Introduction to the Cell Flashcards
Basics of cell and molecular biology.
1
Q
What is the function of the nucleus in a cell?
A
The nucleus controls cellular activities and houses genetic material. It is often called the “brain of the cell”. Specific functions include:
* Storing and protecting DNA
* Regulating gene expression
* Controlling cell division
* Synthesizing RNA
* Producing ribosomes in the nucleolus
2
Q
What is the primary function of mitochondria?
A
Mitochondria are known as the “powerhouse of the cell” because they produce energy through ATP synthesis. They also:
* Balance calcium ions within the cell
* Assist in apoptosis (programmed cell death)
* Help build hormones and blood components
* Detoxify ammonia in liver cells
3
Q
Describe the functions of rough and smooth endoplasmic reticulum.
A
- Rough ER: Synthesizes proteins for the endomembrane system.
- Smooth ER: Synthesizes lipids and detoxifies toxins.
Both types of ER transport materials through the cell
4
Q
What is the function of the rough endoplasmic reticulum (rough ER)?
A
The rough endoplasmic reticulum (rough ER) is primarily responsible for making proteins that are destined to leave the cell, be incorporated into the cell membrane, or be sent to specific organelles.
5
Q
What is the primary function of the Golgi apparatus?
A
The Golgi apparatus modifies, packages, and distributes cellular products. It:
* Receives materials from the ER
* Modifies proteins and lipids
* Packages proteins for secretion or transport within the cell
* Produces lysosomal enzymes and lysosomal vesicles
6
Q
What are the entering and leaving faces of the Golgi?
A
The Golgi apparatus has two distinct faces, each with a specific role in processing and transporting proteins and lipids:
- Cis Face (Entering Face):
* Location: The cis face is located near the rough endoplasmic reticulum (ER).
* Function: This is the “receiving” side of the Golgi. Vesicles containing proteins and lipids from the rough ER fuse with the cis face, delivering their contents into the Golgi. - Trans Face (Leaving Face):
* Location: The trans face is oriented toward the plasma membrane.
* Function: This is the “shipping” side of the Golgi. Processed proteins and lipids are packaged into vesicles at the trans face and sent to their final destinations, such as: The cell membrane (for secretion or integration).
* Lysosomes or other organelles.
7
Q
What is the main function of lysosomes?
A
Lysosomes contain digestive enzymes for breaking down cellular waste. They are often called “suicidal bags” because they:
* Digest and remove cellular waste materials
* Break down dead and damaged cells
* Aid in cellular recycling processes
8
Q
What is the primary function of peroxisomes?
A
Peroxisomes are involved in oxidation reactions, particularly fatty acid breakdown. They also:
* Detoxify harmful substances
* Produce hydrogen peroxide as a byproduct
* Break down long-chain fatty acids
9
Q
What is the main function of ribosomes?
A
Ribosomes are the site of protein synthesis. They:
* Translate mRNA into proteins
* Can be found free in the cytoplasm or attached to the rough ER
* Are composed of two subunits that come together during protein synthesis
10
Q
What is the primary function of the cell membrane?
A
The cell membrane controls what enters and exits the cell. It:
* Acts as a selective barrier
* Maintains cell homeostasis
* Facilitates cell signaling
* Provides structure and support to the cell
* Allows for cell recognition
11
Q
Describe the ‘Fluid Mosaic’ model of the cell membrane.
A
The fluid mosaic model describes the cell membrane as a flexible, dynamic lipid bilayer with embedded proteins that move laterally, functioning in transport, signaling, and structural support. The lipids in the membranes can move laterally, can rotate, and can flip faces of the membrane (Using the enzyme, Flippase).
12
Q
What is the purpose of the enzyme, flippase?
A
Flippase is an enzyme that helps maintain membrane asymmetry by flipping specific phospholipids from one leaflet of the lipid bilayer to the other, typically moving lipids from the outer to the inner layer. This process is ATP-dependent.
13
Q
What is the cytoskeleton?
A
The cytoskeleton is a dynamic network of protein filaments that extends throughout the cell, providing structural support and facilitating various cellular functions.
14
Q
What are the three main components of the cytoskeleton?
A
Microfilaments, intermediate filaments, and microtubules
15
Q
What are microfilaments and their main function?
A
Microfilaments are the smallest cytoskeletal components, made of F-actin. They provide mechanical support, maintain cell shape, and participate in cell movement and contraction.
16
Q
What are intermediate filaments and their primary function?
A
Intermediate filaments are sturdy protein fibers that provide structural support to the cell and anchor organelles. Their composition varies depending on cell type.
17
Q
What are microtubules and their main functions?
A
Microtubules are hollow tubes made of tubulin. They serve as tracks for intracellular transport, help in cell division, and are components of cilia and flagella.
18
Q
List three main functions of the cytoskeleton.
A
- Maintains cell shape and provides mechanical support
- Organizes and transports cellular components
- Facilitates cell movement and division
19
Q
Name three motor proteins associated with the cytoskeleton.
A
Kinesin, dynein, and myosin
20
Q
What is the centrosome and its role in the cytoskeleton?
A
The centrosome is a spherical structure near the nucleus that serves as a microtubule organization center (MTOC), supporting growth and elongation of microtubules.
21
Q
What is the nucleolus and its primary function?
A
The nucleolus is a small, dense structure within the nucleus that is responsible for producing and assembling ribosomal subunits. It occupies approximately 25% of the nucleus’s volume and plays a crucial role in protein synthesis by creating the components needed for ribosome formation.
Key Details:
* Located inside the nucleus
* Not membrane-bound
* Primary function: Ribosome subunit production
* Composed of proteins and ribosomal RNA (rRNA)
* Essential for protein synthesis and cellular protein production
22
Q
What are phospholipids and their basic structure?
