Lecture 1 Flashcards

1
Q

State nine properties of cells

Here are some difficult MCQs assessing the properties of cells:

A) Highly Complex and Organized
B) Evolve
C) Can Reproduce Themselves
D) Carry Out Chemical Reactions

**
### 2. Which property is primarily associated with the cellular ability to maintain internal conditions and respond to changes in their environment?
A) Acquire and Utilize Energy
B) Highly Complex and Organized
C) Are Capable of Self Regulation
D) Possess a Genetic Program and the Means to Use It

**s.*

A) Carry Out Mechanical Activities
B) Acquire and Utilize Energy
C) Evolve
D) Respond to Stimuli

.*

A) Carry Out Chemical Reactions
B) Possess a Genetic Program and the Means to Use It
C) Evolve
D) Highly Complex and Organized

**
### 5. Which property is essential for cells to adapt to environmental changes and survive in varying conditions?
A) Highly Complex and Organized
B) Respond to Stimuli
C) Carry Out Mechanical Activities
D) Evolve

**
### 6. Which property allows cells to undergo genetic variations and adaptation over generations?
A) Carry Out Chemical Reactions
B) Evolve
C) Acquire and Utilize Energy
D) Can Reproduce Themselves

**
### 7. Which of the following is not a typical characteristic of cells?
A) Carry Out Mechanical Activities
B) Evolve
C) Acquire and Utilize Energy
D) Non-specific Response to External Factors

**
### 8. Which property of cells is directly involved in the formation of cellular structures and movement?
A) Highly Complex and Organized
B) Carry Out Mechanical Activities
C) Possess a Genetic Program and the Means to Use It
D) Are Capable of Self Regulation

**.*

A) Highly Complex and Organized
B) Carry Out Chemical Reactions
C) Are Capable of Self Regulation
D) Evolve

** Here are MCQs designed to test your ability to determine which options are properties specific to cells:

A) Ability to reproduce through binary fission or mitosis
B) Ability to exhibit seasonal migration
C) Ability to undergo ecological succession
D) Ability to perform photosynthesis in the atmosphere

**
### 2. Which of the following properties is specific to cellular structures?
A) Ability to exhibit symbiosis
B) Ability to engage in energy transformation through metabolic pathways
C) Ability to migrate in response to environmental stimuli
D) Ability to participate in genetic drift

*

A) Ability to form ecosystems
B) Ability to maintain homeostasis at the cellular level
C) Ability to display learned behaviors
D) Ability to evolve through natural selection

**
### 4. Which of the following is a defining feature of cells rather than of multicellular organisms or ecological systems?
A) Ability to undergo meiosis
B) Ability to communicate through pheromones
C) Ability to regulate tissue growth
D) Ability to form complex social structures

**

A) Ability to form and maintain organ systems
B) Ability to undergo cellular respiration
C) Ability to exhibit complex behaviors
D) Ability to influence climate change

**

A) Ability to divide and form new cells
B) Ability to evolve populations over generations
C) Ability to interact with other species in an ecosystem
D) Ability to regulate whole-organism homeostasis

**
### 7. Which of these options describes a property specific to cellular function?
A) Ability to adapt to ecological niches
B) Ability to synthesize proteins based on genetic information
C) Ability to migrate in response to environmental changes
D) Ability to form symbiotic relationships

**

A

1.Highly Complex and Organized
2.Acquire and Utilize Energy
3.Possess a Genetic Program and the Means to Use It
4.Can Reproduce
Themselves
5.Evolve
6.Carry Out Chemical Reactions
7.Are Capable of Self Regulation
8.Carry Out Mechanical
Activities
9.Respond to Stimuli

Here are some difficult MCQs assessing the properties of cells:

A) Highly Complex and Organized
B) Evolve
C) Can Reproduce Themselves
D) Carry Out Chemical Reactions

Answer: C) Can Reproduce Themselves
Explanation: While other properties can apply to biological systems broadly, the ability to reproduce themselves is specific to cells.

A) Acquire and Utilize Energy
B) Highly Complex and Organized
C) Are Capable of Self Regulation
D) Possess a Genetic Program and the Means to Use It

Answer: C) Are Capable of Self Regulation
Explanation: Self-regulation involves maintaining internal conditions and responding to environmental changes, which is specific to cells.

A) Carry Out Mechanical Activities
B) Acquire and Utilize Energy
C) Evolve
D) Respond to Stimuli

Answer: B) Acquire and Utilize Energy
Explanation: This property involves metabolic activities and energy transformations, a fundamental characteristic of cells.

A) Carry Out Chemical Reactions
B) Possess a Genetic Program and the Means to Use It
C) Evolve
D) Highly Complex and Organized

Answer: B) Possess a Genetic Program and the Means to Use It
Explanation: This property refers to the cell’s ability to use its genetic code to guide the synthesis of proteins and other essential molecules.

A) Highly Complex and Organized
B) Respond to Stimuli
C) Carry Out Mechanical Activities
D) Evolve

Answer: B) Respond to Stimuli
Explanation: Cells must be able to detect and respond to changes in their environment to survive and adapt.

A) Carry Out Chemical Reactions
B) Evolve
C) Acquire and Utilize Energy
D) Can Reproduce Themselves

Answer: B) Evolve
Explanation: Evolution involves genetic changes and adaptation over generations, a property specific to living organisms including cells.

A) Carry Out Mechanical Activities
B) Evolve
C) Acquire and Utilize Energy
D) Non-specific Response to External Factors

Answer: D) Non-specific Response to External Factors
Explanation: Cells typically have specific responses to external stimuli rather than non-specific responses.

A) Highly Complex and Organized
B) Carry Out Mechanical Activities
C) Possess a Genetic Program and the Means to Use It
D) Are Capable of Self Regulation

Answer: B) Carry Out Mechanical Activities
Explanation: Mechanical activities such as movement and structural formation are specific to cellular functions.

A) Highly Complex and Organized
B) Carry Out Chemical Reactions
C) Are Capable of Self Regulation
D) Evolve

Answer: C) Are Capable of Self Regulation
Explanation: Self-regulation allows cells to maintain internal stability and function despite external fluctuations.

Here are MCQs designed to test your ability to determine which options are properties specific to cells:

A) Ability to reproduce through binary fission or mitosis
B) Ability to exhibit seasonal migration
C) Ability to undergo ecological succession
D) Ability to perform photosynthesis in the atmosphere

Answer: A) Ability to reproduce through binary fission or mitosis
Explanation: Reproduction through binary fission or mitosis is a fundamental property of cells.

A) Ability to exhibit symbiosis
B) Ability to engage in energy transformation through metabolic pathways
C) Ability to migrate in response to environmental stimuli
D) Ability to participate in genetic drift

Answer: B) Ability to engage in energy transformation through metabolic pathways
Explanation: Cells engage in energy transformation through metabolic pathways, a core cellular function.

A) Ability to form ecosystems
B) Ability to maintain homeostasis at the cellular level
C) Ability to display learned behaviors
D) Ability to evolve through natural selection

Answer: B) Ability to maintain homeostasis at the cellular level
Explanation: Maintaining homeostasis at the cellular level is a unique property of cells.

A) Ability to undergo meiosis
B) Ability to communicate through pheromones
C) Ability to regulate tissue growth
D) Ability to form complex social structures

Answer: A) Ability to undergo meiosis
Explanation: Meiosis is a process specific to cells, particularly in reproduction.

A) Ability to form and maintain organ systems
B) Ability to undergo cellular respiration
C) Ability to exhibit complex behaviors
D) Ability to influence climate change

Answer: B) Ability to undergo cellular respiration
Explanation: Cellular respiration is a fundamental process occurring within individual cells.

A) Ability to divide and form new cells
B) Ability to evolve populations over generations
C) Ability to interact with other species in an ecosystem
D) Ability to regulate whole-organism homeostasis

Answer: A) Ability to divide and form new cells
Explanation: Cell division is a property specific to cells, though it contributes to overall organismal growth.

A) Ability to adapt to ecological niches
B) Ability to synthesize proteins based on genetic information
C) Ability to migrate in response to environmental changes
D) Ability to form symbiotic relationships

Answer: B) Ability to synthesize proteins based on genetic information
Explanation: Protein synthesis based on genetic information is a fundamental cellular function.

These questions will help you identify which characteristics are intrinsic to cells versus those that may apply to broader biological contexts.

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2
Q

State the characteristics of prokaryotic cells(prokaryotes are bacteria and archaea cells)

A

Cell wall
•Peptidoglycan cell wall in bacteria and pseudopeptidoglycan cell wall in archaea
•Gives shape, protects against environment and dehydration

Nucleoid region
•single Circular chromosome containing genetic material(DNA)(the DNA in eukaryotes are straight not circular )
•Non-membrane bound so they don’t have a membrane bound nucleus. Their genetic material is in the nucleoid or nucleoid region. Some prokaryotes have DNA fragments called plasmids. Yes, a bacterium can have both a nucleoid and plasmids. The nucleoid is the region within the cell where the main bacterial chromosome, typically a single circular DNA molecule, is located. This chromosome contains the essential genetic information necessary for the bacterium’s growth, reproduction, and basic functions.

Plasmids, on the other hand, are smaller, circular DNA molecules that exist independently of the chromosomal DNA. They often carry additional genes that can provide the bacterium with advantageous traits, such as antibiotic resistance, virulence factors, or the ability to metabolize unusual substances. Plasmids can be transferred between bacteria through processes such as conjugation, thereby spreading these beneficial traits within bacterial populations.

Flagellum
•For movement

Pilus
•Conjugation (exchange of nuclear material)

Fimbria
•Attachment to surfaces

Ribosomes
•Protein synthesis from mRNA
•70S made up of 2 subunits (50S and 30S)

.they don’t have membrane bound organelles. All their cellular processes occur in the cytoplasm or cell membrane

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3
Q

State four characteristics of eukaryotes (fungi,animals,protists(protists include amoeba,paramecium,plasmodium,giardia lamblia,helminths)
State three differences between prokaryotes and eukaryotes
Are viruses and prions prokaryotes or eukaryotes or neither?
Give the two main types of prokaryotes

A

Larger than prokaryotic cells

•Have no capsule or cell wall. Note: some protists and fungi have capsule or cell wall even though eukaryotes don’t have cell wall.

•Nuclear material bound in membrane called nucleus

•Possesses no pilus, fimbria or flagella

•Membrane bound organelles

Differences Between Protists (Eukaryotes) and Prokaryotes:prokaryotes include bacteria and viruses.

1.	Cell Structure:
•	Protists (Eukaryotes): Have a true nucleus enclosed by a nuclear membrane and possess membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum).
•	Prokaryotes: Lack a true nucleus; their genetic material is located in a nucleoid region. They do not have membrane-bound organelles.
2.	Genetic Material:
•	Protists (Eukaryotes): Their DNA is linear and organized into chromosomes within the nucleus.
•	Prokaryotes: Their DNA is usually circular and found in the cytoplasm without a surrounding membrane.
3.	Cell Size:
•	Protists (Eukaryotes): Typically larger, ranging from 10 to 100 micrometers.
•	Prokaryotes: Generally smaller, usually around 1 to 10 micrometers.
4.	Reproduction:
•	Protists (Eukaryotes): Reproduce by mitosis and meiosis; can have complex life cycles.
•	Prokaryotes: Reproduce asexually through binary fission;

Prokaryotes:

1.	Bacteria:
•	Single-celled organisms that lack a true nucleus and membrane-bound organelles.
•	Examples: Escherichia coli (E. coli), Staphylococcus aureus, Bacillus anthracis.
2.	Archaea:
•	Another group of single-celled organisms similar to bacteria in structure but genetically distinct.
•	Often found in extreme environments (e.g., hot springs, deep-sea vents).
•	Examples: Halobacterium (found in salty environments), Thermoplasma (found in hot, acidic environments).

Non-Prokaryotic Entities:

1.	Viruses:
•	Not considered living organisms, and not classified as prokaryotes or eukaryotes.
•	They consist of genetic material (DNA or RNA) enclosed in a protein coat and require a host cell to replicate.
•	Examples: HIV, influenza virus, SARS-CoV-2.
2.	Prions:
•	Misfolded proteins that can cause other proteins to misfold, leading to disease.
•	Not classified as living organisms, and not considered prokaryotic or eukaryotic
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4
Q

What are the components of the plasma membrane?
What is its main function?
How does it carry out its main function?
State two other functions

A

Composition:
1.Phospholipids (bilayer)
2.Proteins (cell recognition, transport, signalling)
3.Cholesterol
4.Others (carbohydrates, other lipids)

Function:
The main function of the plasma membrane is that it acts as a physical barrier between the external environment and the inner cell organelles.

How does it perform its main function?
The plasma membrane is a selectively permeable membrane, which permits the movement of only certain molecules both in and out of the cell.

Other functions:
The plasma membranes also play an important role in both the endocytosis and exocytosis processes.

The plasma membrane also functions by facilitating communication and signalling between the cells.

Here’s how the plasma membrane facilitates endocytosis, exocytosis, and cell communication:

  1. Endocytosis and Exocytosis:
    • Endocytosis: The plasma membrane engulfs external substances, forming a vesicle that brings the materials into the cell. This process can be specific (e.g., receptor-mediated endocytosis) or non-specific.
    • Exocytosis: The plasma membrane expels materials from the cell. Vesicles containing the substances fuse with the membrane, releasing their contents outside the cell. This is crucial for processes like neurotransmitter release and hormone secretion.
  2. Communication and Signaling:
    • Receptors: Integral membrane proteins act as receptors that bind to specific signaling molecules (ligands), such as hormones or neurotransmitters. This binding triggers a cascade of intracellular events.
    • Signal Transduction: Once a ligand binds to a receptor, it can initiate signal transduction pathways that alter cellular activities. This process often involves secondary messengers and changes in enzyme activity or gene expression.
    • Cell Recognition: Glycoproteins and glycolipids on the membrane surface facilitate cell recognition and interaction, which is important for immune responses and tissue formation.

These functions allow cells to interact with their environment, take in necessary substances, expel waste, and communicate with other cells.

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5
Q

Fungi and protists don’t have cell wall but some do. Give examples of the ones that do

A

While most eukaryotic cells do not have cell walls, many protists and fungi do. Here are examples of protists and fungi that possess cell walls:

  1. Algae:
    • Green Algae: Such as Chlamydomonas and Volvox, which have cell walls made primarily of cellulose.
    • Brown Algae: Such as kelp, with cell walls containing alginates.
    • Red Algae: Such as Porphyra, which have cell walls containing agar and carrageenan.
  2. Diatoms: These are a type of algae with cell walls composed of silica, forming intricate and beautiful glass-like structures known as frustules.
  3. Dinoflagellates: Some species have cell walls made of cellulose plates, which can contribute to their distinctive shapes and structures.
  1. Yeasts:
    • Saccharomyces cerevisiae (baker’s yeast), which has cell walls composed of glucans and mannoproteins.
  2. Molds:
    • Aspergillus and Penicillium, with cell walls primarily made of chitin and glucans.
  3. Mushrooms:
    • Agaricus bisporus (common mushroom) and other basidiomycetes, with cell walls made of chitin.
  • Protists: Many algae (green, brown, and red algae), diatoms, and some dinoflagellates have cell walls.
  • Fungi: Yeasts, molds, and mushrooms all possess cell walls, primarily composed of chitin and other polysaccharides.

These cell walls provide structural support, protection, and help maintain the shape of these organisms, similar to the role of cell walls in plants.

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6
Q

What is the importance of phospholipids structure of the cell membrane?
What is the importance of cholesterol in the cell membrane
What is the importance of protein transporters for the cell membrane?
What is the importance of the semi permeable membrane
Why can’t potassium enter the cell anyhow it wants? What does it need to enter?

