Protein structure and functional types

Question 1

How are proteins constructed (4)

Answer 1

1. Enclosed within base pairs from mRNA translation
2. Range of functions (antibodies, enzymes, etc..)
3. Assembled with various amino acid sequences and folded
4. Folded shape depends on linear amino acid sequence & interactions with protein and solvent.

Question 2

What are amino acids (5)

Answer 2

1. Side chain attached to chiral carbon
2. Chiral carbon determines stereochemistry - L or D
3. Eukaryotic enzymes recognise L
4. Bacteria utilise D
5. Bacteria synthesis D-alanine & D-glutamate for crosslinking peptidoglycan wall

Question 3

What are the types of amino acids (7)

Answer 3

1. Small
2. Neuleophilic
3. Hydrophobic
4. Aromatic
5. Acidic
6. Amide
7. Basic

Question 4

What are the different chemistries and properties of side chains (3)

Answer 4

1. non-polar side chains
2. positive or negative charges
3. polar but unchanged side chains

Question 5

What is the importance of amino acid side chains (2)

Answer 5

1. critical to understanding and maintaining protein structure.
2. Due to side chain interactions, the sequence and location of amino acids in a particular protein guides where bends and folds occur in that protein

Question 6

What happens when amino acids condense (3)

Answer 6

1. making a peptide bond
2. resulting in a primary sequence which can be designated with certain letters.
3. Within these proteins, the peptides are linked together forming a chain resulting in the primary structure.

Question 7

How are primary amino acid structures named (4)

Answer 7

1. 5 amino acids = pentapeptide
2. Name from N-terminus to C-terminus
3. N-terminus has (-NH₂)
4. C-terminus has (-COOH)

Question 8

What are the levels of protein structure (4)

Answer 8

1. Primary - sequence
2. Secondary - interactions between chains
3. Tertiary - bonds between chains
4. Quaternary - proteins interacting with each other

Question 9

What are protein secondary structures (3)

Answer 9

1. alpha helix - hydrogen bonds, prolines, charged residues
2. Random coil
3. Beta pleated sheets - anti-parallel, hydrogen bonds, N→C then C→N, more stable (H-bonds)

Question 10

How do peptides/proteins fold (2)

Answer 10

1. Hydrophobic residues cause proteins to fold adjacent to one another
2. Hydrophilic areas on the surface are exposed to solvent.

Question 11

What makes secondary structures fold into tertiary structures (8)

Answer 11

1. Adopted by the most energetically favourable protein
2. Tested various conformations before the final form
3. Stabilised by interactions between amino acids
4. Chemical forces between protein and environment contribute to shape and stability
5. Covalent bonds, non-covalent bonds
6. Folded proteins have function
7. Cytoplasmic proteins have hydrophilic side chains, and hydrophobic elements inside
8. Cell membrane proteins have hydrophobic groups on surface exposed to membrane lipids

Question 12

What can quaternary protein structures do (4)

Answer 12

1. Associate with one another = monomer
2. Interact with one another = homodimer
3. Interact with genetic material
4. Communication between subunits

Question 13

How is haemoglobin structured (4)

Answer 13

1. Globular protein (ball-shaped)
2. tetrametric (alpha-1, beta-2) quaternary structure
3. 4 subunits in tetrahedral arrangement
4. H-bonds, electrostatic interactions, sulphide bond

Question 14

How is insulin held together

Answer 14

Interactions with central zinc ion

Question 15

What are the protein function types (5)

Answer 15

1. structural proteins - maintain cell shape
2. enzymes - catalyse the biochemical reactions that occur in cells
3. signalling proteins - work as monitors, changing shape and activity in response to metabolic signals or messages from outside the cell
4. Cells also secrete various proteins that become part of the extracellular matrix or are involved in intercellular communication
5. Transport proteins - move cargo around the body and cell

Question 16

What are the types of proteins (4)