A
Phospholipids are amphipathic molecules composed of a hydrophilic head group, a glycerol molecule, and two hydrophobic fatty acid tails4. They spontaneously form bilayers in aqueous solutions, with hydrophobic tails inside and polar head groups exposed to water.
23
Q
What is the phospholipid bilayer and its importance?
A
The phospholipid bilayer is the fundamental structure of all biological membranes. It forms a stable barrier between two aqueous compartments, with hydrophobic tails facing inward and hydrophilic heads facing outward.
24
Q
Name two main types of phospholipids found in cell membranes.
A
- Phosphatidylcholine (PC)
- Phosphatidylethanolamine (PE)
25
List two primary functions of phospholipids in cell membranes.
* Provide structural integrity to cell membranes
* Contribute to membrane fluidity and flexibility, allowing for membrane dynamics and cell movements
26
Describe the structure of cholesterol in relation to the cell membrane.
Cholesterol is an amphipathic molecule with a hydrophilic hydroxyl (-OH) group aligning towards phospholipid heads and a hydrophobic steroid ring and hydrocarbon tail associating with phospholipid tails.
27
How does cholesterol affect membrane properties?
Cholesterol moderates membrane properties by:
* Reducing membrane fluidity and permeability to small water-soluble molecules
* Preventing membrane crystallization
* Helping secure peripheral proteins by forming lipid rafts
28
How does cholesterol's effect on membrane fluidity change with temperature?
At low temperatures, cholesterol increases fluidity by disrupting phospholipid clustering. At high temperatures, it decreases fluidity by pulling phospholipids together.
29
What factors affect membrane fluidity?
Membrane fluidity is affected by:
* Fatty acid tail length
* Temperature
* Cholesterol content
* Degree of saturation in fatty acid tails
30
How does cholesterol concentration affect membrane fluidity and permeability?
Higher cholesterol concentration generally decreases membrane fluidity and permeability by restricting the motion of membrane molecules.
31
How does cholesterol position itself in the lipid bilayer?
Cholesterol fits most of its structure into the lipid bilayer with only the small hydroxyl group facing the external environment. Its steroid rings are in close proximity to neighboring lipids' hydrocarbon chains, creating a condensing effect on lipid packing.
32
What is the glycocalyx and its main components?
The glycocalyx is a protective layer on the cell surface composed of glycoproteins, glycolipids, and polysaccharides. It acts as a selective barrier, retains beneficial proteins, and filters harmful materials.
33
List three key functions of the glycocalyx.
* Protects the cell membrane
* Facilitates cell-to-cell recognition and communication
* Aids in water retention and cell hydration
34
What are glycoproteins and how are they formed?
Glycoproteins are proteins with oligosaccharide chains covalently attached to amino acid side-chains. They are formed through glycosylation, where carbohydrates are added to proteins after synthesis or during protein growth.
35
Name three functions of glycoproteins.
* Aid in stabilizing and protecting proteins
* Vital for blood grouping
* Allow certain proteins to perform their functions efficiently
36
What are glycolipids and their basic structure?
Glycolipids are molecules composed of a lipid joined to a sugar by a glycosidic bond. They have an amphipathic nature with a hydrophilic sugar head and a hydrophobic fatty acid tail.
37
List three functions of glycolipids.
* Cell recognition
* Cell adhesion
* Cell signaling
38
What are peripheral membrane proteins?
Peripheral membrane proteins are proteins that temporarily adhere to the membrane surface or interact with integral membrane proteins. They are not embedded in the lipid bilayer.
39
What are integral membrane proteins?
Integral membrane proteins are permanently embedded within the lipid bilayer of the cell membrane. They typically span the entire membrane and have hydrophobic regions interacting with the lipid core.
40
What is a GPI anchor and its function?
A GPI (glycosylphosphatidylinositol) anchor is a glycolipid that can attach proteins to the extracellular surface of the cell membrane. It anchors proteins on the extracellular side of the membrane.
41
What is a farnesyl anchor and how does it function?
A farnesyl anchor is a 15-carbon isoprenoid lipid modification that attaches proteins to the cytosolic surface of cell membranes. It helps anchor proteins to the membrane and can influence their interactions with lipid rafts.
42
What are lipid rafts and their key characteristics?
Lipid rafts are small (10-200 nm), heterogeneous, and highly dynamic microdomains in cellular membranes with the following key characteristics:
* Composition: Enriched in cholesterol and sphingolipids
* Structure: More ordered and tightly packed than the surrounding bilayer
* Function: Compartmentalize cellular processes and serve as organizing centers for signaling molecules
* Dynamics: Float freely within the membrane but can cluster to form larger platforms
* Location: Primarily in the plasma membrane, but also found in other cellular compartments like the Golgi apparatus
* Regulation: Influence membrane fluidity, protein trafficking, and signal transduction
Lipid rafts play crucial roles in various cellular processes, including protein sorting, signal transduction, and membrane trafficking.
43
What are proteins, their structure, and main functions?
* Structure: Polymers of amino acids linked by peptide bonds
* Levels of structure: Primary, secondary, tertiary, and quaternary
* Functions:
1. Catalyze biochemical reactions (enzymes)
2. Provide structural support (e.g., collagen)
3. Transport molecules (e.g., hemoglobin)
4. Cell signaling and communication
5. Immune response (antibodies)
44
What are lipids, their structure, and main functions?
* Structure: Diverse group of hydrophobic or amphipathic molecules
* Types: Triglycerides, phospholipids, steroids, waxes
* Functions:
1. Energy storage (triglycerides)
2. Cell membrane structure (phospholipids)
3. Hormones and signaling molecules (steroids)
4. Insulation and protection (waxes)
45
What are carbohydrates, their structure, and main functions?
* Structure: Molecules composed of carbon, hydrogen, and oxygen (Cn(H2O)n)
* Types: Monosaccharides, disaccharides, and polysaccharides
* Functions:
1. Energy source and storage (glucose, starch, glycogen)
2. Structural components (cellulose in plants, chitin in arthropods)
3. Cell recognition and signaling (glycoproteins, glycolipids)
46
What are nucleic acids, their structure, and main functions?
