B122 Review

Question 1

Describe structure of an atom

Answer 1

an atom consists of a nucleus with protons and neutrons. The nucleus is surrounded by an electron cloud of electrons

The protons and neutrons make up the mass of the atom, while the electrons orbit the nucleus in various energy levels or shells.

Question 2

describe covalent, ionic, polar covalent (polar bond) and hydrogen bonds and

what is their relative strength.

Answer 2

covalent bond
- Formed when two atoms share one or more pairs of electrons to achieve a stable electron configuration. The strongest type of bond.

ionic bond
- Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities,

polar covalent bond
A polar covalent bond occurs when atoms are shared unequally in a covalent bond. Specifically, when the difference in electronegativities of the two atoms in the bond is between 0.4 and 1.7. The terms polar bond and polar covalent bond are generally used interchangeably.

hydrogen bonds
A hydrogen bond is a weak interaction that occurs when a hydrogen atom covalently bonded to a highly electronegative atom (such as oxygen, nitrogen, or fluorine) is attracted to another electronegative atom in a different molecule or a different part of the same molecule. This interaction results from the partial positive charge on the hydrogen atom and the partial negative charge on the electronegative atom.

strongest -> weakest
1. Covalent Bonds: Strong and stable.
2. Ionic Bonds: Strong, but weaker than covalent in aqueous environments.
3. Polar Covalent Bonds: Strong, with an added aspect of polarity.
4. Hydrogen Bonds: Weak, but significant in large numbers for biological structures and interactions.

Question 3

Define solute, solvent, and solution.

Answer 3

solute
A substance that is dissolved in a solvent to form a solution. The minor component in a solution

solvent
A substance that dissolves a solute, resulting in a solution. The solvent is typically present in greater quantity than the solute.

solution
A homogeneous mixture composed of two or more substances, where a solute is uniformly distributed within a solvent.

Question 4

define acids and bases

Answer 4

acids
Acids are substances that can donate a proton (H⁺ ion) to another substance in a chemical reaction. In aqueous solutions, acids increase the concentration of hydrogen ions (H⁺).

bases
Bases are substances that can accept a proton (H⁺ ion) or donate a hydroxide ion (OH⁻) in a chemical reaction. In aqueous solutions, bases increase the concentration of hydroxide ions (OH⁻).

Question 5

describe the pH scale.

Answer 5

The pH scale is a logarithmic scale used to measure the acidity or alkalinity of a solution. It ranges from 0 to 14, with each value representing the concentration of hydrogen ions (H⁺) in the solution.

pH 0: acidic -> 1 mol H+ ion per liter of water
pH 7: neutral -> 10^-7 moles H+ per liter of water
pH 14: basic -> 10^-14 moles H+ per liter of water

Question 6

Define reactants, products, and chemical equilibrium.

Answer 6

reactants
Reactants are the starting substances that undergo a chemical reaction. They are present at the beginning of the reaction and are consumed during the process to form products.

products
Products are the substances formed as a result of a chemical reaction. They are present at the end of the reaction and are produced from the reactants.

chemical equilibrium
Chemical equilibrium is the state in a reversible chemical reaction where the rate of the forward reaction equals the rate of the reverse reaction. At equilibrium, the concentrations of reactants and products remain constant over time.

Question 7

What is the law of mass action

Answer 7

The law of mass action states that the rate of a chemical reaction is proportional to the product of the concentrations of the reactants, each raised to a power equal to the coefficient of that reactant in the balanced chemical equation.. It explains and predicts behaviors of solutions in dynamic equilibrium. Specifically, it implies that for a chemical reaction mixture that is in equilibrium, the ratio between the concentration of reactants and products is constant.

reaction rate increases as the concentration of the reactants increases

General reversible reaction:
aA+bB⇌cC+dD

Question 8

Define metabolism.

Answer 8

Metabolism is the sum of all chemical reactions that occur within a living organism to maintain life. These reactions are organized into metabolic pathways, which can be divided into two main categories: anabolism and catabolism.

anabolism
The set of metabolic pathways that construct molecules from smaller units. These reactions require energy input. Require energy (endergonic)

catabolism
The set of metabolic pathways that break down molecules into smaller units, releasing energy in the process. Release energy (exergonic)

• Metabolism involves the transfer of energy. Catabolic pathways release energy that is captured and used to drive anabolic pathways.
• Metabolic reactions are facilitated and regulated by enzymes, which ensure that the reactions occur at rates sufficient to meet the needs of the organism.

Question 9

Define monomers and polymers.

Answer 9

monomers

Monomers are small, simple molecules that can join together to form larger, more complex molecules called polymers. They are the basic building blocks of polymers. Amino acids are the monomers of proteins, nucleotides the monomers of nucleic acids.

polymers
polymers are large, complex molecules made up of repeating units of monomers linked together by covalent bonds. They can have various structures and properties depending on the types and arrangements of their monomers.