Answer 16

1. Globular
2. Fibrous
3. Simple
4. Complex

Question 17

What are globular proteins (3)

Answer 17

1. roughly ball-shapes (sphere-proteins)
2. usually water soluble - polar groups on surface
3. e.g. blood albumin, haemoglobin and most enzymes)

Question 18

What are fibrous proteins (4)

Answer 18

1. Long and thin shapes (scleroprotein)
2. many fitted together in simple repeat units
3. usually insoluble in water
4. (e.g. collagen, keratin (structural proteins))

Question 19

What are simple proteins

Answer 19

Only a polymer of amino acids that folds into a protein

Question 20

What are complex proteins (2)

Answer 20

1. A polymer of amino acids with other molecules attached (e.g. phosphates, sugars, lipids)
2. Their tertiary/quaternary structure relates to their function and role in biological systems

Question 21

What are protein families (2)

Answer 21

1. Related shapes therefore interact in similar ways
2. Long stretches of similar amino acid sequences within the primary structure

Question 22

What are membrane proteins (4)

Answer 22

1. In plasma membrane
2. Help cells interact with the environment
3. Hydrophobic amino acids = contact lipids in membrane bilayer
4. hydrophilic amino acids = extend to water-based cytoplasm, modified by addition of sugar molecules

Question 23

What is collagen (6)

Answer 23

1. Fibrous proteins
2. Long polypeptide chain and trimetric helix
3. Most abundant protein in animals
4. Forms most connective tissues
5. Used in reconstructive surgery
6. Structural

Question 24

What are lipoproteins (5)

Answer 24

1. Transport protein
2. Important in the vascular system because fats don’t dissolve in water
3. Lipoproteins carry fats where they need to go
4. LDL (low-density) - transport fats to cells
5. HDL - transports cholesterol away from arteries to the liver

Question 25

How do enzymes work (3)

Answer 25

1. Aid biochemical reactions
2. Lower the activation energy of the reaction, making it faster
3. Highly specific to their substrates, except frug metabolism

Question 26

What happens with post-translational modification (4)

Answer 26

1. After translation and folding is complete
2. transferase adds small modifier groups (e.g. phosphates, carboxyl)
3. Covalent modifications change conformation, turning protein on and off
4. PTM are reversible, different enzymes catalyse reverse reactions

Question 27

What are phosphoproteins (2)

Answer 27

1. Addition of negatively charged phosphate group
2. phosphorylation in controlling protein function is usually involved in cell signalling

Question 28

What are nucleoproteins (3)

Answer 28

1. Associated with nucleic acids as a way of packaging DNA
2. PTM by lysine acetylation - neutralise positive charge
3. PTM makes DNA more accessible for transcription

Question 29

what affects protein stability (6)

Answer 29

1. Extreme conditions
2. Salts
3. Oxidation/Reduction
4. Mutations
5. Ligand/cofactor bonding
6. Protein sequence

Question 30

What is denaturation (4)

Answer 30

1. process in which proteins lose the quaternary, tertiary and secondary structure
2. irreversible
3. affect the activity of the protein.
4. Can be degraded in vivo due to proteolysis.

Question 31

What happens with protein misfolding (5)

Answer 31

1. Folding is reversible and transient
2. Proteopathy = Denaturation, pathological misfolding
3. Unfolded proteins usually refold
4. Misfolding = cellular malfunctioning & diseases
5. Aggregation = insoluble fibrils accumulate in tissue, Alzheimer’s

Question 32

What is Mad cow disease (BSE) and Creutzfeldt-Jakob’s disease (CJD) (2)

Answer 32

1. Transmitted through contact with infected tissue, body fluids, or contaminated medical instruments.
2. Normal sterilisation procedures do not get rid of these and fail to render prions non-infective.

Question 33

What is the difference between L and D amino acids (2)

Answer 33

1. L-amino acids have the amino (NH) group on the left
2. D-amino acids have the amino (NH) group on the right