* Structure: Polymers of nucleotides (sugar, phosphate, nitrogenous base)
* Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
* Functions:
1. Store and transmit genetic information (DNA)
2. Transcribe and translate genetic information (RNA)
3. Regulate gene expression
4. Catalyze biochemical reactions (ribozymes)
47
Compare the four main types of macromolecules.
* Proteins: Most diverse in function, composed of amino acids
* Lipids: Hydrophobic, energy storage, membrane structure
* Carbohydrates: Energy source and structural components
* Nucleic Acids: Genetic information storage and transmission
48
What are amino acids and their role in proteins?
Amino acids are the building blocks of proteins. They consist of an amino group, a carboxyl group, and a unique side chain. There are 20 standard amino acids used in protein synthesis.
49
What is the primary structure of a protein?
The primary structure is the linear sequence of amino acids in a polypeptide chain, linked by peptide bonds.
50
What are the two main types of protein secondary structure?
* Alpha helix: A spiral structure stabilized by hydrogen bonds
* Beta sheet: A pleated structure formed by hydrogen bonding between parallel or antiparallel chains
51
What is protein tertiary structure?
The overall three-dimensional shape of a single protein molecule, formed by interactions between side chains, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
52
What is protein quaternary structure?
The arrangement of multiple polypeptide subunits in a multi-subunit protein complex.
53
What are triglycerides and their function?
Triglycerides are lipids consisting of three fatty acids attached to a glycerol backbone. They are the main form of energy storage in animals.
54
What are phospholipids and their role?
Phospholipids are amphipathic molecules with a hydrophilic head and two hydrophobic tails. They are the main components of cell membranes, forming a bilayer.
55
What are steroids and an example of their function?
Steroids are lipids with a characteristic four-ring structure. An example is cholesterol, which is essential for membrane fluidity and is a precursor for steroid hormones.
56
What are monosaccharides and give examples?
Monosaccharides are the simplest carbohydrates, consisting of a single sugar unit. Examples include glucose, fructose, and galactose.
57
What are disaccharides and give examples?
Disaccharides are formed by the bonding of two monosaccharides. Examples include sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose).
58
What are polysaccharides and give examples?
Polysaccharides are long chains of monosaccharides. Examples include starch and glycogen (energy storage), cellulose (structural component in plants), and chitin (structural component in arthropods).
59
Describe the structure of DNA
DNA is a double helix composed of two antiparallel strands. Each strand consists of a sugar-phosphate backbone and nucleotide bases (A, T, C, G) that pair with complementary bases on the other strand (A with T, C with G).
60
How does RNA structure differ from DNA?
RNA is typically single-stranded, uses the sugar ribose instead of deoxyribose, and uses uracil (U) instead of thymine (T). It can form complex secondary structures through base pairing.
61
Name three main types of RNA and their functions
* mRNA (messenger RNA): Carries genetic information from DNA to ribosomes for protein synthesis
* tRNA (transfer RNA): Brings amino acids to ribosomes during protein synthesis
* rRNA (ribosomal RNA): Forms part of the structure of ribosomes
62
What is the Central Dogma of Molecular Biology?
The Central Dogma describes the flow of genetic information: DNA is transcribed into RNA, which is then translated into proteins.
63
What are the key structural features of enzymes?
* Enzymes are globular proteins composed of amino acid chains
* They have a specific three-dimensional structure with:
1. Primary structure: Linear sequence of amino acids
2. Secondary structure: Local structures like α-helices and β-sheets
3. Tertiary structure: Overall 3D fold of a polypeptide chain
4. Quaternary structure: Arrangement of multiple subunits (if applicable)
* Active site: Small cleft where the reaction occurs
* Size range: From 62 amino acids (4-oxalocrotonate tautomerase) to over 2,500 (animal fatty acid synthase)
64
Describe the enzyme active site and its function.
* Small portion of enzyme (2-4 amino acids) directly involved in catalysis
* Contains:
1. Catalytic site: Where the reaction occurs
2. Binding site(s): Orient substrates
* Highly specific to substrate shape and chemistry
* Two models of substrate binding:
1. Lock and key: Substrate fits perfectly into active site
2. Induced fit: Active site shape adjusts upon substrate binding
65
How do enzymes catalyze reactions?
* Provide alternative reaction pathway with lower activation energy
* Form enzyme-substrate (ES) complex
* Stabilize the transition state
* Mechanisms include:
1. Covalent catalysis
2. General acid-base catalysis
3. Catalysis by approximation
4. Metal ion catalysis
* Do not alter reaction equilibrium
* Increase reaction rate by lowering activation energy
66
What are the key concepts in enzyme kinetics?
* Studies rates of enzyme-catalyzed reactions
* Characterized by saturation kinetics
* Key parameters:
1. Vmax: Maximum reaction rate at enzyme saturation
2. Km: Substrate concentration at half Vmax
* Follows Michaelis-Menten equation: v0 = (Vmax[S]) / (Km + [S])
* Assumptions:
1. Quasi-steady-state
2. Constant total enzyme concentration
3. No product inhibition or cooperativity
67
What are the six main categories of enzymes?
* Oxidoreductases: Catalyze oxidation and reduction reactions
* Transferases: Transfer chemical groups between compounds
* Hydrolases: Catalyze hydrolysis of chemical bonds
* Lyases: Add or remove groups from substrates
* Isomerases: Catalyze structural shifts within a molecule
* Ligases: Join two molecules with covalent bonds
68
What factors influence enzyme activity?
* Substrate concentration
* Enzyme concentration
* Temperature
* pH
* Presence of activators or inhibitors
* Cofactors (if required)
* Allosteric regulation (for some enzymes)
69
What are the main types of enzyme inhibition?