Question 10

What are the four types of macromolecules? What are the monomers of each macromolecule?

Answer 10

1. carbohydrates -> monomer: monosaccharides -> polymer polysaccharides
2. proteins -> monomer: amino acid -> polymer polypeptide chains
3. nucleic acids -> monomers: nucleotides
4. lipids -> building block: glycerol + fatty acids

Question 11

What are the four levels of protein structure

Answer 11

primary structure
The sequence of amino acids in a polypeptide chain, determined by the gene encoding the protein. Peptide bonds between the amino acids.

secondary structure
Local folding of the polypeptide chain into structures like alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds. involves hydrogen bonds

tertiary structure
he overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the side chains (R groups) of the amino acids. Includes hydrogen bonds, ionic bonds, disulfide bridges (covalent), hydrophobic interactions, van der Waals forces

quaternary structure
The arrangement and interaction of multiple polypeptide chains (subunits) to form a functional protein complex.

Question 12

Define enzyme. Why is enzyme binding described as a “lock and key” mechanism? What is the function of the active site on an enzyme?

Answer 12

An enzyme is a biological catalyst, typically a protein, that accelerates chemical reactions in living organisms by lowering the activation energy required for the reaction to occur. Enzymes are highly specific for their substrates and are not consumed in the reaction, allowing them to be used repeatedly.

The “lock and key” mechanism is a model used to describe how enzymes bind to their substrates. According to this model:

• The enzyme (lock) has a specific active site with a unique shape that fits precisely with the substrate (key).
• Only the correctly sized and shaped substrate can fit into the enzyme’s active site, similar to how only the correct key fits into a lock.
• This specificity ensures that enzymes catalyze only particular reactions, reducing the likelihood of undesired side reactions

active site
The region on the enzyme where substrates bind and reactions are catalyzed, crucial for the enzyme’s specificity and catalytic activity.

Question 13

What is the effect of high temperature on proteins in general and enzymes in particular

Answer 13

high temperature causes proteins to denature. heat disrupts the hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges that hold the protein in its specific shape. Denatured proteins often lose their functional shape, which is critical for their biological activity.

Enzymes are proteins, so they are also subject to denaturation at high temperatures. When an enzyme denatures, its active site loses its specific shape, preventing the substrate from binding effectively. This results in a loss of catalytic activity.

Question 14

Define optimal pH for an enzyme.

Answer 14

The optimal pH for an enzyme is the specific pH value at which the enzyme exhibits its maximum activity. At this pH, the enzyme’s structure is in its most favorable conformation, and the active site is best suited to bind the substrate and catalyze the reaction efficiently.

stomach pH ~ 2
plasma pH - between 7.35 and 7.45

Question 15

What is cell theory?

Answer 15

cell theory is a scientific theory first formulated in the mid-nineteenth century, that living organisms are made up of cells, that they are the basic structural/organizational unit of all organisms, and that all cells come from pre-existing cells. Cells are the basic unit of structure in all living organisms and also the basic unit of reproduction.

Question 16

Define intracellular fluid (ICF) and extracellular fluid (ECF).

Answer 16

intracellular fluid
Definition: Intracellular fluid (ICF) is the fluid contained within the cells of the body. It makes up about two-thirds of the total body water.

extracellular fluid
Extracellular fluid (ECF) is the fluid outside the cells. It makes up about one-third of the total body water.

Question 17

Where are cytosol (or cytoplasm) and interstitial fluid located?

Answer 17

cytosol / cytoplasm
The cytosol is the liquid component of the cytoplasm, found inside the cell. The cytoplasm includes the cytosol and the organelles suspended within it, excluding the nucleus.

interstitial fluid
The interstitial fluid is found in the extracellular space, specifically between the cells of tissues. It surrounds and bathes the cells.

Question 18

Describe the structure of a cell membrane.

What do we mean by semi-permeable or selectively permeable?

Answer 18

The cell membrane is a phospholipid bilayer with embedded proteins, cholesterol, and carbohydrates. head of phosopholipid is hydrophilic, tails is hydrophobic

Semi-permeable or selectively permeable means that the cell membrane allows certain molecules or ions to pass through it while blocking others. This selective permeability is crucial for maintaining homeostasis within the cell.

Question 19

Describe membrane receptors

Answer 19

Membrane receptors are specialized protein molecules embedded in the cell membrane that receive and transmit signals from the external environment to the inside of the cell. These receptors play a crucial role in cell communication, allowing the cell to respond to various stimuli such as hormones, neurotransmitters, and other signaling molecules.

Question 20

Define diffusion and osmosis.