A

Phospholipids structure in the plasma membrane helps the cell exist in its aqueous environment.
Phospho or phosphate group binds to a glycerol molecule. The glycerol molecule is bound to two fatty acids(they’re hydrophobic)

Phosphate groups (they’re hydrophilic. Hydrophilic heads) face outward and fatty acids face inwards (they’re hydrophobic. Hydrophobic tails) so they don’t come into contact with the water in the cell

Cholesterol gives rigidity to the cell membrane. Cholesterol contributes to the rigidity of the cell membrane. It helps to stabilize the membrane’s structure and reduce its fluidity, making it less permeable to small water-soluble molecules. So cholesterol doesn’t make the cell fluid

Protein transporters help transport molecules
Integral proteins can serve as transporters
Glycoprotein(sugar and protein)
Glycolipids(sugar and lipids)

Endocytosis and exocytosis

Semi permeable membrane:
Allows Uncharged or hydrophobic molecules enter into the cell
Does not allow Potassium and other molecules to just enter the cell unless they use transport proteins cuz they are charged molecules

Your summary is mostly correct, but here are some clarifications:

  • Integral Proteins: These proteins span the cell membrane and can function as transporters, channels, or receptors. They help move molecules across the membrane, including those that cannot diffuse freely.
  • Glycoproteins: These are proteins with carbohydrate groups attached. They are involved in cell recognition and communication.
  • Glycolipids: These are lipids with carbohydrate groups attached. They also play a role in cell recognition and stability of the membrane.
  • Semi-Permeable Membrane: This type of membrane allows certain molecules to pass through while blocking others.
    • Uncharged or Hydrophobic Molecules: These can diffuse through the membrane more easily.
    • Charged Molecules: Like potassium ions (K+), which cannot easily pass through the hydrophobic core of the membrane, typically require specific transport proteins or channels to cross the membrane.
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7
Q

State the three main parts of the nucleus
Which structure in the nucleus has a double membrane ?
What is the function of nuclear pores?
What is chromatin
What is the importance of the nucleolus

A

Main parts of nucleus: nucleolus, nucleoplasm and genetic material

nuclear envelope is a double-membrane structure that constitutes the nucleus’ outermost portion
The nuclear pores control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm.

•Chromatin describes the material that makes up the chromosomes both when condensed and decondensed.

•The Nucleolus assembles individual parts of the ribosomes to synthesis the complete ribosomes

In MCQ settings, the main parts of the nucleus typically include:

  1. Nucleolus: The site of ribosomal RNA synthesis and ribosome assembly.
  2. Nucleoplasm: The substance within the nucleus that supports the nuclear components.
  3. Nuclear Envelope: The double membrane that encloses the nucleus, separating it from the cytoplasm. It includes nuclear pores that regulate the movement of molecules between the nucleus and cytoplasm.

The genetic material (DNA and chromatin) is often considered part of the nuclear contents rather than a separate structural component, but it’s crucial to mention in the context of nuclear function and organization.

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8
Q

What is the importance of mitochondria ?
Which part of the mitochondria folds inward to form cristae?
Mitochondria has its own ribosomes and DNa true or false?
Mitochondria makes ATP from what two main reduced equivalents?
Electron transport and oxidative phosphorylation occur in which part of the mitochondria?
Citric acid cycle ,fatty acid oxidation and initial steps of heme synthesis occur in which part of the mitochondria

A

Powerhouses” or “energy factories”. Responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule.
•From reduced equivalents (FADH2 and NADH)
•Possess their own ribosomes and DNA.
Protein synthesis

Mitochondrion- has dna,ribosomes, inner and other membrane

It receives electrons from FADH to NADH. Passes them thru electron transport chain, generate protons which reenter the inner membrane of mitochondria to generate Atp

The mitochondrial matrix is the space enclosed by the inner membrane of the mitochondrion. It contains the mitochondria’s own DNA, ribosomes, and various enzymes involved in metabolic processes such as the citric acid cycle (Krebs cycle).

To summarize the main parts of the mitochondrion:

  • Outer Membrane: The lipid bilayer that encloses the entire organelle.
  • Inner Membrane: The lipid bilayer that folds inward to form structures called cristae, which increase the surface area for energy production.
  • Matrix: The space inside the inner membrane, where metabolic activities occur.
  • Intermembrane Space: The space between the outer and inner membranes.

Electron transport, oxidative phosphorylation occur in the inner membrane of the mitochondria

Inner Mitochondrial Membrane:
- Electron Transport Chain (ETC)
- ATP Synthesis (Oxidative Phosphorylation)

Mitochondrial Matrix:
- Krebs Cycle (Citric Acid Cycle)
- Heme Synthesis (initial steps)
- Fatty Acid Oxidation
- Amino Acid Metabolism (partially)

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9
Q

In the endomembrane system What are the functions of the endoplasmic reticulum and smooth endoplasmic reticulum ?
What gives the rough endoplasmic reticulum its rough appearance and what is the function of this thing?

What are the difference sim the functions of the ER and the Golgi apparatus

A

ER is responsible for manufacture and folding of proteins.
Smooth ER- cholesterol and other lipids

Rough endoplasmic reticulum-Membranes of these structures are lined withribosomeson their outer surfaces, giving them a rough appearance
The ribosomes on the rough endoplasmic reticulum manufactureproteinswhich enter the channels of the endoplasmic reticulum

Smooth endoplasmic reticulum-Plays a major role in synthesizinglipidsby means of enzymes embedded in these smooth membranes
it produces thephospholipidsandcholesterolused in membrane formation, and along with the membrane proteins

While both the endoplasmic reticulum (ER) and Golgi apparatus are involved in processing proteins and lipids, their roles differ in focus and timing:

  1. Endoplasmic Reticulum (ER):
    • Synthesis and Folding: The rough ER is involved in the synthesis of proteins, particularly those that are to be secreted, incorporated into the plasma membrane, or sent to lysosomes. It also helps in folding proteins and adding modifications like glycosylation.
    • Quality Control: The ER monitors the quality of newly synthesized proteins. Misfolded proteins are usually retained and directed to the cytoplasm for degradation (ER-associated degradation or ERAD).
  2. Golgi Apparatus:
    • Processing and Modification: After proteins and lipids leave the ER in transport vesicles, they arrive at the Golgi apparatus. Here, they undergo further modifications, including additional glycosylation, phosphorylation, and sulfation.
    • Sorting and Packaging: The Golgi apparatus sorts and packages proteins and lipids into vesicles that are then directed to their appropriate destinations, such as the plasma membrane, lysosomes, or secretion outside the cell.

In summary, the ER is primarily involved in the initial synthesis and quality control of proteins, while the Golgi apparatus is responsible for the final modifications, sorting, and distribution of these molecules.

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10
Q

What is the function of the smooth ER in the liver cells?
What are the functions of the Golgi apparatus in the endomembrane and system?
What is the function of the lysosome?
Why is the lysosome a membrane bound organelle?

A

In liver cells the smooth ER contains enzymes for the detoxification of harmful drugs and metabolic by-products

Golgi apparatus
Acts to process and package the macromolecules such asproteinsandlipidsthat are synthesized by the cell
A major function is the modifying, sorting and packaging of proteins for secretion.
It is also involved in the transport of lipids around the cell, and the creation oflysosomes.

Lysosome
Contain digestiveenzymes
The main function of lysosomes is to accomplish digestion of food particles

Lysosomes are membrane bound. They contain toxic things to destroy foreign bodies that have been phagocytosed. If the lysosomes weren’t membrane bound, they would destroy regular cells

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11
Q

Which organelle is the quality control officer of the cell?
What would be the consequence of the dysfunction of this organelle?

A

Golgi apparatus- cis phase (facing ER) and trans phase(facing plasma membrane).
It is the quality control officer of the cell. If the golgi wasn’t there, there would be improper folding of the proteins and release of poorly formed proteins or substance

The Golgi apparatus indeed has two faces, but its role is more complex than just quality control, and some details in your statement need clarification:

  1. Cis and Trans Faces of the Golgi Apparatus:
    • Cis Face: This side is oriented towards the endoplasmic reticulum (ER), not necessarily the nucleus. It receives newly synthesized proteins and lipids from the ER.
    • Trans Face: This side is oriented towards the plasma membrane. It is responsible for sorting and packaging proteins and lipids into vesicles for transport to their final destinations, such as the plasma membrane, lysosomes, or secretion outside the cell.
  2. Quality Control in the Cell:
    • The endoplasmic reticulum (ER) is primarily responsible for the initial folding of proteins and ensuring they are correctly folded. If proteins are improperly folded, they are typically retained in the ER and may be degraded if they can’t be corrected.
    • The Golgi apparatus modifies proteins (e.g., glycosylation, sulfation) and plays a role in ensuring that proteins are properly modified before being sent to their final destination. However, it is not the primary site for folding proteins.
  3. What Would Happen Without the Golgi Apparatus:
    • Without the Golgi apparatus, cells would struggle to modify, sort, and properly distribute proteins and lipids. However, protein folding issues primarily arise in the ER, not the Golgi. So, the absence of the Golgi would lead to problems with protein modification, sorting, and secretion, rather than folding.
  • The Golgi apparatus is crucial for modifying, sorting, and shipping proteins and lipids to their correct locations.
  • The ER is the main site for protein folding and quality control. Without the Golgi, proteins wouldn’t be properly modified or sent to the right destinations, but folding problems would mainly originate from the ER.
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12
Q

What are the functions of the CIs and trans Golgi apparatus?
Which is located closer to the ER
Which is away from it

A

The Golgi apparatus has two main phases: the cis-Golgi network (CGN) and the trans-Golgi network (TGN). The cis-Golgi network is located closer to the endoplasmic reticulum (ER) and receives vesicles containing proteins and lipids from the ER. The trans-Golgi network is located further from the ER and is involved in sorting these proteins and lipids and directing them to their final destinations, either within the cell or for secretion outside the cell.

Actually, the cis face of the Golgi apparatus primarily functions in receiving and processing newly synthesized proteins and lipids from the endoplasmic reticulum (ER).

Here’s a clearer breakdown:

  • Cis Face:
    • This is the “receiving” side of the Golgi apparatus.
    • Proteins and lipids from the ER arrive here in transport vesicles.
    • The cis face doesn’t do the actual packaging; instead, it is more involved in initial processing steps like modifying the proteins and lipids as they enter the Golgi.
  • Trans Face:
    • This is the “shipping” side of the Golgi apparatus.
    • Here, the processed proteins and lipids are packaged into vesicles.
    • These vesicles are then sorted and directed to their final destinations, such as the plasma membrane, lysosomes, or secretory pathways.

In summary, the cis face does not package but rather receives and processes, while the trans face is responsible for the final packaging and sorting.

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13
Q

Explain how the ribosomes work with the Golgi apparatus to get proteins

A

Ribosomes after producing the proteins, sends it to the ER FOR FOLDING AND THEN SENDS IT TO THE GOLGI APPARATUS FOR CLEAVAGE AND MODIFICATION to make sure the proteins were folded right .

Ribosomes and the Golgi apparatus work together in the process of protein synthesis, modification, and packaging within the cell.

  1. Protein Synthesis by Ribosomes: Ribosomes are the cellular machinery responsible for protein synthesis. They translate the genetic code from messenger RNA (mRNA) into a specific sequence of amino acids to form a protein.
  2. Protein Modification in the Endoplasmic Reticulum (ER): Once synthesized, many proteins undergo post-translational modifications in the endoplasmic reticulum (ER). These modifications include folding, glycosylation (addition of sugar molecules), and disulfide bond formation, among others.
  3. Transport to the Golgi Apparatus: After modification in the ER, proteins are transported to the Golgi apparatus via vesicles. These vesicles bud off from the ER and fuse with the cis-Golgi network (CGN), delivering their cargo of newly synthesized proteins.
  4. Further Processing in the Golgi Apparatus: Within the Golgi apparatus, proteins undergo further modifications, including glycosylation and proteolytic cleavage. This processing is mediated by various enzymes present within the Golgi compartments.
  5. Sorting and Packaging: The Golgi apparatus also plays a role in sorting proteins to their appropriate destinations within the cell. Depending on specific signals present in the protein sequence, proteins may be directed to different compartments within the cell, including other organelles or the plasma membrane for secretion.
  6. Export via Secretory Vesicles: Once fully processed and sorted, proteins are packaged into transport vesicles that bud off from the trans-Golgi network (TGN). These vesicles then move to the cell membrane, where they fuse and release their contents (e.g., proteins) outside the cell through a process called exocytosis.

In summary, ribosomes synthesize proteins, which are then modified in the ER and further processed, sorted, and packaged within the Golgi apparatus before being transported to their final destinations inside or outside the cell.

Or

You are correct that the endoplasmic reticulum (ER) plays a significant role in quality control, but here’s how the process works:

  1. Ribosomes: Synthesize proteins either free in the cytoplasm or bound to the rough ER. Proteins synthesized on the rough ER are directly inserted into the ER lumen.
  2. Endoplasmic Reticulum (ER): In the rough ER, proteins undergo folding and initial post-translational modifications. The ER has quality control mechanisms to ensure proteins are correctly folded and assembled. Misfolded proteins are typically retained and targeted for degradation.
  3. Golgi Apparatus: After the initial processing in the ER, proteins are transported to the Golgi apparatus. The Golgi further modifies, sorts, and packages proteins into vesicles. This includes additional post-translational modifications such as glycosylation and cleavage.

In summary:
- The ER is responsible for initial folding and quality control.
- The Golgi apparatus further modifies and sorts the proteins after they have left the ER.

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14
Q

Which organelles dysfunction will cause a problem with insulin?

A

Insulin is a protein so a problem with insulin not functioning well could be a Golgi apparatus or ER problem.
So they can put different types or combinations of organelles there and ask you where the insulin problem could be coming from then you pick.

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15
Q

Which of the organelles dominate the liver cells?
Which dominate the smooth muscles? Example to remember this one is for gyming
Which organelle synthesized and converts bile acids in the liver?
Which organelle causes beta oxidation of very long chain fatty acids so they’re broken down into smaller pieces to be sent to the mitochondria for more work to be done on them

A

Different organelles will dominate different cell types.
Example is the liver which is for detoxyfying bad stuff so it will have high amounts of ER specifically the smooth one.
Peroxisomes too dominate liver cells cuz they synthesize and convert bile acids and release them

Smooth muscles during gyming need a lot of muscle bulk and the msucles need ATP which is produced by mitochondria so in the muscle, there’s a high amount of mitochondria compared to something like the Golgi apparatus. Cuz they don’t produce anything for exporting.

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16
Q

What are Peroxisomes and what are their functions?
Which organelle breaks down fatty acids and amino acids

A

They have a single bilayer membrane. Peroxisomesare small, round organelles enclosed by single membranes.

They carry out oxidation reactions that break down fatty acids and amino acids.

Functions:
-α-oxidation ofbranched fatty acids such as phytanic acid
-β-oxidation of unbranched very-long-chain and polyunsaturated fatty acids
-biosynthesis of plasmalogens: Plasmalogens are a type of phospholipid found in cell membranes, particularly abundant in the membranes of neurons, myelin sheaths, heart muscle cells, and sperm cells.
-conjugation of cholic acid as part of bile acid synthesis

They have special set of enzymes that let them break down very long chain fatty acids (more than 18 carbon atoms) that the mitochondrion can’t break down
They also synthesize, convert bile acids and releasing them. They will be dominant in the liver cells.
Glyogenesis- building fatty acids from scratch

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17
Q

How do Peroxisomes detoxify poisons that enter the body

A

They also detoxify many poisons that may enter the body. (Many of these oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, catalase enzymes safely break down the H2O2into oxygen and water.)