* Competitive inhibition: Inhibitor competes with substrate for active site
* Non-competitive inhibition: Inhibitor binds to allosteric site, changing enzyme shape
* Uncompetitive inhibition: Inhibitor binds only to enzyme-substrate complex
* Mixed inhibition: Combination of competitive and non-competitive inhibition
70
Explain the Michaelis-Menten model of enzyme kinetics.
* Describes relationship between substrate concentration [S] and reaction rate v0
* Key equation: v0 = (Vmax[S]) / (Km + [S])
* At low [S]: Rate increases linearly with [S]
* At high [S]: Rate approaches Vmax asymptotically
* Km: [S] at which v0 = 1/2 Vmax
* Assumes single substrate and no cooperativity
* Used to determine Vmax and Km experimentally
71
What are the main types of cellular transport mechanisms?
1. Passive transport:
* Simple diffusion
* Facilitated diffusion
* Osmosis
2. Active transport:
* Primary active transport
* Secondary active transport
3. Vesicular transport:
* Endocytosis
* Exocytosis
72
What factors determine the type of transport used by a cell?
* Concentration gradient
* Molecule size and polarity
* Membrane permeability
* Energy requirements
* Presence of specific transport proteins
73
Describe simple diffusion.
* Passive transport mechanism
* Molecules move directly through the phospholipid bilayer
* Follows concentration gradient (high to low)
* No energy required
* Limited to small, nonpolar molecules (e.g., O2, CO2)
74
What is facilitated diffusion?
* Passive transport mechanism
* Requires transport proteins (channels or carriers)
* Follows concentration gradient (high to low)
* No energy required
* Allows passage of larger or polar molecules
* Can be regulated by the cell
75
Explain osmosis.
* Special type of passive transport
* Movement of water molecules across a semipermeable membrane
* Moves from an area of high water concentration to low water concentration
* Driven by differences in solute concentration
76
What is primary active transport?
* Directly uses ATP for energy
* Moves molecules against their concentration gradient
* Example: Na+/K+ ATPase pump [3 sodiums out / 2 potassiums in]
* Transports a single type of molecule
77
Describe secondary active transport.
* Uses energy from electrochemical gradient created by primary active transport
* Moves two types of molecules simultaneously
* One molecule moves down its concentration gradient, providing energy for the other to move against its gradient
* Example: Glucose-sodium cotransporter (SGLT)
78
What is vesicular transport?
* Involves movement of large molecules or particles
* Two main types:
1. Endocytosis: Brings materials into the cell
2. Exocytosis: Releases materials out of the cell
* Requires energy (ATP)
* Utilizes membrane-bound vesicles
79
Compare passive diffusion and facilitated diffusion.
* Passive diffusion:
1. Molecules move directly through the phospholipid bilayer
2. No energy required
3. Limited to small, nonpolar molecules
* Facilitated diffusion:
1. Requires transport proteins (channels or carriers)
2. No energy required
3. Allows passage of larger or polar molecules
* Can be regulated by the cell
80
What types of molecules typically use passive diffusion?
* Small, nonpolar molecules
* Examples: O2, CO2, steroid hormones
81
Give examples of molecules that use facilitated diffusion.
* Glucose (via GLUT transporters)
* Amino acids
* Ions (through ion channels)
* Water (through aquaporins)
82
Compare primary and secondary active transport.
* Primary active transport:
1. Directly uses ATP for energy
2. Moves molecules against their concentration gradient
3. Transports a single type of molecule
* Secondary active transport:
1. Uses energy from electrochemical gradient created by primary active transport
2. Moves two types of molecules simultaneously
3. One molecule moves down its gradient, providing energy for the other to move against its gradient
83
Describe the Na+/K+ ATPase pump as an example of primary active transport.
* Found in neurons and other cells
* Maintains resting membrane potential
* For every ATP molecule hydrolyzed:
1. 3 Na+ ions are pumped out of the cell
2. 2 K+ ions are pumped into the cell
* Creates and maintains electrochemical gradients for both Na+ and K+
84
Explain how the glucose-sodium cotransporter (SGLT) in kidney tubules works as an example of secondary active transport.
* Found in kidney tubules and small intestine
* Uses Na+ concentration gradient created by Na+/K+ ATPase
* Na+ moves down its concentration gradient into the cell
* This energy is used to transport glucose against its concentration gradient
* Results in glucose reabsorption from the filtrate or absorption from the intestinal lumen
85
What is a symporter?
* An integral membrane protein that transports two or more different molecules across the cell membrane in the same direction
* Uses secondary active transport
* One molecule moves down its concentration gradient, providing energy for the other to move against its gradient
* Example: SGLT1 (sodium-glucose cotransporter) in intestinal epithelium
86
Describe the mechanism of SGLT1 symporter.
* Located in intestinal epithelium and kidney tubules
* Transports 1 glucose molecule and 2 sodium ions into the cell simultaneously
* Sodium moves down its concentration gradient (created by Na+/K+ ATPase)
* Energy from sodium movement is used to transport glucose against its concentration gradient
* Important for glucose absorption in intestines and reabsorption in kidneys
87
What is a uniporter?
* A membrane transport protein that passively transports a single type of molecule or ion across a cell membrane
* Uses facilitated diffusion (no energy required)
* Moves solutes down their concentration gradient
* Can be either channels or carriers
* Examples: glucose transporters (GLUTs), mitochondrial calcium uniporter (MCU)
88
Describe the mechanism of uniporter transport.
1. Substrate binds to specific site on one side of the membrane
2. Transporter undergoes conformational change
3. Substrate is translocated across the membrane
4. Another conformational change releases the substrate on the other side
5. Transporter returns to original conformation
Process is driven by concentration gradient of the substrate
89
What is an antiporter?
* An integral membrane protein that uses secondary active transport
* Moves two or more molecules in opposite directions across a membrane
* Uses the energetically favorable movement of one molecule to power the unfavorable movement of another
* Example: Na+/Ca2+ exchanger in plasma membranes
90
Describe the mechanism of the Na+/Ca2+ antiporter.
