B1.2: Proteins

Question 1

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

Answer 1

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Question 2

Define dipeptide, oligopeptide and polypeptide.

Answer 2

Dipeptide: 2 amino acids are linked by a condensation reaction

Oligopeptide: 20 amino acids in a chain linked by a condensation reaction

Polypeptide: The main component of proteins and are a longer chain of amino acids

Question 3

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

Answer 3

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Question 4

State where in the cell polypeptide formation occurs.

Answer 4

Cell polypeptide formation occurs in ribosomes in cells

Question 5

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

Answer 5

Plants: Can make all amino acids using photosynthesis

Animals: Obtain essential amino acids from their food only as they can’t synthesise it themselves

Question 6

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

Answer 6

Essential: Body can’t produce

Non-essential: Body can produce from other amino acids or by the breakdown of proteins

Question 7

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

Answer 7

People eating a vegan diet must ensure that they have enough ESSENTIAL amino acids consumed

• Adequate amounts of these protein sources are consumed for optimal health

Question 8

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

Answer 8

Infinite variety of possible peptide chains arise from the ability to combine the 20 different amino acids in any sequence.

Question 9

Examples of polypeptides

Answer 9

• Lysozyme: present in saliva
• Alpha-Neurotoxins: present in snake venom
• Glucagon: secreted from the pancreas
• Myoglobin: found in muscle tissues

Question 10

Define denaturation.

Answer 10

A process in which the structure of a protein’s altered causing it to lose function permanently

Question 11

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

Answer 11

• pH too high/too low: affects protein solubility and shape by altering protein’s charge leading to irreversible changes in protein structure resulting in inactivity. Denaturation is caused
• temp. too high: Breaks weak Hydrogen bonds holding the protein structure together causing the protein to unfold and lose function. Denaturation is caused. Substrates can no longer bind to the protein. A protein’s shape is specific to its function.

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

• Hydrophobic R-groups are non polar only
• Hydrophilic R-groups are 1) polar or charged 2) acidic or basic
• Polar R-groups have partial charges that interact with water molecules whereas charged R-groups can be +vely charged (basic) or -vely charged (acidic)

Question 13

Identify the “backbone” of a polypeptide.

Answer 13

• Repeating sequence of atoms linked by covalent bonds
  —C—C—N—C—C—N—

Question 14

Define “confirmation” as related to protein structure.

Answer 14

Confirmation refers to the specific 3D arrangement of atoms in a polypeptide or protein.

Question 15

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

Answer 15

Primary Structure
- Linear and specific sequence of amino acids joined together to form a polypeptide chain
- Peptide bonding is involved and holds amino acids in place

Question 16

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

Answer 16

• The unique sequence of amino acids determines how the polypeptide chain will fold which leads to the 3D structure of the protein
• a change in this sequence of amino acids can result in significant changes to protein structure and function

Question 17

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

Answer 17

Secondary Structure
- Involves 2 common types of secondary structures: alpha helices (forms coils) and beta-pleated sheets (forms pleats)
- Hydrogen bonding is involved which exists between the carboxyl group of one non-polar amino acid and the amino group of another non-polar amino acid in a different part of the polypeptide chain
which stabilise the formation of secondary structure.

Question 18

What and where is the bonding in alpha helices?

Answer 18

• Consists of non polar amino acids that have hydrogen bonding between non-adjacent amino acids and these 2 shapes maximise the number of hydrogen bonds

Question 19

What and where is the bonding in beta pleated sheets?

Answer 19

• Consists of non polar amino acids that have hydrogen bonding between adjacent amino acids and these 2 shapes maximise the number of hydrogen bonds

Question 20

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

Answer 20

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Question 21

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

Answer 21

Tertiary Structure:
- Further folding of the polypeptide that is dependent on the interaction between R groups which may form Hydrogen Bonds, Ionic Bonds, Disulfide Covalent Bonds and Hydrophobic Interactions

Question 22

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

Answer 22

Effects of Polar R groups:
- Hydrophilic polar amino acids face outside towards aqueous environment

Effects of Non-polar R groups:
- Hydrophobic non-polar amino acids are protected in the core, minimising interactions with water molecules

Question 23

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

Answer 23

• The R-group can undergo binding of Hydrogen ions resulting in a +vely or -vely charged state
• These charged R-groups can interact with oppositely charged atoms hence, forming ionic bonds

Question 24

What is a disulfide covalent bond and whats its function

Answer 24

• A disulfide covalent bond can occur between pairs of cysteine amino acids - this is the strongest bond present
• Critical for stabilising the tertiary and quaternary structures of proteins

Question 25

Where do the hydrophobic interactions occur

Answer 25

Hydrophobic interactions occur between non-polar amino acids as water is a polar molecule and forms hydrogen bonds with polar amino acids

• This means the non-polar amino acids arent able to interact with water thus, they clump together into the hydrophobic clusters in the interior of the protein to minimise contact with water molecules

Question 26

How can amino acids be hydrophobic or hydrophilic

Answer 26

This depends on the properties of the R-group.

Question 27

Discuss the arrangement of amino acids in soluble globular proteins.

Answer 27

• Hydrophilic amino acids on their surface where they are in contact with water as globular proteins need to be soluble in water as they carry out their function in an aqueous solution outside the cell or in the cytoplasm
• Hydrophobic amino acids are clustered in the centre where water is excluded
• This arrangement stabilises tertiary structure of the proteins as it maximises hydrophobic interactions and hydrogen bonding

Question 28

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

Answer 28

• Hydrophobic amino acids on parts of their surface where they contact the non-polar hydrocarbon core of the membrane
• This arrangement both stabilises the tertiary structure and ensures that it remains positioned correctly in the membrane where its function can be performed

Question 29

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

Answer 29

• Allow hydrophilic solutes/water to diffuse across the hydrophobic core of membrane
• Consist of hydrophilic regions with a hydrophobic region in between which holds them in a transmembrane position
• The width and charge distribution of this channel allows specific hydrophilic ions or molecules to pass through

Question 30

Describe the quaternary structure of a protein.

