B1.2 Fix answers

Question 1

Draw the generalized structure of an amino acid.

Answer 1

H
|
H O
H | /
N - C —-C /
H | \ \
R \ \
O

Alpha carbon

Amino Side. Carboxyl group
Group. Chain

monomers that are used to make proteins.

Question 2

Label the amine group, carboxyl group, alpha carbon and R group on an amino acid.​

Answer 2

H
|
H O
H | /
N - C —-C /
H | \ \
R \ \
O

Alpha carbon

Amino Side. Carboxyl group
Group. Chain

monomers that are used to make proteins.

Question 3

Define dipeptide, oligopeptide and polypeptide.

Answer 3

Dipeptide: 2 amino acids.
Oligopeptide: 2-20 amino acids.
Polypeptide: More than 20 amino acids.

Amino acids join together through a condensation reaction (Interactive 1). A peptide bond is formed when the carboxyl group (–COOH) of one amino acid reacts with the amino group (–NH2) of another amino acid to form a dipeptide. A molecule of water (H2O) is released as a byproduct. The peptide bond formed is a type of covalent bond and, therefore, is very stable.

The N-terminal (amino-terminal) end of the dipeptide refers to the free amino group that is not involved in the peptide bond, while the C-terminal (carboxyl-terminal) end refers to the unbound carboxyl group. More amino acids can be added to the dipeptide through the formation of a new peptide bond between an incoming amino acid and the C-terminal (carboxyl terminal) of the dipeptide. This process can be repeated multiple times to form longer chains of amino acids, called polypeptides. Every time an amino acid joins the growing polypeptide strand and a new peptide bond is formed, another water molecule is released. Subtopic D1.2 covers the formation of polypeptides.

Question 4

Draw peptide bond formation in a condensation reaction between two amino acids.

Answer 4

In a condensation reaction, two amino acids form a peptide bond by joining the carboxyl group of one amino acid with the amino group of another, releasing a water molecule.
amino acid + amino acid → dipeptide + 1 water molecule
Condensation reaction between two amino acids. Once the water is removed, the C bonds to the N in a peptide bond.

Question 5

State where in the cell polypeptide formation occurs.
​.

Answer 5

Ribosomes

Question 6

Compare the source of amino acids by plant and animal cells.

Answer 6

Plant Cells:

Synthesize amino acids from inorganic nitrogen sources (nitrate or ammonium).
Use carbon skeletons from photosynthesis to build amino acids.
Animal Cells:

Obtain amino acids from dietary protein intake.
Break down ingested proteins into amino acids through digestion.

Question 7

Define “essential” and “non-essential” as related to dietary amino acids.

Answer 7

Essential amino acids are the amino acids that your body cannot produce and therefore you must obtain them from the food that you eat.

Non-essential amino acids can be produced by the body from other amino acids or by the breakdown of proteins. both important

Question 8

Outline why vegan diets require attention to food combinations to ensure essential amino acids are consumed.

Answer 8

Vegan diets can provide all the essential amino acids necessary for a healthy diet through plant-based protein sources such as beans, lentils, nuts, seeds and tofu (Figure 2). However, if following a vegan diet, it is necessary to ensure that adequate amounts of these protein sources are consumed for optimal health

Question 9

Outline why there is a limitless diversity of DNA base sequences.​

Answer 9

The infinite variety of possible peptide chains arises from the ability to combine the 20 different amino acids in any sequence. This allows for creation of an almost limitless number of unique proteins with different structures and functions. The genetic code, combined with the ability to generate diverse combinations of amino acids, is what makes the complexity and diversity of life possible. The genetic code is composed of codons, which are groups of three nucleotides that specify the type of amino acid or stop signal required. There are 64 different codons in total, but only 20 amino acids

Question 10

Define denaturation.

Answer 10

Denaturation is a process in which the structure of a protein is altered causing it to lose function, usually permanently

Question 11

Explain the effect of pH on temperature on protein structure and function.​

Answer 11

All proteins have a specific range of temperature and pH for their optimal activity. As all enzymes are proteins, it is essential for them to be exposed to their ideal conditions to maintain efficiency. Extreme changes in pH can affect protein solubility and shape by altering the protein’s charge. This can lead to irreversible changes in protein structure, causing inactivity. For example, the enzyme pepsin requires an acidic environment to function, while an alkaline environment will render it inactive.