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18
Q

Cell cycle and cell division:
If cells don’t go through interphase properly, they will mutate.
what are the three Check points in the cell cycle that the cell checks what has Been produced to see if everything is in the right order and If it’s not, it causes the cell to die
Both G1 and G2 check for DNA damage but they check for different aspects of DNA damage. State those different aspects

A

. If abnormalities are detected at these checkpoints, the cell may undergo apoptosis (programmed cell death) to prevent the propagation of damaged or abnormal cells. Here are the main checkpoints:

  1. G1 Checkpoint (Restriction Point):
    • Occurs near the end of the G1 phase.
    • Checks for cell size, nutrient availability, growth factors, DNA damage, and proper internal signaling.
    • If conditions are favorable and DNA is undamaged, the cell proceeds to the S phase to initiate DNA replication. Otherwise, it may enter a quiescent state (G0, G0 is a phase where cells exit the cell cycle and cease to actively divide. ) or undergo apoptosis.
  2. G2 Checkpoint:
    • Occurs at the end of the G2 phase, before entry into mitosis.
    • Checks for DNA replication completeness, DNA damage, and proper cell size.
    • If DNA replication is complete and undamaged, and cell size is adequate, the cell proceeds to mitosis. Otherwise, it may pause for repair or undergo apoptosis.
  3. Metaphase Checkpoint:
    • Occurs during metaphase of mitosis.
    • Ensures that all chromosomes are properly attached to the mitotic spindle and aligned at the metaphase plate.
    • If chromosomes are not correctly aligned or attached, the checkpoint delays the onset of anaphase until the issues are resolved, preventing unequal distribution of genetic material.

These checkpoints are crucial for maintaining genomic integrity and preventing the proliferation of damaged or abnormal cells. If the cell detects significant abnormalities or fails to pass these checkpoints, it may undergo programmed cell death (apoptosis) to eliminate the potentially harmful cell.

Both G1 and G2 phases include checkpoints to ensure DNA integrity, but they focus on different aspects of DNA assessment.

  • G1 Checkpoint:
    • The G1 checkpoint, often referred to as the restriction point, ensures that the cell is ready to proceed to DNA replication. It checks for:
      • Nutrient availability: Ensures the cell has the resources needed for DNA replication.
      • DNA damage: Assesses if the DNA is intact and free from significant damage before replication begins.
      • Growth factors and signals: Determines if external signals are appropriate for cell division.
  • G2 Checkpoint:
    • The G2 checkpoint occurs after DNA replication but before mitosis. It checks:
      • DNA replication: Ensures that DNA replication is complete and accurate.
      • DNA damage: Assesses if there are any errors or damage in the replicated DNA before mitosis.
      • Repair mechanisms: Confirms that any damage has been repaired.
  • G1 Phase: Checks for DNA damage and readiness to enter the S phase for DNA replication.
  • G2 Phase: Checks for DNA damage and the accuracy of DNA replication before proceeding to mitosis.
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19
Q

Cell cycle occurs only in eukaryotic cells
True or false

A

True

20
Q

Explain the cell cycle
Which of the phases causes the cell to enter apoptosis if there’s any damage?
Which causes it to enter G0
Which mitotic phase does the Chromosomes condense, the nuclear envelope breaks down, and spindle fibers form?
Which mitotic phase do Sister chromatids separate and move toward opposite poles of the cell?
Which mitotic phase do Chromosomes decondense, nuclear envelopes reform around the separated chromatids, and spindle fibers disassemble?
Which mitotic phase do Chromosomes line up at the metaphase plate, and spindle fibers attach to the centromeres?

During which phase of interphase is the restriction point located, a critical checkpoint that determines whether a cell will proceed with division?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) G0 phase
In which phase of interphase does the cell check for DNA damage and ensure all the DNA has been accurately replicated before proceeding to mitosis?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) G0 phase
Which of the following proteins is crucial for the transition from the G1 phase to the S phase, by regulating the cell cycle’s progression?
• A) Cyclin D
• B) Cyclin E
• C) Cyclin B
• D) Cyclin A
During interphase, the nucleolus is most prominent in which of the following stages?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) The nucleolus is not visible during interphase

In cancer cells, the regulation of the cell cycle is often disrupted. Which phase of interphase is most commonly affected by mutations leading to uncontrolled cell division?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) All of the above equally

A

In cancer cells, the regulation of the cell cycle is often disrupted. Which phase of interphase is most commonly affected by mutations leading to uncontrolled cell division?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) All of the above equally
• Answer: A) G1 phase
• Explanation: The G1 phase is where many of the key regulatory checkpoints occur, and mutations in proteins regulating this phase (such as p53) are often implicated in cancer.

Which of the following proteins is crucial for the transition from the G1 phase to the S phase, by regulating the cell cycle’s progression?
• A) Cyclin D
• B) Cyclin E
• C) Cyclin B
• D) Cyclin A
• Answer: B) Cyclin E
• Explanation: Cyclin E binds to CDK2, facilitating the transition from the G1 phase to the S phase, where DNA replication occurs.

During interphase, the nucleolus is most prominent in which of the following stages?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) The nucleolus is not visible during interphase
• Answer: A) G1 phase
• Explanation: The nucleolus is most prominent during the G1 phase, where it is actively involved in ribosomal RNA synthesis.

During which phase of interphase is the restriction point located, a critical checkpoint that determines whether a cell will proceed with division?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) G0 phase
• Answer: A) G1 phase

In which phase of interphase does the cell check for DNA damage and ensure all the DNA has been accurately replicated before proceeding to mitosis?
• A) G1 phase
• B) S phase
• C) G2 phase
• D) G0 phase
• Answer: C) G2 phase

Explanation for Question 1:

The restriction point is a critical checkpoint during the G1 phase of interphase. This point determines whether a cell will proceed with the cell cycle and eventually divide.

Why G1 Phase and Not G2?
- The restriction point in the G1 phase (also called the “Start” checkpoint in yeast or “Restriction Point” in mammals) ensures that the cell is ready to enter the S phase (where DNA replication occurs). If conditions are not favorable or there are errors, the cell may enter a resting state called G0.
- The G2 phase comes after DNA replication (S phase) and checks for DNA damage or incomplete replication. However, the G2 phase checkpoint is not the restriction point; it is a separate checkpoint called the G2/M checkpoint that determines if the cell can proceed to mitosis.

Explanation for Question 2:

During the G2 phase of interphase, the cell checks for DNA damage and ensures that all the DNA has been accurately replicated before proceeding to mitosis.

Why G2 Phase and Not S Phase?
- The S phase is when DNA replication occurs. The cell focuses on replicating its DNA accurately during this phase.
- However, it is in the G2 phase that the cell performs a quality control check. This is the G2/M checkpoint, where the cell checks for DNA damage post-replication and ensures that replication is complete and accurate. Only after passing this checkpoint will the cell proceed to mitosis (M phase).

In summary:
- The G1 phase contains the restriction point that checks whether the cell should proceed to DNA replication.
- The G2 phase includes the checkpoint that verifies DNA replication integrity and checks for any damage before mitosis.

Summary
1.Interphase
Three stages
-Growth 1 (G1) -accumulates building blocks of chromosomal DNA and the associated proteins. Accumulatesenough energy reserves to complete the task of replicating each chromosome in the nucleus
Or Cell Growth: The cell grows in size and synthesizes proteins and organelles.
• Normal Functions: The cell performs its normal physiological functions.
-DNA Synthesis (S) -DNA replication results in the formation of two identical copies of each chromosome (sister chromatids)OR DNA Replication: Each chromosome is duplicated, resulting in two sister chromatids per chromosome.
• Centrosome (the thing that houses the centrioles) Duplication: Centrosomes also duplicate to prepare for mitosis.
-Growth 2 (G2) -cell replenishes its energy stores and synthesizes the proteins necessary for chromosome manipulation.Some cell organelles are duplicated
Final Preparations: The cell continues to grow and produce proteins necessary for mitosis.
• Check for Errors: DNA is checked for replication errors and repaired.

  1. Mitotic phase (M)(formation of two identical daughter cells)
    -Mitosis
    -Karyokinesis:divisions of nucleus
    -Cytokinesis:divisions of cytoplasm

The cell cycle is the process by which a cell duplicates its contents and divides into two daughter cells. It consists of four main stages:

  1. G1 Phase (Gap 1): The cell grows and carries out its normal functions. It also checks for adequate resources and conditions to proceed to the next phase.
  2. S Phase (Synthesis): DNA replication occurs, resulting in the synthesis of two identical copies of each chromosome. At the end of this phase, the cell contains twice the amount of DNA it had at the beginning.
  3. G2 Phase (Gap 2): The cell continues to grow and prepares for cell division. It synthesizes proteins and organelles necessary for division and checks for DNA damage.
  4. M Phase (Mitotic Phase): The cell divides into two daughter cells through a process called mitosis, followed by cytokinesis. Mitosis consists of several stages: karyokinesis occurs in the prophase,metaphase,anaphase and telophase
    • Prophase: Chromosomes condense, the nuclear envelope breaks down, and spindle fibers form.
    • Metaphase: Chromosomes line up at the metaphase plate, and spindle fibers attach to the centromeres(the thing that holds the two sister chromatids together. On a regular, a chromosome has one chromatin but during cell cycle, it duplicates to become two sister Chromatids (the sister chromatid are two chromatins joined by a centromere)
    • Anaphase: Sister chromatids separate and move toward opposite poles of the cell.
    • Telophase: Chromosomes decondense, nuclear envelopes reform around the separated chromatids, and spindle fibers disassemble.
    • Cytokinesis: The cytoplasm divides, resulting in two distinct daughter cells.

Cell division is crucial for growth, development, tissue repair, and reproduction in multicellular organisms. It ensures that each daughter cell receives a complete set of genetic information and the necessary cellular components to function properly.

Understanding which phase a question is referring to often depends on the context given in the question. Let’s clarify the checkpoints and how to differentiate them:

  1. G1 Checkpoint (Restriction Point):
    • Main Function: Determines whether the cell will proceed to DNA synthesis (S phase) or exit the cell cycle into G0.
    • Focus: Checks for DNA damage, adequate cell size, and availability of nutrients and growth signals.
    • Key Proteins: p53, Rb (Retinoblastoma protein).
    • Implications: Mutations here can lead to cancer as it might allow cells with DNA damage to replicate.
  2. S Phase Checkpoint:
    • Main Function: Ensures that DNA replication proceeds correctly and that there are no replication errors or DNA damage.
    • Focus: Monitoring the replication process and ensuring the integrity of the newly synthesized DNA.
    • Key Proteins: ATR, ATM, and other DNA repair proteins.
    • Implications: Errors here could lead to mutations, but this checkpoint is more about the ongoing process of replication rather than a stop/go decision like G1 and G2.
  3. G2 Checkpoint:
    • Main Function: Verifies that DNA replication in S phase has been completed successfully without errors and that the cell is ready for mitosis.
    • Focus: Checks for DNA damage, completeness of DNA replication, and readiness for mitosis.
    • Key Proteins: p53 (also functions here), Cyclin B/Cdk1.
    • Implications: If errors or damage are detected, the cell cycle is halted, allowing for repair or triggering apoptosis if repair isn’t possible.
  • G1 Checkpoint Questions:
    • Look for references to deciding whether the cell should commit to division.
    • Key terms: “Restriction point,” “cell size,” “nutrients,” “p53,” “Rb.”
    • Example: “Which checkpoint determines whether a cell enters S phase?”
  • S Phase Checkpoint Questions:
    • Look for references to DNA replication accuracy and integrity during the synthesis phase.
    • Key terms: “DNA replication,” “replication fork,” “ATR,” “ATM.”
    • Example: “Which checkpoint ensures that DNA replication occurs without errors?”
  • G2 Checkpoint Questions:
    • Look for references to ensuring that DNA has been fully and correctly replicated and that the cell is ready for mitosis.
    • Key terms: “Prepares for mitosis,” “DNA damage check,” “Cyclin B/Cdk1.”
    • Example: “Which checkpoint prevents cells with damaged or incomplete DNA from entering mitosis?”
  • G1: Decides whether the cell should enter S phase.
  • S: Monitors ongoing DNA replication.
  • G2: Ensures the cell is ready for mitosis.

When answering MCQs, focus on the specific terms and phrases used in the question to identify which checkpoint it’s referring to.

21
Q

Explain mitosis
Learn more about mitosis and meiosis in the cards I did for Legon biology
Remember that interphase is not part of mitosis
Which phase do the centrosomes move toward opposite poles?
Which phase do kinetochores appear at the centromeres?

A

Interphase first then

Prophase:
• Chromosomes condense and become visible
• Spindle fibers emerge from the centrosomes
• Nuclear envelope breaks down
• Centrosomes (not chromatids) move toward opposite poles

Prometaphase:
• Chromosomes continue to condense
• Kinetochores appear at the centomeres(Kinetochores are protein complexes on the centromere that attach chromosomes to spindle fibers and ensure accurate chromosome segregation during cell division. They also play a role in the spindle assembly checkpoint to prevent errors in chromosome distribution.)
• Mitotic spindle microtubules
attach to
kinetochores

Metaphase:
• Chromosomes are lined up at the metaphase plate
• Each sister chromatid is attached to a spindle fiber opposite poles

Anaphase:
• Centromeres split in two
• Sister chromatids (now called chromosomes)
are pulled toward opposite poles
• Certain fibers begin to elongate the cell

Telophase:
• Chromosomes arrive at opposite poles and begin to decondense
. Nuclear Envelope
material surrounds each set of chromosomes
• The mitotic spindle breaks down
• Spindle fibers continue to push poles apart

Cytokinesis
• Animal cells: a cleavage furrow separates the daughter cells
• Plant cells: a cell plate, the precursor to a new cell wall, separates the daughter

prometaphase is not part of metaphase; it is a distinct phase that occurs between prophase and metaphase during mitosis.

Here’s a quick breakdown of the stages:

1.	Prophase: Chromosomes condense, the nuclear envelope starts to break down, and the mitotic spindle begins to form.
2.	Prometaphase: The nuclear envelope fully disintegrates, kinetochores form at the centromeres of chromosomes, and spindle microtubules attach to kinetochores.

The confusion likely arises from the different structures being discussed:

  • Centrosomes (the microtubule-organizing centers) move to opposite poles during prophase (and finish moving by prometaphase) to help set up the mitotic spindle.
  • Sister chromatids (the identical copies of a chromosome) move apart during anaphase.

Here is a clarification:

  1. Prophase: Centrosomes begin to move apart toward opposite poles of the cell, initiating spindle formation.
  2. Prometaphase: Centrosomes reach opposite poles, and the spindle fibers extend from them and attach to the kinetochores of chromosomes.
  3. Anaphase: Sister chromatids, which were aligned at the metaphase plate, are pulled apart by the spindle fibers attached to the kinetochores and move toward opposite poles.

So, centrosomes move apart during prophase/prometaphase, while sister chromatids separate and move apart during anaphase.

22
Q

State the four molecules of life and their beginning products

A

Molecules of life:
Nucleotides-DNa/RNA
Sugars-carbs
Fatty acids-lipids
Amino acids -proteins

23
Q

Amino acid structure is made up of an amine,alpha carbon and carboxylic acid. Amino Group: -NH₂
2. Alpha Carbon: The central carbon atom to which the other groups are attached.
3. Carboxyl Group: -COOH

Additionally, each amino acid has a unique side chain (R group) attached to the alpha carbon, which varies between different amino acids and determines their specific properties.
true or false
What are essential amino acids,non essential and semi essential amino acids ?
How many amino acids are essential and how many are non essential?
Which amino acid is gotten from phenylalanine?
Is that amino acid essential or non essential

A

Essential proteins: Body doesn’t produce these amino acids by themselves cuz the energy requirements are so high that they can’t produce them

Tyrosine is produced from phenyalanine so if phenylalanine isn’t in your diet, you won’t get tyrosine
Nn Yes, you’re right—tyrosine is considered a non-essential amino acid because the body can synthesize it, but it can only do so if there’s enough phenylalanine in the diet.