Answer 30

Quaternary Structure
- Arrangement and interaction of 2 or more polypeptide chains to form a functional protein

Question 31

Compare the structure of conjugated and non-conjugated proteins.

Answer 31

Structure of Conjugated proteins:
- Have non-protein components in addition to having polypeptide subunits which increase a protein’s diversity and functionality

Structure of Non-Conjugated proteins:
- Only consist of polypeptide subunits

Question 32

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

Answer 32

Conjugated protein:
- Hemoglobin: has 4 polypeptide chains - 2 alpha and 2 beta chains. Called a conjugated protein as it contains Haem - iron that binds oxygen allowing this protein to transport oxygen

Non-conjugated protein:
- Collagen: has 3 polypeptide subunits
- Insulin: has 2 polypeptide subunits

Question 33

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

Answer 33

Structure of fibrous proteins:
- Collagen has a long and narrow shape and is insoluble in water. Consists of 3 polypeptide chains that are twisted together in a triple helix structure held together by Hydrogen bonds and VDW forces

Function of fibrous proteins:
- Provide structural support and stability to cells and tissues like skin, tendons and bone

Question 34

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

Answer 34

Structure of globular proteins:
- Insulin has a compact and spherical structure with a hydrophilic interior and hydrophobic exterior. Consists of 2 polypeptide chains - alpha and beta chain

Specificity of globular proteins:
- Insulin binds to specific receptors on cells which allows glucose to enter the cells and be used for energy or stored for later use.

Question 35

What amino acid is involved in making the disulfide covalent bond (the strongest bond which causes the tertiary structure to bend)

Answer 35

Cysteine amino acid

Question 36

What types of amino acids are involved in hydrophobic interactions

Answer 36

non polar amino acids

Question 37

What types of amino acids are involved in ionic bonds

Answer 37

polar amino acids

Question 38

What structure determines the final folding of the tertiary structure

Answer 38

Primary structure - depends on the sequence of amino acids

Question 39

Differences between globular and fibrous proteins

Answer 39

GP:
- Shape: roughly spherical
- Function: specialised (act as enzymes, hormones, etc)
- Examples: Hemoglobin, Insulin and enzymes
- Solubility: Soluble

FP:
- Shape: Long strands
- Function: structural functions
- Examples: Collagen, fibrin and myosin
- Solubility: Insoluble

Question 40

Name 3 proteins and their functions

Answer 40

• Hemoglobin: O2-carrying protein found in rbc
• Insulin: A hormone produced by the pancreas to lower blood glucose levels
• Collagen: Structural protein found in muscle, tendons, ligaments and the skin of vertebrate

Question 41

What are histone proteins and where are they found

Answer 41

• They are found in the nucleus and help with supercoiling DNA into chromosomes

Question 42

What is lipase

Answer 42

Enzyme used to break down lipids into fatty acids and glycerol with the use of hydrolysis

Question 43

What is the polar and non-polar part of lipase

Answer 43

Non-polar (hydrophobic) part is the lipid and the polar (hydrophilic) part is its outer part

Question 44

Outline the role of interactions and bonding in the determination of protein 3D structure

Answer 44

• Hydrophobic interactions result in hydrophobic amino acids facing inside of the protein
• Peptide bonds between amino acids to give their primary structure
• Ionic bonding between oppositely charged amino acids
• Disulfide covalent bonding between pairs of cysteines and to give their tertiary structure

Question 45

Name 7 proteins and state their functions

Answer 45

• Insulin: Used to reduce blood glucose concentrations
• Collagen: It’s a structural protein
• Rhodopsin: Used as an eye pigment
• Hemoglobin: Used to transport oxygen
• Immunoglobins: Used as antibodies
• Rubisco: Used as an enzyme
• Spider Silk: Used to make webs

Question 46

Describe the structure of proteins (9 marks)

Answer 46

• Primary structure: Chain of amino acids
• consisting of 20 different amino acids
• linked by peptide bonds
• Secondary structure: Formed by interaction between amino group on one nucleotide and carboxyl group on another nucleotide of the same polypeptide chain
• weak hydrogen bonds formed
• Alpha helices formed / Beta pleated sheets formed
• Tertiary Structure: Folding up of the polypeptide
• Stabilised by disulfide covalent bonds / other bonds named
• Quarternary structure: Several polypeptides join
• Conjugated proteins are proteins which combine with other non-protein molecules
• E.g. Hemoglobin

Question 47

Explain how the bonds between amino acids contribute to the structure of proteins (8 marks)

Answer 47

Primary structure:
- Sequence of amino acids
- linked via peptide bonds in the polypeptide chain

Secondary structure:
- formation of Alpha helices or beta pleated sheets
- H bonding betw. carboxyl and amino group of the same polypeptide chain

Tertiary Structure:
- Formed by interactions between R groups of amino acids
- Gives polypeptide chain its 3D shape
- Disulphide covalent bonds form between cysteines in R groups
- Polar R groups form H bonds with other Polar R groups
- +vely charged R groups interact with -vely charged R groups

Quaternary Structure:
- Formed in proteins with more than one polypeptide chain
- Formed by the interactions between R groups on different polypeptide chains