Answer 20

difusion
Diffusion is the passive movement of molecules or ions from an area of higher concentration to an area of lower concentration until equilibrium is reached. This process occurs due to the random motion of particles and does not require energy.

osmosis
Osmosis is the spontaneous net movement or diffusion of solvent molecules through a selectively-permeable membrane from a region of high water potential to a region of low water potential, in the direction that tends to equalize the solute concentrations on the two sides.

Question 21

What is the difference between simple diffusion and facilitated diffusion?

Answer 21

simple diffusion
Simple diffusion is the passive movement of molecules or ions from an area of higher concentration to an area of lower concentration without the aid of membrane proteins. Small, non-polar molecules

facilitated diffusion
Facilitated diffusion is the passive movement of molecules or ions across a biological membrane via specific transmembrane integral proteins. Larger, polar molecules or ion

• typically neither require energy

Question 22

Describe channel proteins? What is a leakage channel?

Answer 22

Channel proteins are integral membrane proteins that form pores or channels in the cell membrane, allowing specific molecules or ions to pass through. These channels facilitate the passive transport of substances down their concentration gradient.

Leakage channels are a type of ion channel that is always open, allowing ions to “leak” across the membrane at all times. These channels contribute to the resting membrane potential of cells by maintaining a steady flow of ions.

Question 23

What is the difference between a ligand-gated channel, a voltage-gated channel, and a mechanically gated channel?

Answer 23

Ligand Gated

Ligand-gated channels are ion channels that open or close in response to the binding of a specific chemical messenger (ligand) to the channel.

voltage Gated
Voltage-gated channels are ion channels that open or close in response to changes in the electrical potential (voltage) across the cell membrane.

mechanically gated channel
Mechanically gated channels are ion channels that open or close in response to mechanical forces or pressure applied to the cell membrane.

Question 24

Describe carrier proteins and pumps. How are they different?

Answer 24

carrier protein

A carrier protein is a type of membrane protein that facilitates the movement of specific molecules or ions across the cell membrane. It works by binding to the substance on one side of the membrane, undergoing a conformational change, and then releasing the substance on the other side. This process can be either passive (facilitated diffusion) or active (requiring energy).

Ex/ sodium glucose (cotransport/symport

pump proteins
Pumps are membrane proteins that actively transport ions or molecules across the cell membrane against their concentration gradient. Require energy (ATP) to function.

Ex/ Sodium-potassium pump (contratransport / antiport)

Question 25

Describe cotransport and countertransport.

Answer 25

cotransport
Cotransport, or symport, is a type of transport where a carrier protein moves two different molecules or ions in the same direction across the cell membrane.

Ex/ sodium-glucose cotransporter

countertransport / aniport
countertransport, or antiport, is a type of transport where a carrier protein moves two different molecules or ions in opposite directions across the cell membrane.

Ex / Sodium-calcium exchanger

Question 26

Describe active transport.

Answer 26

Active transport is the process by which cells move molecules or ions across the cell membrane against their concentration gradient, using energy in the form of ATP. Facilitated by carrier proteins and pumps. Primary active transport uses ATP directly, while secondary active transport uses the energy from an existing gradient created by primary active transport.

Question 27

Describe the sodium-potassium pump

Answer 27

The sodium-potassium pump is a type of primary active transport mechanism that moves sodium (Na⁺) and potassium (K⁺) ions across the cell membrane, against their concentration gradients, using energy from ATP.

Utilizing ATP pumps three sodium ions out of the cell and two potassium ions into the cell.

Creates a charge difference across the membrane, contributing to the membrane potential.

Regulates cell volume by controlling the osmotic balance of ions.

Question 28

Describe microvilli and cilia. What are their functions?

Answer 28

Microvilli

Microvilli are small, finger-like projections found on the surface of epithelial cells (primarily columnar), particularly those lining the intestines and the kidneys. Microvilli significantly increase the surface area of the cell, enhancing its ability to absorb nutrients, ions, and other substances.

cilia

Cilia are hair-like structures that extend from the surface of epithelial cells (primarily columnar and pseudostratified). Cilia can move in coordinated waves, propelling fluids and particles across the surface of the cell.

Question 29

Describe vesicular transport: endocytosis, exocytosis, phagocytosis, pinocytosis, receptor-mediated endocytosis.