Phenylalanine is an essential amino acid, meaning it must be obtained from the diet because the body cannot synthesize it. If phenylalanine is lacking in the diet, the body won’t be able to produce enough tyrosine, even though tyrosine itself is classified as non-essential.

Semi essential proteins- cuz new babies can’t produce these proteins so they rely on the proteins from mother’s diet. Once they grow, the enzymes that produce these proteins kick in and so they’re easily produced now

Yes, the term “semi-essential” or “conditionally essential” is used to describe these amino acids. They are typically non-essential in healthy adults because the body can synthesize them, but under certain conditions (such as in infancy, illness, or stress), they become essential because the body cannot produce enough to meet its needs.

Examples include:

  • Arginine
  • Cysteine
  • Tyrosine
  • Glutamine
  • Glycine
  • Proline

In infants, for instance, these amino acids might need to be supplied through the diet until the body develops the capacity to synthesize them adequately.

Amino acids are the building blocks of proteins and are categorized into three groups based on the body’s ability to synthesize them:

  1. Essential Amino Acids: These are amino acids that the body cannot produce on its own and must be obtained from the diet. There are nine essential amino acids:
    • Histidine
    • Isoleucine
    • Leucine
    • Lysine
    • Methionine
    • Phenylalanine
    • Threonine
    • Tryptophan
    • Valine

PVT TIM HALL- Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine
2. Non-Essential Amino Acids: These are amino acids that the body can synthesize on its own, so they do not need to be obtained from the diet. There are eleven non-essential amino acids:
- Alanine
- Arginine
- Asparagine
- Aspartic acid
- Cysteine
- Glutamic acid
- Glutamine
- Glycine
- Proline
- Serine
- Tyrosine

Almost All Girls Go Crazy After Getting Taken Prom Shopping Again,which stands for Alanine, Asparagine, Glutamate, Glutamine, Cysteine, Aspartate, Glycine, Tyrosine, Proline and Serine,Arginine

  1. Semi-Essential Amino Acids: These are amino acids that are normally non-essential but may become essential under certain conditions such as illness or stress when the body’s demand for them exceeds its ability to produce them. One example of a semi-essential amino acid is:
    -histidine
    • Arginine: Under certain conditions such as growth, trauma, and illness, arginine becomes essential and must be obtained from the diet.

Histidine is generally classified as an essential amino acid. It is required in the diet because the body cannot produce it in sufficient quantities, especially during periods of rapid growth, such as in infants and children.

However, in adults, histidine can sometimes be considered “semi-essential” or “conditionally essential” under certain circumstances, such as in cases of significant metabolic stress or illness, where the body’s demand for histidine may exceed its capacity to produce it.

In summary, histidine is primarily essential, especially in children, but can have characteristics of a semi-essential amino acid under certain conditions.

These distinctions are important because they determine the dietary requirements for amino acids and help ensure adequate intake for proper protein synthesis and overall health

24
Q

State the 20 amino acids as well as whether they are essential or not and their short forms

A

Alanine Ala non-essential
Arginine Arg semi-essential
Asparagine Asn non-essential
Aspartic acid Asp nonessential
Cysteine Cys non-essential*
Glutamine GIn non-essential
Glutamic acid Glu non-essential
Glycine Gly non-essential
Histidine His semi-essential
Isoleucine lle essential
Leucine Leu essential
Lysine Lys essential
Methionine Met essential
Phenylalanine Phe essential
Proline Pro non-essential
Serine Ser non-essential
Threonine Thr essential
Tryptophane Trp essential
Tyrosine Tyr non-essential*
Valine Val essential

25
Q

What is the amino acid structure and classification?
For each classification,state three examples of amino acids under them

A

Non polar amino acids -examples:glycine,alanine,valine,leucine,isoleucine,tyrosine,phenylalanine,tryptophan,methionine,proline

Non-polar side chains:Grandma Always Visits London In May For Winston’s Party.
G: Glycine (Gly).
A: Alanine (Ala).
V: Valine (Val).
L: Leucine (Leu).
I: Isoleucine (Ile).
M: Methionine (Met).
F: Phenylalanine (Phe).
W: Tryptophan (Trp).
P: Proline

Polar but not charged amino acids-cysteine,serine,threonine,asparagine,glutamine

Clever Sweethearts Test All Genotypes”
Breakdown:
• Cysteine
• Serine
• Threonine
• Asparagine
• Glutamine

Tyrosine is polar and aromatic
Polar Charged basic amino acids(are positive) -
arginine,lysine,histidine
Love And Happiness are positives

Polar Charged acidic amino acids(are negative)
-aspartic acid(Asp D) and glutamic acid(Glu E)

Anger and Greed are negative feelings

Acid and basic amino acids are charged amino acids
2. All aliphatic amino acids, as well as methionine - a sulfur-containing amino acid - and phenylalanine and tryptophan, which are aromatic amino acids, are nonpolar amino acids
3. All alcohols and amides, as well as cysteine, which is a sulfur-containing amino acid, and tyrosine, which is an aromatic amino acid, are polar amino acids

The alcohols are serine and threonine
Amides are glutamine and asparagine

26
Q

What is the amino acid structure and classification?
For each classification,state three examples of amino acids under them

A

Non polar amino acids -examples:glycine,alanine,valine,leucine,isoleucine,tyrosine,phenylalanine,tryptophan,methionine,proline
Polar but not charged amino acids-cysteine,serine,threonine,asparagine,glutamine
Charged basic amino acids(these are positively charged)-arginine,lysine,histidine
Charged acidic amino acids(these are negatively charged)-aspartic acid(Asp D) and glutamic acid(Glu E)

27
Q

Most amino acids are under what classification?
glutamate is the anionic form of glutamic acid that predominates at physiological pH.

A

Most amino acids are non polar. Nonpolar amino acids are those that have hydrophobic (water-repelling) side chains. These amino acids tend to be found in the interior of proteins, where they contribute to the protein’s structural stability by forming hydrophobic interactions with other nonpolar amino acids.

Here are the nonpolar amino acids:

  1. Glycine (Gly): Although glycine itself is polar due to its hydrogen atom side chain, it is often considered nonpolar because of its small size and high flexibility, allowing it to fit into tight spaces within protein structures.
  2. Alanine (Ala)
  3. Valine (Val)
  4. Leucine (Leu)
  5. Isoleucine (Ile)
  6. Methionine (Met)
  7. Proline (Pro): Proline is unique in that its side chain forms a covalent bond with the amino group, resulting in a rigid, cyclic structure. While it is classified as nonpolar, its structure and properties differ from other nonpolar amino acids.
  8. Phenylalanine (Phe)
  9. Tryptophan (Trp)

These nonpolar amino acids tend to cluster together in the interior of proteins, away from the surrounding aqueous environment, helping to stabilize the protein’s structure. These non polar proteins hide in the interior part of the protein structure while the charged and polar proteins are exposed to the exterior part

Glutamic acid is for red blood cell normality. If it’s swapped with valine, you’ll get sickle cell. So, glutamate is the anionic form of glutamic acid that predominates at physiological pH.

Glutamic Acid: This term typically refers to the non-ionized or protonated form of the amino acid at a low pH. In this form, glutamic acid has a carboxyl group that is protonated, making it more acidic.
2. Glutamate: This is the deprotonated or ionized form of glutamic acid, which occurs at physiological pH (around 7.4). In this form, one of the carboxyl groups has lost a proton, giving glutamate a negative charge at physiological pH.

28
Q

State three aromatic amino acids and two sulphuric containing amino acids

A

Aromatic:
Phenylalanine
Tryptophan
Tyrosine

Please Take The rings.

Sulphuric:
Cysteine
Methionine

Sulfur Creates More

29
Q

What is Pka?
What is ka
What’s the relationships between ka and pka
If an acid has a low ka what does it mean?
If it has a high ka, what does it mean?
At a ph higher than the pka, does the acid tend to accept protons or donate protons?
When it accepts, is it positive or negative ?
When it donates, is it positive or negative?
How does the pka of an acid relate to its pH?
What would you expect of a strong acid with very low pka values when it encounters a ph much higher than its pka

A

The lower the pka, the easier the amino acids can easily give away their hydrogen ions when placed in solution

Actually, pKa is not the pH at which an acid dissolves completely; rather, it’s the pH at which the acid is half dissociated.

Here’s a clearer explanation:

  1. pKa and Dissociation: The pKa of an acid is the pH at which half of the acid molecules are dissociated (i.e., they have donated a proton) and half remain undissociated. At this pH, the concentrations of the acid (HA) and its conjugate base (A⁻) are equal.
  2. pKa and pH Relationship: When the pH of a solution is equal to the pKa of the acid, there’s an equilibrium between the protonated (HA) and deprotonated (A⁻) forms. If the pH is lower than the pKa, the acid will mostly remain in its protonated form (HA). If the pH is higher than the pKa, the acid will mostly be in its deprotonated form (A⁻).
  3. Complete Dissociation: Strong acids (with very low pKa values) are often completely dissociated at a pH much higher than their pKa, meaning almost all of the acid molecules have donated their protons. However, for weak acids, the dissociation is partial and depends on the pH relative to the pKa.

In summary, pKa is the pH at which half of the acid is dissociated, not the pH at which the acid dissolves or dissociates completely.

. It is defined as the negative logarithm (base 10) of the acid dissociation constant (Ka) of the substance. The pKa value indicates the degree to which a molecule or ion will donate or accept a proton (H+ ion) in a substance(could be water or something else).

At a pH higher than the pKa, the amino acid tends to accept protons and exist predominantly in its deprotonated (negative) form, while at a pH lower than the pKa, it tends to donate protons and exist predominantly in its protonated (positive) form.

Ka is the degree to which an acid dissociates in a water or another substance.
A high ka means that the acid easily dissociates in water hence it is a strong acid.
A high ka means a low pka because they are inversely proportional.
The acid is strong if it easily dissociates in water because it is highly reactive in acid base reactions due to the fact that it easily dissociates in water.
Strong acids means lower ph because The more H⁺ ions an acid releases into a solution, the lower the pH of that solution, making it more acidic. Strong acids significantly lower the pH because they donate many H⁺ ions.

It looks like there may be some confusion regarding acids and their behavior in different environments, particularly with respect to proton donation and acceptance. Let’s clarify how acids behave in acidic environments and how this relates to amino acids:

  1. Definition of an Acid: An acid is defined as a substance that can donate protons (H⁺) in solution. When an acid donates a proton, it becomes a conjugate base (which often has a negative charge).
  2. Acidic Environment: An acidic environment is characterized by a high concentration of H⁺ ions (low pH). In this situation:
    • Acids in an Acidic Environment: Strong acids will dissociate completely, donating protons and existing mostly in their deprotonated (conjugate base) form. Weak acids, however, may not dissociate completely.
    • Protonation of Bases: In an acidic environment, weak bases (which can accept protons) will tend to become protonated.
  • Amino Acid Behavior: Amino acids contain both an amine group (–NH₂) and a carboxylic acid group (–COOH). The behavior of these groups is influenced by pH:
    • At Low pH (Acidic Environment):
      • The carboxylic acid group (–COOH) is protonated (stays as –COOH) and does not release its proton, meaning it retains a neutral charge.
      • The amine group (–NH₂) becomes protonated (–NH₃⁺), resulting in a positive charge overall.
      • If the side chain of the amino acid is also acidic (like in glutamic acid or aspartic acid), it can still lose a proton, but overall, the amino acid can have a net positive charge.
  • At High pH (Basic Environment):
    • The carboxylic acid group deprotonates (–COO⁻), leading to a negative charge.
    • The amine group may remain protonated (–NH₃⁺) depending on how high the pH is, potentially leading to a zwitterionic state (where the amino acid has both positive and negative charges but is overall neutral).
  • In an acidic environment, weak acids can remain protonated (not donating protons) and bases become protonated, leading to positive charges.
  • In a basic environment, acids tend to lose protons (deprotonate) and become negatively charged.

So, while it is true that acidic substances tend to release protons, it’s essential to consider the specific context of the chemical groups involved (like those in amino acids) and how they interact with protons in different pH environments.

30
Q

Explain electrophoresis in amino acids?
Where do positively charged amino acids migrate to in electrophoresis ?
What about negatively charged amino acids?

A

Electrophoresis: solution in a rectangular shape basin with a cathode and an anode
Mixture of amino acids to separate them. Apply electric current to the basin. Manipulate the ph to the point where the amino acids will either release the hydrogen ions or hold on to it. Those who retain their positive charge will migrate to the negatively charged electrode (cathode) and those who are negatively charged will migrate to the positively charged electrode (anode)

31
Q

Question:, where will a peptide containing the amino acids aspartic acid, serene and lysine migrate to when placed in a solution with ph of 6.

A

Solution: calculate overall net charge of each amino acid.
Serene net charge is zero or uncharged, aspartic acid is -1, lysine is +1
The net charge for all combined is 0 and so at a ph of 6, it wil have a net negative charge and hence migrate to the anode or either anode or cathode (I don’t understand this part well)

To predict the migration behavior of a peptide containing the amino acids aspartic acid (Asp), serine (Ser), and lysine (Lys) in a solution with a pH of 6, we need to consider the pKa values of the ionizable groups in each amino acid.

  1. Aspartic Acid (Asp):
    • Aspartic acid has two ionizable groups: the carboxyl group (pKa ~ 2.1) and the side chain carboxyl group (pKa ~ 3.9).
    • At pH 6, both carboxyl groups will be predominantly deprotonated (-COO⁻), as the pH is higher than their pKa values.
  2. Serine (Ser):
    • Serine is uncharged (pKa ~ 13.0).
    • At pH 6, the hydroxyl group will be mostly protonated (-OH), as the pH is significantly lower than its pKa value.
  3. Lysine (Lys):
    • Lysine has one ionizable group: the amino group on its side chain (pKa ~ 10.5).
    • At pH 6, the amino group will be mostly protonated (-NH3⁺), as the pH is lower than its pKa value.

Considering the net charge of the peptide at pH 6:
- Aspartic acid contributes a negative charge (-1).
- Serine is uncharged so zero and lysine contribute positive charge
- The overall charge of the peptide is 0.

Since the overall charge of the peptide is neutral at pH 6, it will migrate towards the region in the gel where molecules with no net charge typically migrate, which is near the center of the gel during gel electrophoresis.

To address the question and solution provided, let’s break down the process:

1. Determine the Net Charge of Each Amino Acid:

  • Aspartic Acid: Has a side chain carboxyl group with a pKa of around 4.0, which is deprotonated and carries a -1 charge at pH 6.
  • Serine: Has a side chain hydroxyl group with a pKa far above 6 (typically around 13), so it remains uncharged (0 charge) at pH 6.
  • Lysine: Has a side chain amino group with a pKa around 10.5, which is protonated and carries a +1 charge at pH 6.

2. Calculate the Overall Net Charge:

  • Aspartic Acid: -1
  • Serine: 0
  • Lysine: +1

Net Charge = -1 (Aspartic Acid) + 0 (Serine) + +1 (Lysine) = 0

At pH 6, the peptide overall has a net charge of 0, meaning it is at its isoelectric point and does not migrate towards either the anode or cathode in an electric field.