* Found in plasma membranes of many cells
* Exchanges 3 sodium ions for 1 calcium ion in opposite directions
* Typically moves sodium into the cell and calcium out
* Can reverse direction under certain conditions (e.g., cell depolarization)
* Important for regulating intracellular calcium levels and cardiac muscle contraction
91
Compare symporters, uniporters, and antiporters.
92
What are the main stages of the cell cycle?
Interphase (G1, S, G2), Mitotic phase (Mitosis, Cytokinesis), and G0 phase (optional).
93
Diagram of the Cell Cycle.
94
What happens during G1 phase of interphase?
Cell growth and preparation for DNA synthesis.
95
What occurs in the S phase of interphase?
DNA replication.
96
What is the purpose of the G2 phase?
Preparation for mitosis.
97
What are the two parts of the mitotic phase?
Mitosis (nuclear division) and Cytokinesis (cytoplasmic division).
98
What is the G0 phase?
A quiescent or senescent state where the cell is not actively dividing.
99
What happens during prophase in mitosis?
Chromatin condenses, the nuclear envelope breaks down, and spindle fibers form.
100
Describe the key event of metaphase.
Chromosomes align at the metaphase plate.
101
What occurs during anaphase?
Sister chromatids separate and move to opposite poles of the cell.
102
What are the events of telophase?
Chromosomes decondense, nuclear envelopes reform, and cytokinesis begins.
103
What is the function of totipotent stem cells?
They can form all cell types, including embryonic and extra-embryonic tissues (e.g., zygote).
104
What types of cells can pluripotent stem cells form?
Most cell types in the body (e.g., embryonic stem cells).
105
What are multipotent stem cells capable of?
Forming multiple cell types within a specific lineage (e.g., hematopoietic stem cells).
106
Define unipotent stem cells.
Stem cells that can only differentiate into one cell type (e.g., spermatogonial stem cells).
107
What are the therapeutic potentials of stem cells?
Regenerative medicine, tissue engineering, disease modeling, and drug screening.
108
Why is balancing cell division and apoptosis important?
To maintain tissue homeostasis, proper organ function, prevent diseases (e.g., cancer), support embryonic development, and regulate the immune system.
109
What are the main events of Meiosis I?
Homologous chromosomes pair, crossover, and separate.
110
What happens during Meiosis II?
Sister chromatids separate, resulting in four haploid gametes.
111
How does meiosis differ from mitosis?
* Meiosis produces haploid gametes; mitosis produces diploid cells.
* Meiosis involves two rounds of division; mitosis involves one.
* Meiosis includes genetic recombination; mitosis does not.
* Meiosis occurs in germ cells; mitosis occurs in somatic cells.
112
What are the similarities between meiosis and mitosis?
Both involve DNA replication and cell division.
113
What are the major components that make up the human genome?
* Nuclear DNA: 23 pairs of chromosomes
* Mitochondrial DNA: Circular DNA in mitochondria
* Genes: Protein-coding sequences
* Regulatory elements: Promoters, enhancers, silencers
* Non-coding DNA: Introns, repetitive sequences
* Telomeres: Protective end sequences of chromosomes
114
What is nuclear DNA in the context of the human genome?
Nuclear DNA consists of 23 pairs of chromosomes located in the nucleus of human cells.
115
Describe mitochondrial DNA.
Mitochondrial DNA is circular DNA found in the mitochondria, which are organelles responsible for energy production in cells.
116
What are genes in the human genome?
Genes are protein-coding sequences within the DNA that contain instructions for producing specific proteins.
117
What are regulatory elements in the human genome?
Regulatory elements are DNA sequences that control gene expression, including promoters, enhancers, and silencers.
118
What is non-coding DNA?
Non-coding DNA refers to DNA sequences that do not code for proteins, including introns and repetitive sequences.
119
What are telomeres and their function?
Telomeres are protective end sequences of chromosomes that help maintain chromosome integrity during cell division.
120
What are the major enzymes involved in DNA replication and their functions?
* DNA helicase: Unwinds the DNA double helix
* DNA primase: Synthesizes RNA primers
* DNA polymerase III: Main replicative enzyme, extends DNA strands
* DNA polymerase I: Removes RNA primers, fills gaps
* DNA ligase: Joins Okazaki fragments
121
What is the function of DNA helicase in replication?
DNA helicase unwinds the DNA double helix, separating the two strands to allow for replication.
122
What does DNA primase do during DNA replication?
DNA primase synthesizes short RNA primers that serve as starting points for DNA synthesis.
123
What is the role of DNA polymerase III in replication?
DNA polymerase III is the main replicative enzyme that extends DNA strands by adding nucleotides complementary to the template strand.
124
How does DNA polymerase I contribute to DNA replication?
DNA polymerase I removes RNA primers and fills the gaps left behind with DNA nucleotides.
125
What is the function of DNA ligase in replication?
DNA ligase joins Okazaki fragments on the lagging strand by forming phosphodiester bonds between adjacent DNA segments.
126
What are Okazaki fragments?
Okazaki fragments are short sequences of DNA nucleotides synthesized discontinuously during DNA replication. They are:
* Produced on the lagging strand during DNA replication
* Essential for the synthesis of the lagging strand, as DNA polymerase can only add nucleotides in the 5' to 3' direction
* Initially contain an RNA primer at the 5' end
* Later joined by DNA ligase to form a continuous lagging strand
Key steps in Okazaki fragment processing:
* RNA primer removal by DNA polymerase I
* Gap filling by DNA polymerase
* Fragment joining by DNA ligase
Additional enzymes involved:
* Flap endonuclease 1 (FEN1): Processes Okazaki fragments by removing RNA primers and displaced DNA flaps
* DNA2 helicase/endonuclease: Assists in efficient Okazaki fragment maturation
127
What are the similarities between DNA replication in eukaryotic and prokaryotic cells?