Answer 29

Vesicular transport is a cellular process that involves the movement of materials within vesicles, small membrane-bound sacs, to different locations in the cell or to the cell’s exterior.

endocytosis
Endocytosis is the process by which cells internalize substances from their external environment.

exocytosis
Exocytosis is the process by which cells expel materials to the extracellular environment.

phagocytosis
Known as “cell eating.” Involves the engulfment of large particles, such as debris or microorganisms, by the cell.
The cell membrane extends around the particle, forming a phagosome, which then fuses with a lysosome for digestion.

pinocytosis
Known as “cell drinking.” Involves the ingestion of fluid and dissolved solutes by the cell.
The cell membrane invaginates to form small vesicles that take in extracellular fluid and its contents.

receptor-mediated endocytosis
Highly specific process where cells absorb metabolites, hormones, proteins, or viruses by the inward budding of the cell membrane. This process involves receptor proteins on the cell surface that bind to specific ligands, forming a coated vesicle. (cholesterol uptake)

Question 30

Describe the parts of a cell and their functions, including the nucleus, mitochondrion, Golgi apparatus, smooth and rough endoplasmic reticulum, ribosomes, lysosomes, centrioles.

Answer 30

A cell is composed of various specialized structures, each with distinct functions essential for cellular operations. The nucleus serves as the control center, housing the cell’s DNA and coordinating activities such as growth, metabolism, and reproduction through the regulation of gene expression. Mitochondria, known as the powerhouses of the cell, generate ATP through oxidative phosphorylation, providing energy for cellular functions. The Golgi apparatus functions as the cell’s packaging and distribution center, modifying, sorting, and packaging proteins and lipids for secretion or delivery to other organelles.

The endoplasmic reticulum (ER) is divided into two regions: smooth and rough. The rough endoplasmic reticulum (RER) is studded with ribosomes, which are the sites of protein synthesis. These newly synthesized proteins are folded and processed within the RER. The smooth endoplasmic reticulum (SER), lacking ribosomes, is involved in lipid synthesis, detoxification processes, and calcium ion storage. Ribosomes themselves, whether free-floating in the cytoplasm or attached to the RER, are the molecular machines that translate mRNA into proteins.

Lysosomes are the cell’s digestive system, containing hydrolytic enzymes that break down macromolecules, old cell parts, and foreign substances. Centrioles, cylindrical organelle involved the the devrelopment of spinkdle fibers in cell division.

Question 31

what are the four bases that form the genetic code, and how do they code for proteins

Answer 31

The four bases that form the genetic code are adenine (A), thymine (T), cytosine (C), and guanine (G). In RNA, thymine is replaced by uracil (U).

These bases pair up (A with T or U, and C with G) and form the rungs of the DNA double helix. One strand is the template strand (the antisense strand) used to create mRNA, the other strand is the coding strand.

The genetic code is composed of sequences of three bases called codons. Each codon (base-triplet) specifies a particular amino acid or a stop signal during protein synthesis. There are 64 possible codons (4 bases x 4 bases x 4 bases), and these codons code for the 20 amino acids used to build proteins, along with start and stop signals.

During transcription, the antisense strand of DNA is copied into messenger RNA (mRNA) in the nucleus. This mRNA carries the genetic information from DNA to the ribosome, where translation occurs.

During translation, the ribosome reads the mRNA sequence in codons, starting at a specific start codon (AUG, which codes for methionine). Transfer RNA (tRNA) molecules, each carrying a specific amino acid, bind to the corresponding codon on the mRNA through their anticodon. The ribosome links the amino acids together in the correct order to form a polypeptide chain, which folds into a functional protein. This process continues until a stop codon (UAA, UAG, or UGA) is reached, signaling the end of protein synthesis.

Question 32

Describe the functions of mRNA, tRNA, and rRNA.

Answer 32

mRNA

Carries the genetic code from DNA in the nucleus to the ribosomes in the cytoplasm. During transcription, mRNA is synthesized based on the DNA template. It then travels to the ribosome, where it serves as a template for assembling amino acids in the correct sequence to form a protein.

tRNA
Transfers specific amino acids to the ribosome during protein synthesis. Each tRNA molecule has an anticodon that is complementary to an mRNA codon and an attached specific amino acid. During translation, tRNA molecules bind to their corresponding codons on the mRNA, bringing the appropriate amino acids into place to form a growing polypeptide chain.

rRNA
Forms the core structural and functional components of the ribosome. rRNA molecules combine with proteins to form ribosomes, which are the sites of protein synthesis. They help ensure the proper alignment of mRNA and tRNA and catalyze the formation of peptide bonds between amino acids.

Question 33

Describe stages of mitosis

Answer 33

1. prophase chromosomes condense and become visible. Nuclear envelop begins to disintegrate. mitotic spindle starts to form the centrosomes.
2. metaphase chromosomes align at the metaphase plate. Spindle fibers attach to the centromeres of the chromosome.
3. anaphase sister chromatids are pulled apart by spindle fibers.
4. telophase chromosomes reach the oposite poles and begin to de-condensel nuclear envelop re-forms around each set of chromosomes. mitotic spindle breaks down.

5 cytokinesis Cytoplasm divides, creating two daughter cells.

PMATC -> please make a twin cell