  1. Peptide: Glycine, Glutamic Acid, and ArginineNet Charge Calculation:
    • Glycine: Neutral (0 charge)
    • Glutamic Acid: -1 (pKa of side chain ~4.0)
    • Arginine: +1 (pKa of side chain ~12.5)
    Net Charge = 0 (Glycine) - 1 (Glutamic Acid) + 1 (Arginine) = 0Migration: At pH 6, the peptide has a net charge of 0 and will not migrate.
  2. Peptide: Alanine, Aspartic Acid, and LysineNet Charge Calculation:
    • Alanine: Neutral (0 charge)
    • Aspartic Acid: -1
    • Lysine: +1
    Net Charge = 0 (Alanine) - 1 (Aspartic Acid) + 1 (Lysine) = 0Migration: At pH 6, the peptide has a net charge of 0 and will not migrate.
  3. Peptide: Glutamine, Aspartic Acid, and HistidineNet Charge Calculation:
    • Glutamine: Neutral (0 charge)
    • Aspartic Acid: -1
    • Histidine: +1 (pKa of side chain ~6.0)
    Net Charge = 0 (Glutamine) - 1 (Aspartic Acid) + 1 (Histidine) = 0Migration: At pH 6, the peptide has a net charge of 0 and will not migrate.
  • Isoelectric Point (pI): If the pH is at the isoelectric point, the peptide will have no net charge and won’t migrate in an electric field.
  • Migration Direction: If the peptide has a net positive charge, it will migrate towards the cathode (negative electrode). If it has a net negative charge, it will migrate towards the anode (positive electrode).

In summary, the key is to calculate the net charge of the peptide at the given pH and predict its migration based on its overall charge.

32
Q

What is peptide?
What is polypeptide?
What is a protein?

A

Peptide = < 50 amino acid long
Polypeptide = > 50 amino acid long
Protein More than 1 polypeptide

33
Q

State the four structures of proteins and define them

A

Each trna has its own amino acid.
Trna brings anticodon and mRNA has codons

Long chain peptides are primary structure of protein. Example is keratin. Bonds here is covalent or peptide

Keratin is mostly helical.

Protein in aqueous solution for coil or helix. Lots of glycine here in the helix structure cuz of the turning plenty.
Bond between each amino acid is colvalent and is a peptide bond.covalent bonds are strong.

Or it forms beta sheets

Bonds holding secondary structure:
Hydrogen bonds across R polar groups.
Polar amino acids form more hydrogen bonds. When you heat it a little, the hydrogen bonds break.

Tertiary structure:
It’s built upon the secondary structure. Has combinations of alpha and beta structures

For tertiary structure to hold, the bonds holding it are sulphide or disulphide bonds (cysteine cysteine disulphide bonds ) that are formed across across. It’s relationship with cystein.
Hydrophobic interactions (example is van der waals) between R groups
Hydrogen bonds too are here

Protein in aqueous solution for coil or helix. Lots of glycine here in the helix structure cuz of the turning plenty.
Bond between each amino acid is colvalent and is a peptide bond.covalent bonds are strong.

Or it forms beta sheets

Quartenary :
Prosthetic group(for hemoglobin, it’s iron heme). Hold something soncerning quartenary structure

4 different peptides in hemoglobin (2alpha globin peptides and 2 beta globin peptides) plus a prosthetic group (iron)

Insulin is tertiary cuz it has disulphide bonds in only one peptide

Ionic bonds in quartenary structure. Ionic bonds are not strong

Primary structure:
Linear arrangement of the amino acid sequences
Peptide bonds are the most important bonds
Example is a line in the polypeptide insulin hormone

Insulin is classified as a quaternary protein.

Here’s why:

  • Primary Structure: This refers to the sequence of amino acids in a protein.
  • Secondary Structure: This involves local folding into alpha-helices and beta-sheets.
  • Tertiary Structure: This is the overall three-dimensional shape of a single polypeptide chain.
  • Quaternary Structure: This refers to the arrangement of multiple polypeptide chains (subunits) into a functional protein complex.

Insulin is composed of two polypeptide chains (A and B chains) linked by disulfide bonds. This combination of multiple polypeptide chains into a single functional unit gives insulin its quaternary structure.

An example of a primary protein structure is the sequence of amino acids in a polypeptide chain.

For instance, the primary structure of insulin includes a specific sequence of amino acids in its polypeptide chains. The sequence of amino acids in one of insulin’s chains might look something like this (simplified for illustration):

Chain A: Glycine - Valine - Glutamic Acid - Cysteine - Phenylalanine - …

This sequence determines the protein’s higher-level structures and functions.

Secondary structure:
The secondary structure of a protein refers to localized folding patterns or arrangements of amino acid residues within a protein chain.

•Within each peptide small regions may adopt specific folding patterns.
•These are called secondary structure.

Tertiary structure:
3-D arrangement of polypeptides
Built upon the secondary structure
Disulphide (-S-S-) bonds, hydrophobic interactions and H-bonds

Quartenary structure:
Multiple polypeptides (subunits) combine to form a functional protein
Held together by weak interactions
Example is hemoglobin

Protein structures refer to the three-dimensional arrangements of atoms within proteins, which are essential for their function and activity. Proteins are polymers made up of amino acids linked together by peptide bonds, and the specific sequence of amino acids determines the protein’s primary structure. However, proteins are not linear; they fold into complex three-dimensional structures dictated by the interactions between amino acid residues.

There are four levels of protein structure:

  1. Primary Structure: The linear sequence of amino acids in a protein chain, which is determined by the genetic code. This sequence is crucial, as it determines how the protein will fold and ultimately its function.
  2. Secondary Structure: Localized folding patterns within a protein chain, primarily driven by hydrogen bonding between the backbone atoms (amino and carboxyl groups) of amino acid residues. The two most common types of secondary structure are alpha helices and beta sheets.
  3. Tertiary Structure: The overall three-dimensional arrangement of a protein chain, resulting from interactions between amino acid side chains (R-groups), such as hydrogen bonding, hydrophobic interactions, van der Waals forces, and disulfide bonds. Tertiary structure determines the overall shape and stability of the protein molecule.
  4. Quaternary Structure: The arrangement of multiple protein subunits (polypeptide chains) to form a functional protein complex. Quaternary structure is only applicable to proteins composed of multiple subunits, such as hemoglobin or DNA polymerase.
34
Q

Which bonds are prominent in tertiary and secondary protein structure ?
What about quartenary structures and primary structures?
Why isn’t collagen soluble in water

A

Alpha helix and beta-pleated sheet

If alpha helix dominates, the protein will be more soluble in water

Collagen isn’t soluble in water cuz the beta plated sheets dominates. It is made of glycine,lysine and propene

• Within these structures, intramolecular interactions, hydrogen bonding between the backbone amine and carbonyl functional groups are critical to maintain 3-dimensional shape Alpha helices and beta sheets are two common types of secondary structures in proteins. Here’s a detailed overview of each:

  • Structure:
    • Shape: Right-handed spiral or coil.
    • Formation: Each turn of the helix involves approximately 3.6 amino acids. The backbone of the polypeptide chain coils around an imaginary axis.
    • Stabilization: Stabilized by hydrogen bonds that form between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid located four residues earlier in the sequence.
  • Properties:
    • R Group Position: The side chains (R groups) of the amino acids extend outward from the helix, avoiding steric clashes with the backbone.
    • Occurrence: Common in many proteins, including structural proteins like keratin.
  • Function:
    • Provides stability and elasticity to proteins. The helical structure contributes to the protein’s overall stability and flexibility.
  • Structure:
    • Shape: Composed of beta strands that are aligned side by side, forming a sheet-like structure.
    • Formation: Each beta strand is a linear segment of the polypeptide chain. The strands are held together by hydrogen bonds between the carbonyl oxygens and amide hydrogens of adjacent strands.
    • Types: Can be parallel (strands run in the same direction) or antiparallel (strands run in opposite directions).
  • Properties:
    • R Group Position: The side chains of the amino acids alternate above and below the plane of the beta sheet.
    • Occurrence: Common in proteins with a high content of beta sheets, such as fibroin in silk.
  • Function:
    • Provides strength and structural support. The beta-sheet structure is often found in proteins that require strength and rigidity, such as in silk fibers and certain enzymes.
  • Shape and Stability:
    • Alpha Helices: Coiled, forming a helical shape with hydrogen bonds stabilizing the coil.
    • Beta Sheets: Extended, forming a pleated sheet with hydrogen bonds between adjacent strands.
  • Bonding:
    • Alpha Helices: Hydrogen bonds are intra-chain (within the same helix).
    • Beta Sheets: Hydrogen bonds are inter-chain (between different strands).
  • Side Chain Orientation:
    • Alpha Helices: Side chains project outward from the helical axis.
    • Beta Sheets: Side chains alternate above and below the plane of the sheet.

These secondary structures contribute significantly to the overall folding and functionality of proteins.

Here is a list of bonds associated with each level of protein structure:

  • Peptide bonds
  • Hydrogen bonds: beta sheets and alpha helices. Alpha helices and beta sheets are stabilized primarily by hydrogen bonds
  • Hydrogen bonds
  • Ionic bonds
  • Disulfide bonds
  • Hydrophobic interactions
  • Van der Waals forces
  • Hydrogen bonds
  • Ionic bonds
  • Disulfide bonds
  • Hydrophobic interactions
  • Van der Waals forces

Tertiary and secondary: hydrogen bonds

Tertiary : hydrogen bonds and di sulphide bonds
Tertiary protein also has di sulphide bonds.
Secondary: hydrogen bonds and peptide bonds

Primary: peptide bonds or amine bonds

Quartenary structures are held by weak van der waals bonds and electrostatic forces

35
Q

Hemoglobin is made form 4 polypeptides
Myoglobin is made from one polypeptide
True or false

A

True

36
Q

Explain meiosis
How’s it different from mitosis
What is synapsis and crossing over and which phase does it occur in
Which phase of meiosis I reduces the chromosome number by half
What is the difference between anaphase I and anaphase II
Which of the types anaphases will cause splitting of the centromeres ?

A

The cell cycle in meiosis is similar to the mitotic cell cycle but includes two rounds of division (meiosis I and meiosis II) and results in four non-identical daughter cells with half the chromosome number of the original cell. Here’s how it works:

  • G1 Phase (First Gap): The cell grows and carries out normal functions.
  • S Phase (Synthesis): DNA is replicated, resulting in chromosomes that consist of two sister chromatids.
  • G2 Phase (Second Gap): The cell continues to grow, produce proteins, and prepare for division.
  • Prophase I: Chromosomes condense, homologous chromosomes pair up forming tetrads(synapsis), and crossing over (exchange of genetic material between each tetrad) occurs between non-sister chromatids (idk how to explain this so watch this video for more understanding of crossing over and you’ll understand non sister chromatids. https://youtu.be/kQu6Yfrr6j0?si=IHvh2NWUNCtAkG1w ) of homologous chromosomes. The nuclear envelope breaks down, and spindle fibers form.
    Tetrads are 4 sister chromatids of paired homologous chromosomes.
  • Metaphase I: Homologous chromosome pairs align at the metaphase plate. Each chromosome attaches to spindle fibers from opposite poles.
  • Anaphase I: Homologous chromosomes are pulled apart to opposite poles of the cell, reducing the chromosome number by half. Sister chromatids remain attached.(so the tetrad divides but retain each sister chromatid retains it centromere until each sister chromatid is finally pulled apart and the centromere is split into two in the anaphase II)
  • Telophase I: The chromosomes arrive at the poles, the nuclear envelope may reform, and the cell may begin to divide.
  • Cytokinesis: The cytoplasm divides, resulting in two haploid daughter cells. These cells have half the number of chromosomes (but each chromosome still consists of two sister chromatids).
  • This is a brief interphase-like stage. There is no DNA replication during this period. The cell prepares for the second round of division.
  • Prophase II: Chromosomes condense again, and the nuclear envelope (if reformed) breaks down. Spindle fibers reform.
  • Metaphase II: Chromosomes align individually along the metaphase plate, similar to mitosis.
  • Anaphase II: Sister chromatids are finally separated and pulled toward opposite poles.
  • Telophase II: Chromatids (now individual chromosomes) arrive at the poles, and the nuclear envelope reforms.
  • Cytokinesis: The cytoplasm divides, resulting in four haploid daughter cells, each with a single set of chromosomes. These cells are genetically distinct due to the recombination and independent assortment of chromosomes during meiosis I.
  • Meiosis I is where the chromosome number is reduced by half (from diploid to haploid).
  • Meiosis II is similar to mitosis but occurs in haploid cells and separates sister chromatids.
  • The result of meiosis is four genetically distinct haploid cells, which are the basis of gametes (sperm and egg cells) in sexually reproducing organisms.

These haploid cells can fuse during fertilization to form a diploid zygote, restoring the diploid chromosome number in the offspring.

You’re correct that the processes of mitosis and meiosis share similarities, but they differ significantly in their outcomes and specific mechanisms. Here’s a breakdown of the key differences:

  1. Number of Divisions:
    • Mitosis: Involves one division, resulting in two daughter cells.
    • Meiosis: Involves two divisions (meiosis I and meiosis II), resulting in four daughter cells.
  2. Number of Daughter Cells:
    • Mitosis: Produces two genetically identical diploid daughter cells (same number of chromosomes as the parent cell).
    • Meiosis: Produces four genetically distinct haploid daughter cells (half the number of chromosomes as the parent cell).
  3. Chromosome Number:
    • Mitosis: Maintains the chromosome number. If the parent cell is diploid (2n), the daughter cells will also be diploid.
    • Meiosis: Reduces the chromosome number by half. If the parent cell is diploid (2n), the daughter cells will be haploid (n).
  4. Genetic Variation:
    • Mitosis: Produces genetically identical cells, with no variation unless a mutation occurs.
    • Meiosis: Introduces genetic variation through crossing over (exchange of genetic material between homologous chromosomes) during prophase I and independent assortment (random separation of homologous chromosomes) during metaphase I.
  5. Pairing of Homologous Chromosomes:
    • Mitosis: Homologous chromosomes do not pair up.
    • Meiosis: Homologous chromosomes pair up and undergo synapsis during prophase I, leading to crossing over.

Point 5: Pairing of Homologous Chromosomes

•	Mitosis:
•	Homologous chromosomes (the two chromosomes of a pair, one from each parent) do not pair up during mitosis. Each chromosome behaves independently.
•	This means that during cell division in mitosis, each daughter cell receives an identical set of chromosomes, ensuring the same genetic material as the parent cell.
•	Meiosis:
•	In prophase I of meiosis, homologous chromosomes pair up in a process called synapsis. This pairing is crucial because it allows for the exchange of genetic material between the paired chromosomes through a process called crossing over.
•	This exchange of genetic material is a key feature of meiosis that contributes to genetic diversity in the resulting gametes
  1. Function:
    • Mitosis: Primarily for growth, repair, and asexual reproduction. It produces cells for tissue growth and regeneration.
    • Meiosis: Produces gametes (sperm and eggs) for sexual reproduction, ensuring genetic diversity in offspring.
  2. Stages:
    • Mitosis: Consists of prophase, metaphase, anaphase, telophase, and cytokinesis (one cycle of these stages).
    • Meiosis: Consists of two cycles of these stages: meiosis I (which includes crossing over and reduction of chromosome number) and meiosis II (which resembles mitosis but starts with haploid cells).
  3. Crossing Over:
    • Mitosis: Does not involve crossing over.
    • Meiosis: Crossing over occurs in prophase I, leading to genetic recombination and variation.

Mitosis:
• Crossing over does not occur in mitosis. The chromosomes replicate and divide, but there is no exchange of genetic material between them.
• As a result, the two daughter cells are genetically identical to the parent cell and to each other.
• Meiosis:
• During prophase I of meiosis, homologous chromosomes undergo crossing over. This is where segments of DNA are exchanged between the paired chromosomes.
• Crossing over creates new combinations of genes, which increases genetic variability in the gametes (sperm and egg cells). This genetic diversity is important for evolution and adaptation in sexually reproducing organisms.