* Both use semiconservative replication
* Both require similar enzymes (helicases, polymerases, ligases)
128
How does the speed and complexity of DNA replication differ between eukaryotes and prokaryotes?
Eukaryotic replication is slower and more complex compared to prokaryotic replication.
129
Compare the origins of replication in eukaryotes and prokaryotes.
Eukaryotes have multiple origins of replication, while prokaryotes have only one origin of replication.
130
What is the difference in the structure of DNA being replicated in eukaryotes and prokaryotes?
Eukaryotes replicate linear chromosomes, whereas prokaryotes replicate circular DNA.
131
How do eukaryotes and prokaryotes differ in telomere maintenance?
Eukaryotes have telomere maintenance mechanisms, while prokaryotes do not require telomere maintenance.
132
Describe DNA replication in eukaryotes.
133
Describe the process of transcription in a eukaryotic cell.
* Initiation: RNA polymerase binds to promoter
* Elongation: RNA synthesis
* Termination: RNA release
* Post-transcriptional modifications: 5' capping, 3' polyadenylation, splicing
134
What occurs during the initiation step of transcription?
During initiation, RNA polymerase binds to the promoter region of the gene.
135
What happens in the elongation phase of transcription?
In the elongation phase, RNA synthesis occurs as the RNA polymerase moves along the DNA template, adding complementary RNA nucleotides
136
Describe the termination step of transcription
During termination, the newly synthesized RNA is released from the DNA template and the RNA polymerase.
137
What post-transcriptional modifications occur in eukaryotic mRNA?
Eukaryotic mRNA undergoes post-transcriptional modifications, including 5' capping, 3' polyadenylation, and splicing.
138
Outline the process of translation in a eukaryotic cell.
* Initiation: Ribosome assembly on mRNA
* Elongation: Amino acid chain formation
* Termination: Release of completed protein
* Post-translational modifications: Folding, chemical modification
139
What happens during the initiation of translation
During initiation, the ribosome assembles on the mRNA, positioning itself at the start codon.
140
Describe the elongation phase of translation
In the elongation phase, the amino acid chain is formed as the ribosome moves along the mRNA, adding amino acids according to the codon sequence.
141
What occurs during the termination of translation
During termination, the completed protein is released from the ribosome when a stop codon is reached.
142
What are post-translational modifications?
Post-translational modifications include protein folding and chemical modifications that occur after the protein is synthesized, which are crucial for proper protein function.
143
What are codons and what is their function?
Codons are sequences of three adjacent nucleotides in DNA or RNA that form a unit of genomic information. Their primary functions are:
* Encoding specific amino acids: 61 of the 64 possible codons specify particular amino acids for protein synthesis.
* Signaling translation termination: 3 codons serve as stop signals to end protein synthesis.
* Initiating protein synthesis: The codon AUG, which codes for methionine, also serves as the start signal for translation.
Key features of codons:
* Composed of three nucleotides (triplets) using A, U, C, and G bases in RNA (T instead of U in DNA)
* Read by ribosomes during protein synthesis to determine the sequence of amino acids
* Interpreted by matching with anticodons on tRNA molecules
* The genetic code is largely universal across species, with some exceptions (e.g., in mitochondria)
* Degeneracy: Most amino acids are coded for by multiple codons, providing redundancy in the genetic code
144
What is tRNA and what is its role in protein synthesis?
tRNA (transfer RNA) is a small RNA molecule that plays a crucial role in protein synthesis:
1. Structure:
* 76-90 nucleotides long
* L-shaped tertiary structure
* Contains an acceptor arm, DHU loop, anticodon loop, TΨC loop, and variable loop
2. Function:
* Acts as an adapter molecule during translation
* Decodes mRNA codons and transfers specific amino acids to the growing polypeptide chain
* Binds to mRNA codons via its anticodon
3. Key features:
* Carries a specific amino acid at its 3' end
* Contains an anticodon complementary to mRNA codons
* Undergoes post-transcriptional modifications for proper function
* Process:
* Binds to specific mRNA codons in the ribosome's A-site
* Transfers amino acids to the growing polypeptide chain
* Moves through the P-site and E-site of the ribosome during translation
4. Importance:
* Essential for decoding genetic information
* Helps maintain translation accuracy and speed
* Plays a role in mRNA frame maintenance
145
Define the term "receptor" in the context of cell signaling.
A receptor is a protein that binds to a specific signaling molecule, triggering a cellular response.
146
List and briefly describe the different membrane proteins that can act as receptors.
* G protein-coupled receptors (GPCRs): Transmembrane receptors that activate G proteins
* Receptor tyrosine kinases (RTKs): Enzymes that phosphorylate specific tyrosine residues on target proteins
* Ion channel-linked receptors: Proteins that allow ions to flow across the membrane in response to signals
* Enzyme-linked receptors: Receptors with intrinsic enzyme activity or associated with enzymes
147
What is the role of G protein-coupled receptors (GPCRs) in cell signaling?
G protein-coupled receptors (GPCRs) are responsible for signal transduction through G proteins. They activate G proteins upon ligand binding, which then trigger various cellular responses.
148
Explain the function of receptor tyrosine kinases (RTKs) in cell signaling.
Receptor tyrosine kinases (RTKs) function by phosphorylating target proteins on specific tyrosine residues. This phosphorylation typically activates or inhibits the target proteins, leading to downstream signaling events
149
How do ion channel-linked receptors contribute to cell signaling?
Ion channel-linked receptors directly control the flow of ions across cell membranes in response to specific signals. This rapid ion movement can lead to changes in membrane potential and trigger various cellular responses.
150
What is the primary function of enzyme-linked receptors in cell signaling?
Enzyme-linked receptors catalyze intracellular reactions upon activation. They either have intrinsic enzyme activity or are closely associated with enzymes, leading to the modification of target molecules and propagation of the signal.