Temperature is another critical factor that can cause protein denaturation. High temperatures can break the weak hydrogen bonds holding the protein structure together, causing the protein to unfold and lose function. Most human proteins function optimally at body temperature (~37 °C). Some organisms that live in extreme high-temperature environments have proteins that can only function at higher temperatures. Low temperatures can also affect protein structure, but to a lesser extent than high temperatures

Question 12

Outline the effect of R-group structure on the properties of an amino acid, with reference to hydrophilic, hydrophobic, polar and charged.

Answer 12

R-groups can be hydrophobic or hydrophilic. Hydrophobic R-groups are non-polar and tend to repel water molecules. Hydrophilic R-groups are polar or charged, acidic or basic, and tend to attract water molecules. Polar R-groups contain partial charges that interact with water molecules, while charged R groups can be either positively charged (basic) or negatively charged (acidic). the R-group is what gives each amino acid its unique characteristics. The R-groups of the amino acids present in a polypeptide determine the properties of the assembled polypeptides

Question 13

Identify the “backbone” of a polypeptide.

Answer 13

Polypeptide Backbone: The repeating sequence of atoms in a protein chain, consisting of
−
N-C-C
−
−N-C-C− units from the amino and carboxyl groups of amino acids.
Structure: N (amide nitrogen) - C
𝛼
α (alpha carbon) - C (carbonyl carbon).
Function: Provides structural support and determines the overall shape of the protein.

Question 14

Define “confirmation” as related to protein structure.

Answer 14

Conformation: The three-dimensional shape or arrangement of a protein molecule.
Importance: Determines protein function and interaction with other molecules.
Factors: Influenced by amino acid sequence, environmental conditions, and molecular interactions.

Question 15

Describe the primary structure of a protein, including the type of bonding involved.

Answer 15

Primary Structure: The linear sequence of amino acids in a polypeptide chain.
Bonding: Peptide bonds link amino acids through condensation reactions.
Significance: Determines higher-level structures and ultimately protein function.

Question 16

Outline how a DNA sequence codes for a polypeptide that will repeatedly fold into the same precise, predictable protein confirmation.

Answer 16

Genetic Code: DNA sequence is transcribed into mRNA, which is translated into a polypeptide.
Codons: Triplets of nucleotides in mRNA specify amino acids.
Folding: Amino acid sequence dictates folding through interactions like hydrogen bonds and hydrophobic interactions.
Consistency: Proteins fold consistently due to specific sequences and interactions.

Question 17

Describe the secondary structure of a protein, including the type and location of the bonds involved.

Answer 17

Secondary Structure: Localized folding patterns within a protein, such as alpha-helices and beta-pleated sheets.
Bonding: Stabilized by hydrogen bonds between the carbonyl oxygen and amide hydrogen of the polypeptide backbone.
Alpha-Helix: Coiled structure with hydrogen bonds every four residues.
Beta-Pleated Sheet: Extended strands with hydrogen bonds between adjacent strands.

Question 18

Identify the alpha-helix and beta-pleated sheet in images of protein structure.

Answer 18

Alpha-Helix: A right-handed coiled structure with a spiral shape.

Characteristics: Hydrogen bonds form between every fourth amino acid.

Beta-Pleated Sheet: A zigzag pattern with strands running parallel or anti-parallel.

Characteristics: Hydrogen bonds form between adjacent strands.

Question 19

Describe the tertiary structure of a protein, including the types of R-group interactions involved.

Answer 19

Tertiary Structure: The overall three-dimensional shape of a protein, formed by the folding of secondary structures.

R-Group Interactions: Include hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

Hydrophobic Interactions: Non-polar side chains cluster away from water.
Hydrogen Bonds: Polar side chains form hydrogen bonds with each other.
Ionic Bonds: Charged side chains form electrostatic interactions.
Disulfide Bridges: Covalent bonds between cysteine residues stabilize structure.

Question 20

Explain the effect of polar and non-polar R-groups of amino acids on tertiary structure of proteins.

Answer 20

Polar R-Groups:

Form hydrogen bonds and interact with water, leading to hydrophilic surfaces.
Often located on the exterior of proteins.
Non-Polar R-Groups:

Cluster together to minimize exposure to water, leading to hydrophobic cores.
Often located in the interior of proteins.