Summary:

•	Point 5 (Pairing): Homologous chromosomes pair up in meiosis (not in mitosis), which is necessary for crossing over and genetic diversity.
•	Point 8 (Crossing Over): Crossing over occurs in meiosis, allowing for the exchange of genetic material and contributing to genetic diversity; it does not happen in mitosis.
  • Mitosis creates two identical daughter cells with the same chromosome number as the parent, used for growth and repair.
  • Meiosis creates four genetically distinct daughter cells with half the chromosome number, used for sexual reproduction and contributing to genetic diversity.

While the processes of division (prophase, metaphase, anaphase, telophase) are similar in both, the critical differences lie in the pairing of homologous chromosomes, the reduction of chromosome number, and the introduction of genetic variation in meiosis.

37
Q

Difference between chromatin and chromosomes
Which of them is the complex of DNA and proteins (primarily histones) that make up the contents of the nucleus during the interphase of the cell cycle?
Which of them occurs when certain fibers undergo condensation, becoming highly organized and compacted into distinct structures leading to condensation?

A

Explanation:

•	Chromatin: This refers to the complex of DNA and proteins (primarily histones) that make up the contents of the nucleus during the interphase of the cell cycle. During this phase, chromatin is loosely packed, allowing for processes like transcription and replication to occur.
•	Chromosome Condensation: As a cell enters mitosis or meiosis, the chromatin fibers undergo condensation, becoming highly organized and compacted into distinct structures called chromosomes. This process is referred to as chromosome condensation.

Summary:

•	Chromatin condensation refers to the initial packing of DNA and proteins into chromatin.
•	Chromosome condensation refers to the further compaction of chromatin into visible chromosomes during cell division.

In the context of cell division, chromosome condensation is the more accurate and commonly used term.

Yes, chromosomes are compacted chromatin.

  • Chromatin is a complex of DNA and proteins (mainly histones) that is loosely packed within the nucleus during interphase.
  • During cell division (mitosis or meiosis), chromatin fibers condense and coil tightly to form chromosomes, which are the distinct, visible structures that ensure accurate distribution of genetic material to daughter cells.
38
Q

Explain the process of protein synthesis (transcription and translation)

Here is an MCQ based on stop codons:

Which of the following codons does NOT serve as a stop signal during protein synthesis?

A) UAA
B) UGA
C) AUG
D) UAG

*

A

Transcription
Translation

Of course! Here’s the explanation with key terms and enzymes included:

Imagine your body is like a big, busy factory that makes lots of different things. One of the most important things the factory makes is proteins, which are like tiny machines that do lots of different jobs in your body, like helping you grow or fixing things when you get hurt.

Here’s how the factory makes these proteins:

  1. Making the Blueprint (Transcription):
    • First, the factory needs a blueprint (which is like a special set of instructions) to make the protein. This blueprint is written in a special language called DNA, which is inside the nucleus of the cell.
    • The factory workers (called RNA polymerase) read the DNA blueprint and make a copy of it called mRNA (messenger RNA). This mRNA is like a message that tells the rest of the factory how to build the protein. RNA polymerase is the enzyme that helps to create this mRNA copy from the DNA. (Transcription)
    1. DNA Blueprint:
      • Inside the nucleus, the DNA holds the instructions for making proteins.
      • The enzyme RNA polymerase reads the DNA and makes a copy called mRNA (messenger RNA).
  2. Building the Protein (Translation):
    • Next, the mRNA message travels out of the nucleus to the part of the cell where proteins are made (called ribosomes).
    • The ribosomes read the mRNA message in small steps and put together the protein by joining tiny building blocks called amino acids. These amino acids are like the parts of a LEGO set that snap together to build something new.
    • tRNA (transfer RNA) brings the amino acids to the ribosome, matching them to the mRNA code. The ribosome uses these amino acids to build the protein.
    • Peptidyl transferase is the enzyme inside the ribosome that helps link the amino acids together to form a chain.

Translation)

2.	Role of rRNA:
•	rRNA (ribosomal RNA) is a key component of the ribosome, which is the part of the cell that assembles proteins.
•	The ribosome is made up of rRNA and proteins and functions like a machine that reads the mRNA message and helps link amino acids together to form the protein.
3.	Role of tRNA:
•	tRNA (transfer RNA) brings the building blocks, or amino acids, to the ribosome.
•	Each tRNA has an anticodon that matches a specific codon on the mRNA. The codons are like codes that tell the ribosome which amino acid to add next.
•	For example, if the mRNA code says “AUG,” the corresponding tRNA with the anticodon “UAC” will bring the amino acid methionine to the ribosome.
•	The tRNA molecules make sure that the amino acids are added in the correct order as specified by the mRNA code.
4.	Protein Assembly:
•	The ribosome reads the mRNA message, and tRNA molecules bring the appropriate amino acids to the ribosome.
•	Inside the ribosome, the enzyme peptidyl transferase helps link the amino acids together to form a chain. This chain then folds into a functional protein.

When all the amino acids are joined in the right order, the new protein is finished!

So, in short, the factory first writes down the instructions (transcription) with the help of RNA polymerase, then follows those instructions to build something (translation) with the help of ribosomes, tRNA, and peptidyl transferase. That’s how your body makes the proteins it needs to keep everything running smoothly!

—Translation:

•	Location: Cytoplasm (specifically at the ribosomes)
•	Process:
1.	Initiation: The mRNA binds to a ribosome. The ribosome reads the mRNA sequence in sets of three nucleotides (codons). The start codon (usually AUG) signals the beginning of translation.
2.	Elongation: Transfer RNA (tRNA) molecules, each carrying a specific amino acid, bind to the complementary mRNA codons through their anticodons. The ribosome facilitates the formation of peptide bonds between adjacent amino acids, elongating the polypeptide chain.
3.	Termination: When the ribosome encounters a stop codon on the mRNA, translation ends. The newly synthesized polypeptide chain is released and folds into its functional three-dimensional structure.
4.	Folding and Post-Translational Modifications: The polypeptide chain folds into its functional shape, often with the assistance of chaperone proteins. It may also undergo post-translational modifications, such as phosphorylation or glycosylation, to become fully functional.

Summary:

•	Transcription: DNA → mRNA
•	Translation: mRNA → Protein

Here is an MCQ based on stop codons:

Which of the following codons does NOT serve as a stop signal during protein synthesis?

A) UAA
B) UGA
C) AUG
D) UAG

Answer: C) AUG

Explanation: UAA, UGA, and UAG are stop codons that signal the end of protein synthesis, while AUG is a start codon that also codes for methionine, marking the beginning of protein synthesis.

39
Q

Certainly! Here are the 15 MCQs with possible answers:

  1. Which enzyme is responsible for unwinding the DNA double helix during replication?A) DNA polymerase
    B) RNA polymerase
    C) Helicase
    D) Ligase
  2. What is the main function of DNA polymerase during DNA replication?A) Synthesizes RNA from a DNA template
    B) Adds nucleotides to a growing DNA strand
    C) Joins Okazaki fragments on the lagging strand
    D) Unwinds the DNA double helix
  3. Which enzyme synthesizes RNA during transcription?A) DNA ligase
    B) RNA polymerase
    C) Topoisomerase
    D) Reverse transcriptase
  4. During translation, which enzyme is responsible for forming peptide bonds between amino acids?A) Peptidyl transferase
    B) Aminoacyl-tRNA synthetase
    C) Helicase
    D) RNA polymerase
  5. Which enzyme is used to charge tRNA molecules with their respective amino acids during translation?A) Aminoacyl-tRNA synthetase
    B) Peptidyl transferase
    C) Helicase
    D) RNA polymerase
  6. Which enzyme catalyzes the removal of supercoils generated ahead of the replication fork during DNA replication?A) DNA polymerase II
    B) Helicase
    C) DNA gyrase
    D) RNA primase
  7. What is the role of topoisomerase during DNA replication?A) Synthesizes RNA primers
    B) Unwinds the DNA double helix
    C) Relieves supercoiling ahead of the replication fork
    D) Adds nucleotides to the growing DNA strand
  8. Which enzyme synthesizes short RNA primers that are necessary for DNA replication to begin?A) DNA polymerase I
    B) Primase
    C) Ligase
    D) RNA polymerase
  9. Which of the following enzymes is involved in the process of RNA splicing in eukaryotic cells?A) Ribonuclease
    B) Spliceosome
    C) RNA polymerase
    D) DNA ligase
  10. Which enzyme is responsible for charging tRNA molecules with their respective amino acids during translation?A) Aminoacyl-tRNA synthetase
    B) Peptidyl transferase
    C) Helicase
    D) RNA polymerase
  11. Which enzyme degrades RNA primers during DNA replication in eukaryotes?A) RNA polymerase
    B) DNA polymerase α
    C) DNA polymerase I
    D) RNase H
  12. During transcription, what is the function of RNA polymerase II in eukaryotic cells?A) Synthesizes ribosomal RNA (rRNA)
    B) Synthesizes transfer RNA (tRNA)
    C) Synthesizes messenger RNA (mRNA)
    D) Synthesizes DNA
  13. What enzyme synthesizes the RNA component of telomerase that elongates telomeres in eukaryotic cells?A) RNA polymerase I
    B) RNA polymerase II
    C) RNA polymerase III
    D) Telomerase
  14. Which enzyme synthesizes the leading strand continuously during DNA replication?A) DNA polymerase III
    B) DNA polymerase I
    C) RNA polymerase
    D) DNA ligase
  15. Which enzyme is responsible for sealing nicks and joining Okazaki fragments on the lagging strand during DNA replication?A) DNA polymerase III
    B) Topoisomerase
    C) DNA ligase
    D) Primase
A

Here are five multiple-choice questions (MCQs) on the common enzymes used in replication, transcription, and translation:

Which enzyme is responsible for unwinding the DNA double helix during replication?

A) DNA polymerase
B) RNA polymerase
C) Helicase
D) Ligase

Answer: C) Helicase

What is the main function of DNA polymerase during DNA replication?

A) Synthesizes RNA from a DNA template
B) Adds nucleotides to a growing DNA strand
C) Joins Okazaki fragments on the lagging strand
D) Unwinds the DNA double helix

Answer: B) Adds nucleotides to a growing DNA strand

Which enzyme catalyzes the synthesis of RNA during transcription?

A) DNA ligase
B) RNA polymerase
C) Topoisomerase
D) Reverse transcriptase

Answer: B) RNA polymerase

During translation, which enzyme is responsible for forming peptide bonds between amino acids?

A) Peptidyl transferase
B) Aminoacyl-tRNA synthetase
C) Helicase
D) DNA polymerase

Answer: A) Peptidyl transferase

Which enzyme is involved in removing RNA primers and filling in the gaps with DNA nucleotides during DNA replication?

A) DNA polymerase I
B) DNA ligase
C) RNA polymerase
D) Primase

Answer: A) DNA polymerase I

These questions cover key enzymes involved in DNA replication, RNA transcription, and protein translation processes.

Here are ten more multiple-choice questions (MCQs) on the common enzymes used in replication, transcription, and translation:

Which enzyme is responsible for sealing nicks and joining Okazaki fragments on the lagging strand during DNA replication?

A) DNA polymerase III
B) Topoisomerase
C) DNA ligase
D) Primase

Answer: C) DNA ligase

What is the role of topoisomerase during DNA replication?

A) Synthesizes RNA primers
B) Unwinds the DNA double helix
C) Relieves supercoiling ahead of the replication fork
D) Adds nucleotides to the growing DNA strand

Answer: C) Relieves supercoiling ahead of the replication fork

Which enzyme synthesizes short RNA primers that are necessary for DNA replication to begin?

A) DNA polymerase I
B) Primase
C) Ligase
D) RNA polymerase

Answer: B) Primase

Which of the following enzymes is involved in the process of RNA splicing in eukaryotic cells?

A) Ribonuclease
B) Spliceosome
C) RNA polymerase
D) DNA ligase

Answer: B) Spliceosome

Which enzyme is used to charge tRNA molecules with their respective amino acids during translation?

A) Aminoacyl-tRNA synthetase
B) Peptidyl transferase
C) Helicase
D) RNA polymerase

Answer: A) Aminoacyl-tRNA synthetase

Which enzyme catalyzes the removal of supercoils generated ahead of the replication fork during DNA replication?

A) DNA polymerase II
B) Helicase
C) DNA gyrase
D) RNA primase

Answer: C) DNA gyrase

During transcription, what is the function of RNA polymerase II in eukaryotic cells?

A) Synthesizes ribosomal RNA (rRNA)
B) Synthesizes transfer RNA (tRNA)
C) Synthesizes messenger RNA (mRNA)
D) Synthesizes DNA

Answer: C) Synthesizes messenger RNA (mRNA)

Which enzyme degrades RNA primers during DNA replication in eukaryotes?

A) RNA polymerase
B) DNA polymerase α
C) DNA polymerase I
D) RNase H

Answer: D) RNase H

What enzyme synthesizes the leading strand continuously during DNA replication?

A) DNA polymerase III
B) DNA polymerase I
C) RNA polymerase
D) DNA ligase

Answer: A) DNA polymerase III

Which enzyme is responsible for the synthesis of the RNA component of telomerase that elongates telomeres in eukaryotic cells?

A) RNA polymerase I
B) RNA polymerase II
C) RNA polymerase III
D) Telomerase

Answer: D) Telomerase

These questions provide a broader understanding of the various enzymes involved in the key biological processes of replication, transcription, and translation.

Question 11: Which enzyme catalyzes the removal of supercoils generated ahead of the replication fork during DNA replication?

Answer: C) DNA gyrase

Explanation:
During DNA replication, the unwinding of the DNA double helix by helicase creates tension and supercoiling ahead of the replication fork. DNA gyrase, a type of topoisomerase (specifically, Topoisomerase II in prokaryotes), is responsible for relieving this supercoiling by cutting both strands of the DNA, allowing it to untwist and then resealing the strands. This action prevents the DNA from becoming too tightly coiled, which would otherwise impede the replication process.

Question 7: What is the role of topoisomerase during DNA replication?

Answer: C) Relieves supercoiling ahead of the replication fork

Explanation:
Topoisomerase is a crucial enzyme during DNA replication that helps manage the topology of DNA. As helicase unwinds the DNA strands, it introduces positive supercoiling ahead of the replication fork. Topoisomerases work by creating temporary nicks in one or both strands of the DNA, allowing the DNA to unwind and relieve the supercoils. There are two main types of topoisomerases:
- Topoisomerase I cuts one strand of the DNA to relieve supercoiling.
- Topoisomerase II (such as DNA gyrase in prokaryotes) cuts both strands of DNA to manage supercoils, which is particularly important during replication and transcription.

Both enzymes play a critical role in maintaining the structural integrity and stability of DNA during cellular processes

40
Q

What is the name of the type of supercoiling that occurs when the DNA helix is overwound and
happens ahead of the replication fork where helicase unwinds the DNA strands?
What is the impact of Overwinding on the DNA strands?

What the type of supercoiling that occurs when the DNA helix is underwound?

A

To relieve supercoils means to reduce the overwinding or underwinding of DNA that occurs when the double helix is unwound during processes like replication or transcription. Supercoiling is a natural consequence of the helical structure of DNA; when the DNA double helix is unwound by enzymes like helicase to allow replication or transcription to occur, it causes stress on the DNA strand, leading to supercoils forming ahead of the unwound region.