151
List and briefly explain the roles of proteins in cell signaling and communication.
* Receptors: Detect and respond to signals
* Signal transducers: Relay and amplify signals
* Enzymes: Modify other proteins
* Scaffold proteins: Organize signaling complexes
* Transcription factors: Regulate gene expression
* Ion channels: Control ion flow and membrane potential
152
How do scaffold proteins contribute to cell signaling?
Scaffold proteins organize signaling complexes by bringing together multiple components of a signaling pathway. This organization enhances the efficiency and specificity of signal transduction.
153
What is the role of transcription factors in cell signaling?
Transcription factors regulate gene expression in response to signaling events. They can be activated or inhibited by signaling pathways, leading to changes in the expression of target genes.
154
Compare and contrast endocrine, paracrine, and autocrine signaling mechanisms.
* Endocrine signaling: Long-distance communication via bloodstream
* Paracrine signaling: Short-distance communication between nearby cells
* Autocrine signaling: Cell signals to itself
155
List four major transduction pathways that can be activated by various signaling mechanisms.
* cAMP pathway
* Phosphoinositide pathway
* JAK-STAT pathway
* MAP kinase pathway
156
Explain the relationship between signaling mechanisms and transduction pathways.
Each signaling mechanism (endocrine, paracrine, or autocrine) can activate various transduction pathways depending on the specific receptor and ligand involved. The type of receptor and the signaling molecule determine which transduction pathway is activated, rather than the signaling mechanism itself.
157
What is the cAMP pathway and how does it function?
The cAMP (cyclic adenosine monophosphate) pathway is a signaling cascade that involves:
1. Conversion of ATP to cAMP by adenylate cyclase (AC)
2. Activation of cAMP-dependent protein kinase A (PKA)
3. Phosphorylation of specific proteins by PKA
4. Regulation of gene transcription through phosphorylation of CREB (cAMP response-element binding-protein)
Key components:
* Adenylate cyclase (AC): Converts ATP to cAMP
* Protein kinase A (PKA): Main effector of cAMP
* Phosphodiesterases (PDEs): Regulate cAMP levels by hydrolysis
* CREB: Transcription factor activated by PKA
The pathway is involved in various cellular functions, including protein synthesis, enzymatic activity regulation, and gene transcription
158
Describe the phosphoinositide pathway and its role in cell signaling.
The phosphoinositide pathway is a lipid signaling system involving:
1. Phosphatidylinositol (PtdIns) and its phosphorylated derivatives
2. Lipid kinases and phosphatases that modify PtdIns
3. Proteins that interact with phosphoinositides
Key features:
* Phosphoinositides: PI3P, PI4P, PI5P, PI(3,4)P2, PI(3,5)P2, PI(4,5)P2, PI(3,4,5)P3
* Main enzymes: PI3K (produces PI(3,4,5)P3), PTEN (dephosphorylates PI(3,4,5)P3)
* Signaling processes: Cell proliferation, survival, metabolism, cytoskeletal changes, vesicle trafficking, autophagy, cell division, migration
The pathway regulates cellular activities through:
* Direct interaction with membrane proteins (e.g., ion channels, GPCRs)
* Recruitment of cytosolic proteins with phosphoinositide-binding domains
* Activation of signaling cascades (e.g., PI3K-Akt pathway)
159
Explain the JAK-STAT signaling pathway and its importance.
The JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway is a signaling cascade involving:
1. Cytokine binding to transmembrane receptors
2. Activation of receptor-associated JAKs
3. Phosphorylation and dimerization of STAT proteins
4. Translocation of STAT dimers to the nucleus
5. Regulation of gene transcription
Key components:
* JAKs: Tyrosine kinases that phosphorylate receptors and STATs
* STATs: Transcription factors that regulate gene expression
* Cytokine receptors: Initiate the signaling cascade
The pathway is crucial for:
* Immunity
* Cell division
* Cell death
* Tumor formation
Disruption of JAK-STAT signaling can lead to various diseases, including skin conditions, cancers, and immune system disorders
160
What is the MAP kinase pathway and its significance in cell signaling?
The MAP (Mitogen-Activated Protein) kinase pathway is a signaling cascade involving:
* Sequential activation of protein kinases
* Transmission of extracellular signals to the nucleus
* Regulation of gene expression and cellular responses
Key features:
* Three-tiered kinase cascade: MAPKKK → MAPKK → MAPK
* Major MAPK families: ERK, JNK, and p38
* Activated by various stimuli: Growth factors, stress, cytokines
*
The pathway is important for:
* Cell proliferation
* Differentiation
* Survival
* Apoptosis
161
What are the five basic principles of enzyme function?
* Lower activation energy of reactions
* Exhibit substrate specificity
* Remain unchanged after catalysis
* Function optimally under specific conditions (pH, temperature)
* Can be regulated by various factors
162
How do enzymes affect the activation energy of reactions?
Enzymes lower the activation energy of reactions, making it easier for the reaction to occur and increasing the reaction rate.
163
What is meant by substrate specificity in enzyme function?
Substrate specificity means that enzymes are selective about the molecules they act upon. Each enzyme is designed to catalyze a specific reaction with a particular substrate or group of related substrates.
164
How do enzymes change during and after catalysis?
Enzymes remain unchanged after catalysis. They are not consumed in the reaction and can be reused multiple times to catalyze the same reaction.
165
How do environmental conditions affect enzyme function?
Enzymes function optimally under specific conditions, particularly pH and temperature. Changes in these conditions can affect the enzyme's structure and activity.
166
What does it mean that enzymes can be regulated?
Enzyme regulation means that their activity can be controlled by various factors, including inhibitors, activators, allosteric regulators, and post-translational modifications.
167
What are the key properties of enzyme kinetics?