Question 21

Explain the effect of positively and negatively charged amino acid R-groups on the tertiary structure of proteins.

Answer 21

Positively Charged R-Groups:

Form ionic bonds with negatively charged groups, stabilizing protein structure.
Negatively Charged R-Groups:

Form ionic bonds with positively charged groups, contributing to protein folding and stability.
Electrostatic Interactions:

These interactions can affect protein shape, solubility, and interaction with other molecules.

Question 22

State that a strong disulfide covalent bond can occur between pairs of cysteine amino acids.

Answer 22

Disulfide Bonds:
Strong covalent bonds form between sulfur atoms of cysteine side chains.
Stabilize protein structure, especially in extracellular proteins.

Question 23

Discuss the arrangement of amino acids in soluble globular proteins.

Answer 23

Globular Proteins: Compact, spherical proteins that are typically soluble in water.
Arrangement:
Hydrophobic Core: Non-polar amino acids are buried inside, away from water.
Hydrophilic Surface: Polar and charged amino acids are on the exterior, interacting with water.

Question 23

State that amino acids can be hydrophobic or hydrophilic depending on the properties of the R-group.

Answer 23

Hydrophobic Amino Acids: Have non-polar R-groups that repel water. Examples include leucine and valine.
Hydrophilic Amino Acids: Have polar or charged R-groups that attract water. Examples include serine and lysine.

Question 24

Discuss the arrangement of amino acids in integral membrane bound proteins.

Answer 24

Integral Membrane Proteins: Span the lipid bilayer, with regions exposed to both the exterior and interior of the cell.
Arrangement:
Transmembrane Domains: Rich in hydrophobic amino acids, interact with the lipid bilayer.
Extracellular and Cytoplasmic Domains: Contain hydrophilic amino acids, interact with aqueous environments.

Question 24

Discuss the arrangement of amino acids in channel proteins in membranes.

Answer 24

Channel Proteins: Facilitate the transport of ions and molecules across cell membranes.
Arrangement:
Pore Lining: Hydrophilic amino acids line the channel, allowing passage of polar molecules.
Membrane-Spanning Regions: Composed of hydrophobic amino acids, anchoring the protein in the lipid bilayer.

Question 25

Describe the quaternary structure of a protein.

Answer 25

Quaternary Structure: The assembly of multiple polypeptide chains (subunits) into a functional protein complex.
Subunit Interactions: Stabilized by non-covalent interactions like hydrogen bonds, ionic bonds, and hydrophobic interactions.
Example: Hemoglobin consists of four subunits, forming a tetramer

Question 26

Compare the structure of conjugated and non-conjugated proteins.

Answer 26

Conjugated Proteins: Contain a non-protein component (prosthetic group) that is essential for function.

Example: Hemoglobin, with heme as a prosthetic group.
Non-Conjugated Proteins: Consist solely of amino acids without additional components.

Example: Myoglobin, which consists only of amino acids.

Question 27

State an example of a conjugated and non-conjugated protein.

Answer 27

Conjugated Protein: Hemoglobin, with a heme group as its prosthetic component.
Non-Conjugated Protein: Myoglobin, consisting only of amino acids without additional components.

Question 28

Describe, with reference to collagen, the structure and function of fibrous proteins.

Answer 28

Fibrous Proteins: Long, insoluble, structural proteins.
Collagen:
Structure: Triple helix of three polypeptide chains, providing strength and flexibility.
Function: Provides structural support in connective tissues, skin, and bones.

Question 29

Describe, with reference to insulin, the structure and specificity of globular proteins

Answer 29

Globular Proteins: Compact, spherical proteins that are typically water-soluble and have dynamic roles, such as enzymes or hormones.

Insulin Structure:

Composition: Two polypeptide chains (A and B) with a total of 51 amino acids, linked by two interchain disulfide bonds and one intrachain disulfide bond in the A chain.
Folding: Hydrophobic interactions and hydrogen bonds stabilize the 3D shape, allowing specific interactions.
Specificity:

Receptor Binding: The 3D structure allows insulin to specifically bind to insulin receptors, regulating glucose uptake.
Function: Insulin’s precise conformation is crucial for its role in lowering blood glucose levels.
Example: Insulin, a hormone that regulates blood sugar, exemplifies the specificity and solubility of globular proteins.