  1. Positive Supercoiling: This occurs when the DNA helix is overwound. It happens ahead of the replication fork where helicase unwinds the DNA strands. Overwinding increases tension and compacts the DNA even more tightly, making it harder to separate the strands.
  2. Negative Supercoiling: This occurs when the DNA helix is underwound. Underwinding can occur naturally and makes it easier to open the DNA strands, which is helpful for processes like transcription and replication.

Topoisomerases are enzymes that manage the level of supercoiling in DNA to maintain stability and allow replication and transcription to proceed smoothly. Here’s how they work:

  • Topoisomerase I: Cuts one strand of the DNA helix, allowing it to rotate and relieve tension. This reduces supercoiling without causing extensive breaks. After relieving the tension, the enzyme reseals the cut strand.
  • Topoisomerase II (e.g., DNA gyrase in prokaryotes): Cuts both strands of the DNA helix, passes another segment of the double helix through the break, and then reseals the cut. This process is particularly useful for untangling DNA molecules that become knotted or supercoiled.

Relieving supercoils is crucial because:

  • Prevents DNA Breakage: Excessive supercoiling can cause the DNA strand to break or become damaged.
  • Facilitates Replication and Transcription: Removing supercoiling helps replication and transcription machinery (such as DNA polymerase and RNA polymerase) move along the DNA strand without obstruction.
  • Maintains DNA Integrity: Proper management of DNA supercoiling ensures that the DNA remains stable and compacted properly within the cell.

Overall, relieving supercoils is essential for the proper functioning of cells and for maintaining the integrity of genetic information during cellular processes.

41
Q

Proteins are polymers of amino acids. Proteins are polymers, meaning they are made up of smaller units called amino acids.

First carbon from amine group is the alpha carbon. At the “center” of each amino acid is a carbon called the α carbon and attached to it are four groups - a hydrogen, an α- carboxyl group, an α-amine group, and an R-group, sometimes referred to as a side chain.

Arginine: body can make but can’t produce enough
Premature children can’t produce arginine.
Histidine and arginine are semi essential

Tyrosine is non essential but is synthesized form phenylalanine so not enough of phenylalanine means you won’t get enough of tyrosine

Function of amino acids in a protein depends on the R group. Also, if it’ll be acid or base or neutral, it’ll depend on the R group or side chain

Aliphatic chain means the amino acid is non polar or hydrophobic
Glycine is the smallest of all the amino acids. Has an R group that’s a hydrogen.
Glycine doesn’t have asymmetrical alpha carbon so glycine can’t rotate left or right when exposed to polarized light

Is clockwise left or right.clockwise is right and counter or anti clockwise is left
The rotation depends on the alpha carbon.
Glycine has a Symmetrical alpha carbon
Alpha carbon serves as a chiral center

Yes, you’re correct about glycine and its unique properties. Here’s a breakdown:

  1. Aliphatic chain: Yes, amino acids with aliphatic side chains (like glycine, alanine, valine, leucine, and isoleucine) are generally non-polar because their side chains are composed mainly of hydrocarbons, making them hydrophobic.
  2. Glycine: It is the smallest amino acid, with an R-group that is simply a hydrogen atom. Because of this, glycine does not have a chiral center (asymmetrical alpha carbon). It is achiral, meaning it does not rotate plane-polarized light, unlike other amino acids which do have asymmetric alpha carbons and are chiral.
  3. Chiral center and rotation: In amino acids with a chiral alpha carbon (i.e., all amino acids except glycine), the arrangement of the four different groups around the alpha carbon determines the molecule’s ability to rotate polarized light.
  4. Clockwise or Counterclockwise: The direction of rotation (clockwise or counterclockwise) refers to how a chiral molecule rotates plane-polarized light.
    • Dextrorotatory (D or +) means the molecule rotates light clockwise (to the right).
    • Levorotatory (L or -) means the molecule rotates light counterclockwise (to the left).

This optical activity depends on the specific configuration of the alpha carbon.

Yes, exactly! All amino acids except glycine have a chiral center (the alpha carbon attached to four different groups), which allows them to rotate plane-polarized light. Glycine, on the other hand, has a symmetrical alpha carbon because its R-group is just a hydrogen atom, making two of the groups attached to the alpha carbon identical (two hydrogen atoms). Oh okay so the R group is opposite the hydrogen group on the alpha carbon. Because glycines R group is a hydrogen, it is symmetrical to the hydrogen that is opposite it on the chiral center or alpha carbon. This lack of asymmetry means glycine is achiral, and as a result, it does not rotate plane-polarized light.

In summary:
- All amino acids except glycine are chiral and rotate light.
- Glycine is achiral and does not rotate light due to its symmetrical alpha carbon.

glycine is achiral, meaning it cannot exist as two mirror-image enantiomers and, therefore, does not rotate plane-polarized light. This is why glycine is optically inactive.

These enantiomers are non-superimposable mirror images of each other.

Humans use more of L form of amino acids so it’s not best to give D form of amino acids

L-amino acids are typically the form found in proteins and rotate light in one direction (often counterclockwise).
• D-amino acids rotate light in the opposite direction and are rarely found in proteins but can occur in some bacteria.

The rotation of light, or optical activity, is a key characteristic of chiral molecules, which is absent in glycine due to its lack of a chiral center.

Valine and isoleucine have branched ethylene groups

Phenylalanine tyrosine and tryptophan have aromatic rings

Proteins tend to fold into three dimensional substances. The three-dimensional (3D) structure refers to the tertiary structure, which includes the overall folding of a polypeptide chain into a complex shape.

So, the secondary structure is 2D in nature, while the tertiary structure is 3D.

Polar but not charged; usually form hydrogen bonds in aqueous soln and have an amine group attached or a hydroxyl group(OH or NH groups): serine and threonine (hydroxyl group is important in proteins)

Cysteine has SH group church helps form hydrogen bones

Aspartame and glutamate relationship with asparagine

Charged basic:

7.4: charged amino acids attract have +1 or -1
Amide group become protonated means you remove H from water which leads to hydroxyl group
Arginine lysine and histidine

Charged acidic:
Have carboxyl group attached at physiologic ph of 7.4 will give off hydrogen ions. COOH gives its hydrogen ions to become COO-

At physiological pH (around 7.4), charged amino acids like arginine, lysine, and histidine (basic amino acids) typically carry a positive charge (+1) because their side chains accept a proton (H⁺).
• Acidic amino acids like aspartate and glutamate have side chains that lose a proton, leaving them with a negative charge (-1) at pH 7.4.

Sickle cell SC:
It changes from glutamate to what?

Sulphur containing amino acids:
Methionine and cysteine.
Cysteine helps maintain structure of an amino acid

Cysteine has SH group church helps form hydrogen bones

Proline: rigid protein
Glycine:??

Memorize Whether the amino acids are polar or non polar or acidic or basic

NB: maximize your strength. Go through the courses and maximize your strength. Focus more on the courses that are easier for you cuz I think each course brings 15 questions
Know the names of the lecturers who taught you and the name sof the faculty that were introduced to you at the start

Each trna has its own amino acid.
Trna brings anticodon and mRNA has codons

Long chain peptides are primary structure of protein. Example is keratin. Bonds here is covalent or peptide

Keratin is mostly helical.

Protein in aqueous solution for coil or helix. Lots of glycine here in the helix structure cuz of the turning plenty.
Bond between each amino acid is colvalent and is a peptide bond.covalent bonds are strong.

Or it forms beta sheets

Bonds holding secondary structure:
Hydrogen bonds across R polar groups.
Polar amino acids form more hydrogen bonds. When you heat it a little, the hydrogen bonds break.

Tertiary structure:
It’s built upon the secondary structure. Has combinations of alpha and beta structures

For tertiary structure to hold, the bonds holding it are sulphide or disulphide bonds (cysteine cysteine disulphide bonds ) that are formed across across. It’s relationship with cystein.
Hydrophobic interactions (example is van der waals) between R groups
Hydrogen bonds too are here

Protein in aqueous solution for coil or helix. Lots of glycine here in the helix structure cuz of the turning plenty.
Bond between each amino acid is colvalent and is a peptide bond.covalent bonds are strong.

Or it forms beta sheets

Quartenary :
Prosthetic group(for hemoglobin, it’s iron heme). Hold something soncerning quartenary structure

4 different peptides in hemoglobin (2alpha globin peptides and 2 beta globin peptides) plus a prosthetic group (iron)

Insulin is tertiary cuz it has disulphide bonds in only one peptide

Ionic bonds in quartenary structure. Ionic bonds are not strong

LIPIDS:

Physical properties are most important for you to call a molecule a lipid.
Soluble in organic solvents

water is classified as an inorganic solvent. Here’s why:

Characteristics of Water as an Inorganic Solvent:

1.	Inorganic Nature: Water (H₂O) does not contain carbon-hydrogen (C-H) bonds, which are characteristic of organic compounds. This makes it an inorganic molecule.

organic compounds are those that contain carbon atoms, often bonded to hydrogen, oxygen, nitrogen, and other elements. The field of organic chemistry focuses on these carbon-containing compounds and their reactions.

Breaking ester bonds in triglycerides using hydrolysis

Carboxylic acids are called fatty acids

Double bonds in aliphatic chain is called unsaturated fatty acid. Aliphatic chains are non polar.

What acid is metabolized in Peroxisomes?This acid is branched chain. To which because of this, children without this enzyme that breaks it down causes mental disease

Acetic acid (vinegar) is soluble
Butyric acid downwards is insoluble.
In nature, fatty acids are in even numbers

Configuration of double bonds in most unsaturated is cis GEOMETRIC isomer

Olive oil is better.

Bulky functional groups on one side are unstable
Those on opposite sides are stable
So opposite sides is trans and cis is same side

But even though cis is unstable, we have enzymes to break down in the body but we dont for trans
Cis; we have enzymes to break them down
Trans; cause health problems from frying for so long using the same oil so it converts cis fatty acids to trans.

Hydrogenation converts cis to trans

Fats or solids will have more of saturated fatty acids and will be stable
Liquids are more unstable cuz of the unsaturated fatty acids and so move in any direction.

Fishes in cold environments have unsaturated fatty acids so their membranes won’t become hard due to the cold environment.

Palm oil which is saturated isn’t bad cuz it produces lots of energy but you have to be active if you want to take lots of palm oil else it’ll go and just produce fat. Palm oil usually becomes hard

To remember the differences between saturated and unsaturated fats, you can use these mnemonic devices and visual cues:

  • Mnemonic: “Saturated = Solid”
    • Saturated fats are typically solid at room temperature (like butter or lard).
  • Double Bonds: “None” (No double bonds)
    • Saturated fats have no double bonds in their fatty acid chains; all carbon atoms are fully “saturated” with hydrogen atoms.
  • Visual Cue: Think of “Saturated” as being “full” or “solid,” like a sponge that can’t absorb any more water. In this case, the sponge is “saturated” with hydrogen.
  • Mnemonic: “Unsaturated = Oily”
    • Unsaturated fats are generally liquid at room temperature (like olive oil or fish oil).
  • Double Bonds: “Double Bonds Present”
    • Unsaturated fats have one or more double bonds in their fatty acid chains, creating “kinks” that prevent the molecules from packing closely together, thus remaining liquid.
  • Visual Cue: Imagine “Unsaturated” as a “less full” sponge with spaces (kinks) where the water (hydrogen) hasn’t been absorbed. The gaps from double bonds prevent the fat from being solid.
  • Saturated Fats: Solid at room temperature, no double bonds.
  • Unsaturated Fats: Liquid at room temperature, one or more double bonds.

These cues help you connect the structural features of fats with their physical state and properties.

Most cholesterol in body is esterified so you need fatty acids to esterification it

Triglyceride is a trihydric alcohol.

Characteristics of triglycerides:
Specific gravity is less than 1.0 so all fats and oils float it water
They are liquids at 20degrees celcius and solid at room temperature

Phospholipids
Most phospholipids are derivatives of??
Phosphatidic acid(phosphate is esterified with the -OH of a suitable alcohol)

Some phospholipids have zero charges but they still form hydrogen bonds

What acid is metabolized in Peroxisomes?This acid is branched chain. To which because of this, children without this enzyme that breaks it down causes mental disease

The acid you’re referring to is likely phytanic acid. It is a branched-chain fatty acid that is metabolized in peroxisomes. A deficiency in the enzyme needed to break down phytanic acid can lead to a disorder called Refsum disease, which can cause various neurological issues.

A

Types of isomers
Structural isomers and stereoisomers.

Structural isomers: have same molecular formula but different structural formula(as in different bonding)
Stereisomers have same structural formula but different spatial arrangements or geometries.
Geometric and optical isomerism as types of stereoisomers.

Here’s a summary of the amino acids you mentioned, categorized by their properties:

  • Valine: Non-polar, branched chain.
  • Isoleucine: Non-polar, branched chain.
  • Phenylalanine: Non-polar, aromatic ring.
  • Tyrosine: Polar, aromatic ring (contains a hydroxyl group).
  • Tryptophan: Non-polar, aromatic ring.
  • Serine: Polar, has a hydroxyl group (–OH).
  • Threonine: Polar, has a hydroxyl group (–OH).
  • Cysteine: Polar, contains a sulfhydryl group (–SH), which can form disulfide bonds.
  • Arginine: Basic, positively charged at physiological pH (7.4).
  • Lysine: Basic, positively charged at physiological pH (7.4).
  • Histidine: Basic, can be positively charged depending on the pH.
  • Aspartate (Aspartic Acid): Acidic, negatively charged at physiological pH (7.4).
  • Glutamate (Glutamic Acid): Acidic, negatively charged at physiological pH (7.4).
  • Asparagine: Neutral, contains an amide group, not charged.
  • Methionine: Non-polar, contains sulfur.
  • Proline: Non-polar, rigid structure due to its unique cyclic form.
  • Glycine: Non-polar, the smallest amino acid, and flexible; it can fit into tight spaces in protein structures.
  • In sickle cell disease, the mutation changes glutamate (an acidic amino acid) to valine (a non-polar amino acid), which affects the protein’s structure and function.
  • Aromatic: Remember the “Phe, Tyr, Trp” trio for phenylalanine, tyrosine, and tryptophan.
  • Polar: Think of serine and threonine as the “hydroxyl heroes” for their –OH groups.
  • Charged: Use the phrase “Positive Arg, Lys, His” for basic and “Negative Asp, Glu” for acidic.
  • Branched: Valine and isoleucine are both “V” for branched.

Feel free to ask if you need more specific details or help with memorization!