* Michaelis-Menten kinetics
* Km (Michaelis constant) and Vmax (maximum velocity)
* Lineweaver-Burk plot for determining kinetic parameters
* Effects of substrate concentration on reaction rate
* Enzyme saturation
168
What is Michaelis-Menten kinetics?
Michaelis-Menten kinetics is a model that describes the kinetics of enzyme-catalyzed reactions. It relates reaction rate to substrate concentration and is characterized by the Michaelis-Menten equation.
169
Define Km (Michaelis constant) and Vmax (maximum velocity).
* Km (Michaelis constant): The substrate concentration at which the reaction rate is half of Vmax. It represents the enzyme's affinity for the substrate.
* Vmax (maximum velocity): The maximum rate achieved by the enzyme at saturating substrate concentrations.
170
What is a Lineweaver-Burk plot and what is its purpose?
A Lineweaver-Burk plot is a graphical method for analyzing enzyme kinetics. It's a double reciprocal plot of 1/v versus 1/[S], used to determine kinetic parameters such as Km and Vmax.
171
How does substrate concentration affect enzyme reaction rate?
As substrate concentration increases, the reaction rate increases until it reaches a maximum (Vmax) when the enzyme becomes saturated with substrate.
172
What is enzyme saturation?
Enzyme saturation occurs when all enzyme active sites are occupied by substrate molecules. At this point, increasing substrate concentration does not increase the reaction rate further.
173
List the six main classifications of enzymes and their functions.
* Oxidoreductases: Catalyze oxidation-reduction reactions
* Transferases: Transfer functional groups between molecules
* Hydrolases: Catalyze hydrolysis reactions
* Lyases: Add or remove groups without hydrolysis
* Isomerases: Catalyze intramolecular rearrangements
* Ligases: Join two molecules using ATP hydrolysis
174
What do oxidoreductases do?
Oxidoreductases catalyze oxidation-reduction reactions, where one molecule is oxidized (loses electrons) and another is reduced (gains electrons).
175
What is the function of transferases?
Transferases transfer functional groups (e.g., methyl, phosphate, amino) from one molecule to another.
176
How do hydrolases work?
Hydrolases catalyze hydrolysis reactions, breaking chemical bonds by adding water.
177
What reactions do lyases catalyze?
Lyases add or remove groups from substrates without hydrolysis, often forming double bonds or rings.
178
What is the role of isomerases?
Isomerases catalyze intramolecular rearrangements, converting one isomer to another.
179
How do ligases function?
Ligases join two molecules together, usually using energy from ATP hydrolysis.
180
List four types of enzyme inhibitors and provide an example of each with its clinical relevance.
* Competitive inhibitors: Compete with substrate for active site (e.g., statins inhibiting HMG-CoA reductase)
* Non-competitive inhibitors: Bind to allosteric site (e.g., aspirin inhibiting cyclooxygenase)
* Irreversible inhibitors: Permanently modify enzyme (e.g., penicillin inhibiting bacterial cell wall synthesis)
* Suicide inhibitors: Enzyme converts inhibitor to reactive form (e.g., acyclovir inhibiting viral DNA polymerase)
181
How do competitive inhibitors work, and what's an example of their clinical use?
Competitive inhibitors compete with the substrate for the enzyme's active site. Example: Statins inhibit HMG-CoA reductase, lowering cholesterol production and reducing cardiovascular disease risk.
182
Explain non-competitive inhibition and provide a clinical example.
Non-competitive inhibitors bind to an allosteric site, changing the enzyme's shape and reducing its activity. Example: Aspirin inhibits cyclooxygenase, reducing inflammation and pain.
183
What are irreversible inhibitors, and how are they used clinically?
Irreversible inhibitors permanently modify the enzyme, often by covalent bonding. Example: Penicillin irreversibly inhibits bacterial cell wall synthesis enzymes, killing bacteria.
184
Describe suicide inhibitors and give an example of their clinical application.
Suicide inhibitors are converted by the enzyme into a reactive form that then inactivates the enzyme. Example: Acyclovir is converted by viral DNA polymerase into a form that inhibits the enzyme, stopping viral replication.
185
What are nuclear receptors, where are they located, what do they do, and what are some examples?
Nuclear receptors are a class of proteins located in the cytoplasm or nucleus of cells. They function as transcription factors that regulate gene expression in response to small, hydrophobic molecules such as hormones, vitamins, and metabolites. When activated by ligand binding, nuclear receptors can:
* Bind directly to DNA at specific hormone response elements (HREs)1
* Control various biological processes including cell proliferation, development, metabolism, and reproduction
* Mediate the cellular response to hormones and other signaling molecules
Examples of nuclear receptors include:
* Thyroid hormone receptor
* Retinoic acid receptor
* Estrogen receptor
* Androgen receptor
* Glucocorticoid receptor
* Peroxisome proliferator-activated receptor (PPAR
186
What are the three main steps in the generalized process of signal transduction?
* Reception: A cell detects a signaling molecule from the outside of the cell.
* Transduction: The signaling molecule changes the receptor protein, initiating a cascade of molecular events inside the cell.
* Response: The cell exhibits a specific change in behavior or function, such as altered gene expression, protein activity, or cellular structure.
## Footnote
* Reception often involves ligands binding to receptor proteins on the cell surface.
* Transduction frequently includes phosphorylation cascades mediated by protein kinases.
* Responses can include changes in motility, cell shape, gene expression, protein localization, cell growth, or programmed cell death.
187
What are feedback loops in biological systems, and what are their two main types?
Feedback loops are regulatory mechanisms in biological systems where the output of a process affects its input, helping to maintain homeostasis. The two main types are:
1. Negative feedback loops:
* Reduce or counteract the initial stimulus
* Tend to stabilize systems and maintain equilibrium
* Example: Body temperature regulation
2. Positive feedback loops:
* Amplify or enhance the initial stimulus
* Can lead to rapid changes or extreme outcomes
* Example: Blood clotting process