42
Q

Methionine starts codon to initiate Protein synthesis.
It and cysteine are the two Sulphur containing amino acids
Tryptophan is the only amino acid with 2 rings
Phenylalanine has a side chain that’s a ring
Serine and threonine are the two alcohols

Proline introduces kinks into the peptide chain

Asparagine has a strong hydrogen bonding in secondary structures
Glutamine transports nitrogen in the body
Histidine is a biological buffer
Glutamate is an excitatory neurotransmitter

Polar uncharged amino acids
Sera Tells her Cyster (Sister) to Try Aspirin Gum
Serine
Threonine
Cysteine Tyrosine
Asparagine Glutamine

Polar Charged Amino Acids
Aspiring Girl Lykes (likes) Art and History
Aspartic Acid
Glumatic Acid
Lysine
Arginine
Histidine

Positively charged or basic amino acids:
Histidine
Arginine
Lysine

Negatively charged or acidic:
Aspartate(not asparagine)
Glutamate (not glutamine)

A
43
Q

Biochem
1. Protein or post translational modification occurs in ER and tagging occurs in Golgi and distributed via the vesicle and transported to plasma membrane and gone by exocytosis
2. Mutation in hydrophobic domain of a protein. Which mutation would most be deleterious. Asn was Valine to lysine.
- [x] 3.A. Cytoplasm also does fatty acid synthesis ???
- [x] 4.A
- [ ] 5.A basic building blocks of ribosomal rna is ribonucleotides.
6. Plants store their starch in amylopectin
7. Amino acid is mostly in the L form. What about the D form? It’s carbohydrates
8.
- [x] 7.B
- [ ] 8.B. If a disease affects the golgi, the plasma membrane will be affected. Cuz it gets regeneration from the golgi
- [ ] 9.B disruption in hydrogen bonding between 2 different polypeptide subunits of a protein will most likely affect affect, the answer is Quartenary and not secondary
- [x] 10.A
- [x] 11.C (which bonds jn dna has a high temp To denature )
- [x] 12.A. Check where the ketose or aldose is to determine whether the thing is left or right to know if it’s L or D. Anomers are either alpha or beta
- [x] 13.B (glycogen and amylose glycosidic bonds) S and R and L forms or something
- [ ] 14.
- [x] 15.D
- [x] 16.A (ions cannot easily diffuse into plasma membrane cuz inside is hydrophobic)(between sodium and potassium, which is bigger in weight)
- [x] 17.C
- [x] 18.D
- [x] 19.C
- [ ] 20. RNA polymerase is involved in catalysing of a phosphodiester bond involving a uracil triphosphate
- [x] 21.C
- [ ] 22????D answer is B. If too much exocytosis and less endocytosis,plasma membrane will increase in size
- [x] 23D
- [ ] 24???C NAD FAD NADP are made up of nucleotides and carbohydrates
- [ ] 25 A examples of carb polymers are chitin cellulose amylopectin but mannose isn’t a polymer of carbohydrate. Becareful of this polymer polymer thing. The big one is a polymer of the small one not the small one being a polymer of the big one. Always remember
Acetyl co A is a precursor to cholesterol
Foam cells in blood vessels
How does cholesterol maintain membrane homeostasis

Limitations of dogma theory:
RNA can replicate itself
DNa can go straight to protein without becoming rna and being translated
RNA can go back to being DNA

Nitrogenous bases form nucleotides.
Phrimidines are 3
Purines are 2

Nitrogenous base reacts with ribose using a covalent bond to form nucleoside

Nitrogenous base is made up of two main groups:
Purines
Pyrmidines.

Pyrimidines have one ring structure
Purines have two ring structures

Base is attached to ribose and ribose is attached to a phosphate.
Phosphate reacts with OH.

RNA serves as a template for synthesis of DNA only in there is reverse transcriptase.
In reverse transcription, if the thing encounters A, what will it put there?
It will put T there.

This is the difference between RNA polymerase and reverse transcriptase

Nucleotide functions and nucleic acid functions

Every phosphate bond broken generates high amount of energy

ATP is made up of which macromolecules: Carbohydrates (ribose)
• Nucleotides/nucleic acids (adenine and phosphate groups)
These are the key macromolecular components of ATP.

Yes, ATP is made up of nucleotides and phosphate groups.

  • Nucleotides: ATP is a nucleotide itself. It consists of:
    1. Adenine (a nitrogenous base, specifically a purine)
    2. Ribose (a five-carbon sugar)
  • Phosphate Groups: ATP has three phosphate groups attached to the ribose sugar. These phosphate groups

Purine and pyrimidines analogues to make drugs as a nucelotide function.
Nucleic acid is for protein synthesis too cuz of the trna and rRNA

A
44
Q

Biochem

Isomerism is constitutional or structural and stereo isomers(example is geometric isomers). Ketose and aldose are structural isomers

Stereo isomers have same molecular formula and connectivity between atoms but are oriented differently in three dimensional space

. Glycine is found in every 3rd position in collagen. Is collagen insoluble? Cuz glycine is non polar.
Glycine is used to synthesize poryphrin which is a component of heme and purine.

Alanine is a major substrate for gluconeogenesis

Transfers methyl groups and is needed to make cysteine: methionine

Branched:leucine isoleucine and valine (LIVe tree. Trees are branched)

Proline: has a side chain with 5 members nitrogen containing ring. Creates conformational rigidity and is stuck in one position all the time. This is important for collagen cuz it’s important for alpha helix formation.
Collagen doesn’t use beta plated sheets. Only alpha. It is a Quartenary structure. It’s insoluble cuz of the triple helix it forms

Proline’s five-membered ring is not aromatic because it lacks the delocalized π-electrons and conjugated double bonds that define aromatic structures. Therefore, it is not classified as an aromatic amino acid, even though it has a ring structure.

Phenylalanine is a precursor to tyrosine.

Tryptophan is needed to synthesize niacin and the indoleamines (serotonin and melatonin)

Polar amino acids have uneven distribution of charges throughout their atoms

Polar amino acids:
Tyrosine is a precursor to melanin,thyroxine and catecholamines

Serine and threonine: undergo post translational modification such as addition of O oligosaccharides in Golgi apparatus for cell trafficking

Asparagine also undergoes post translational modifications such as addition of N oligosaccharides in endoplasmic reticulum for cell trafficking.

Video said cysteine is non polar but confirm from the slides cuz for what I know, it is polar but uncharged and it’s methionine mmom that is not polar

Glutamine:purine and pyrimidines nucleotides.

Acidic: glutamate and Aspartate: have negative charge at body ph. They are hydrophilic.

Basic : also hydrophilic. Arginine, lysine and histidine.

Arginine and lysine are found in histone proteins. Histones need to interact with negatively charged DNA AND THEir positive charge from lysine and arginine helps them do So. This is important in regulation of transcription.

Arginine and histidine are essential for growth so arginine stimulates insulin like growth factor. And they’re semi essential amino acids.
Histidine is neutral at body ph but can accept a proton that’s why it’s considered a basic amino protein.
Histidine is important Especially in children during pregnancy and in anyone recovering from trauma

Types of amino acids in TCA cycle:
Glucogenic-metabolized to glucose during gluconeogenesis. The remaining 13.
Ketogenic-degraded to acetyl coA. Leucine and lysine.
Glucogenic and ketogenic-tyrosine,threonine,tryptophan,phenylalanine,isoleucine

The TCA cycle (tricarboxylic acid cycle), also known as the Krebs cycle or the citric acid cycle, is a crucial metabolic pathway that plays a central role in cellular respiration. Here’s an overview of its key features, functions, and steps:

Overview

•	Location: The TCA cycle takes place in the mitochondrial matrix of eukaryotic cells.
•	Function: The cycle is responsible for the oxidation of acetyl-CoA, derived from carbohydrates, fats, and proteins, to produce energy in the form of ATP, NADH, and FADH₂, as well as carbon dioxide (CO₂) as a waste product.

All non polar amino acids are aliphatic too.

“Non-polar but aliphatic” refers to molecules or parts of molecules that are hydrophobic (non-polar) and have a straight or branched carbon chain structure without aromatic rings (which would be present in aromatic compounds).

In the context of amino acids, this means that the side chain (R-group) consists of simple carbon and hydrogen atoms, forming chains or open structures, making them non-polar and hydrophobic. Examples of non-polar aliphatic amino acids include glycine, alanine, valine, leucine, and isoleucine. These amino acids tend to avoid water and are often found in the interior of proteins, away from aqueous environments.

A
45
Q

A mutation has been detected in a hydrophobic domain of a protein, which of the following mutation would be most deleterious?
A. Valine to lysine.
B. Isoleucine to valine.
C. Leucine to glycine.
D. Glycine to proline.

Why is it A?

The correct answer is A. Valine to lysine because this mutation would introduce a significant change in the chemical properties of the amino acid, leading to a more severe impact on the protein’s structure and function.

Here’s why:
- Valine is a non-polar, hydrophobic amino acid, typically found in hydrophobic domains of proteins, helping stabilize protein structure by interacting with other non-polar residues.
- Lysine is a positively charged, hydrophilic amino acid, which prefers to be in polar environments (like the surface of a protein or in contact with water).

Substituting a hydrophobic residue like valine with a charged, hydrophilic residue like lysine would disrupt the hydrophobic domain’s ability to maintain its structural integrity. This could cause misfolding or functional impairments in the protein, making this the most deleterious mutation.

The other options would not cause as drastic a change:
- B. Isoleucine to valine: Both are non-polar, hydrophobic, and quite similar in structure, so this would likely have minimal impact.
- C. Leucine to glycine: This could affect the protein’s structure, but glycine is small and flexible, which might only cause localized disruptions.
- D. Glycine to proline: While this change might affect protein flexibility due to proline’s rigid structure, it is not as disruptive as introducing a charged residue into a hydrophobic domain.

Thus, Valine to Lysine (A) would be the most deleterious because of the introduction of a charged, hydrophilic residue in a region that needs to remain hydrophobic.

Here are some more questions focusing on mutations involving important amino acids and how they might impact protein structure or function:

A. Glycine to proline
B. Alanine to valine
C. Leucine to isoleucine
D. Serine to threonine

Answer: A. Glycine to proline
Explanation: Glycine is the smallest amino acid and provides flexibility to protein structures, especially in tight turns or loops. Proline, on the other hand, has a rigid ring structure that restricts flexibility and could significantly alter protein conformation.

A. It would significantly increase enzyme activity.
B. It would likely disrupt enzyme activity.
C. No change in enzyme activity.
D. It would enhance substrate binding but reduce catalytic efficiency.

Answer: B. It would likely disrupt enzyme activity.
Explanation: Serine is often involved in catalytic activity (e.g., in serine proteases) due to its ability to participate in nucleophilic attacks. Asparagine, being polar but not nucleophilic, would likely disrupt this function.

A. Phenylalanine to tryptophan
B. Valine to leucine
C. Methionine to arginine
D. Isoleucine to alanine

Answer: C. Methionine to arginine
Explanation: Methionine is a non-polar, hydrophobic amino acid, while arginine is positively charged and hydrophilic. This substitution would introduce a charged group into the hydrophobic core, destabilizing the protein.

A

A. Increase in protein flexibility
B. Loss of phosphorylation site
C. Gain of new hydrogen bonds
D. Introduction of disulfide bridges

Answer: B. Loss of phosphorylation site
Explanation: Tyrosine can be phosphorylated due to the hydroxyl group in its side chain. Phenylalanine lacks this hydroxyl group, so the mutation would eliminate potential phosphorylation, which could affect signaling pathways.

A. Significant disruption due to charge change
B. Minimal effect due to similarity
C. Increased structural rigidity
D. Increased interaction with hydrophobic regions

Answer: B. Minimal effect due to similarity
Explanation: Glutamate and glutamine are both polar, but glutamate is negatively charged, while glutamine is neutral. Since they are similar in size and polarity, this substitution would likely have a minimal effect compared to changes involving non-polar or charged residues.

A. Loss of disulfide bond formation
B. Enhanced hydrophobic interactions
C. Increased protein flexibility
D. Formation of more hydrogen bonds

Answer: A. Loss of disulfide bond formation
Explanation: Cysteine can form disulfide bonds, which are crucial for protein stability. Serine lacks the thiol (-SH) group required for disulfide bonding, so this substitution would prevent the formation of these stabilizing interactions.

A. Loss of hydrogen bonding potential
B. Increase in enzyme specificity
C. Introduction of a positive charge
D. Disruption of hydrophobic interactions

Answer: A. Loss of hydrogen bonding potential
Explanation: Lysine, with its long positively charged side chain, can form hydrogen bonds and electrostatic interactions with substrates. Replacing it with alanine, which is small and non-polar, would likely result in a loss of these interactions, reducing enzyme activity.

A. Leucine to alanine
B. Valine to lysine
C. Isoleucine to threonine
D. Serine to tyrosine

Answer: A. Leucine to alanine
Explanation: Both leucine and alanine are non-polar and hydrophobic. Since transmembrane helices are usually composed of hydrophobic residues, this change would have minimal impact compared to introducing polar or charged residues like lysine or threonine.

A. Increase loop rigidity
B. Decrease loop flexibility
C. Increase loop flexibility
D. Form new disulfide bonds

Answer: C. Increase loop flexibility
Explanation: Proline is rigid and limits flexibility, whereas glycine is small and highly flexible. Replacing proline with glycine would increase flexibility in the loop region.

A. No significant effect
B. Improved stability in non-polar environments
C. Disruption of protein folding and stability
D. Enhanced hydrophobic interactions

Answer: C. Disruption of protein folding and stability
Explanation: Arginine is charged and hydrophilic, whereas leucine is non-polar and hydrophobic. Introducing a hydrophilic residue into a hydrophobic core would destabilize the protein and disrupt proper folding.

These questions are designed to help you understand how changes in amino acids can affect the structure and function of proteins, particularly focusing on their hydrophobic or hydrophilic nature and their roles in protein stability.

Which of these changes would cause the least damage to the protein structure?

A. Alanine to valine
B. Valine to lysine
C. Leucine to arginine
D. Methionine to serine

Answer: A. Alanine to valine
Explanation: Alanine and valine are both small, non-polar amino acids, so this change

Which of the following substitutions would most likely disrupt the center of a protein?

A. Phenylalanine to tryptophan
B. Valine to leucine
C. Methionine to arginine
D. Isoleucine to alanine

Answer: C. Methionine to arginine
Explanation: Methionine is non-polar and likes to be in the center of proteins (away from water), while arginine is charged and prefers water. This change would mess up the protein’s core structure.

Replacing lysine (positively charged) with alanine (neutral) in an enzyme’s active site would likely result in:

A. Loss of enzyme’s ability to bind its substrate
B. More specific enzyme action
C. Introduction of a positive charge
D. Disruption of hydrophobic interactions

Answer: A. Loss of enzyme’s ability to bind its substrate
Explanation: Lysine helps in binding the substrate by forming electrostatic interactions. Replacing it with alanine, which is neutral, would likely weaken substrate binding.

  1. Which substitution would have the least effect on a part of the protein that crosses a cell membrane?

A. Leucine to alanine
B. Valine to lysine
C. Isoleucine to threonine
D. Serine to tyrosine

Answer: A. Leucine to alanine
Explanation: Both leucine and alanine are non-polar and hydrophobic, so swapping one for the other in the membrane region would not cause much disruption

46
Q

A disease directly results from the malfunction of the Golgi Apparatus in human cells, which of the following organelles would be most likely affected?

1.	A. Plasma membrane.
•	Explanation: The Golgi apparatus is essential for processing and packaging proteins and lipids. It modifies proteins synthesized in the endoplasmic reticulum (ER) and sends them to the plasma membrane or other destinations. If the Golgi is malfunctioning, it would affect the delivery of proteins and lipids necessary for maintaining and functioning of the plasma membrane.
A

Question 2:

Disruption in hydrogen bonding between two (2) different polypeptide subunits of a protein will MOST LIKELY affect:

1.	A. Primary structure.
•	Explanation: The primary structure of a protein refers to its linear sequence of amino acids. This structure is determined by peptide bonds (covalent bonds) between amino acids, not hydrogen bonds. Therefore, disruption in hydrogen bonding would not affect the primary structure.
2.	B. Secondary structure.
•	Explanation: The secondary structure refers to local folded structures (like alpha-helices and beta-pleated sheets) formed by hydrogen bonding between backbone atoms in the polypeptide chain. While hydrogen bonds are crucial for stabilizing secondary structures, this question refers to bonds between different subunits, which is more relevant to quaternary structure.
3.	C. Tertiary structure.
•	Explanation: The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, determined by various interactions, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges. However, this question specifically concerns bonds between different subunits, not just a single chain.
4.	D. Quaternary structure.
•	Explanation: The quaternary structure refers to the arrangement and interaction of multiple polypeptide subunits within a protein. Hydrogen bonding plays a significant role in stabilizing these interactions. If hydrogen bonds between different subunits are disrupted, it will directly affect the quaternary structure, potentially leading to loss of function or stability