3.2 - Protein structure and function

Question 1

what does a proteins sequence always start with and what is it coded by?

Answer 1

Met, coded for by AUG

Question 2

N-terminus (2)

Answer 2

1. start of polypeptide chain
2. amino group (NH2)

Question 3

C-terminus (2)

Answer 3

1. end of protein chain
2. carboxyl group (COOH)

Question 4

what does the 5’-3’ of the mRNA sequence correspond to

Answer 4

the N-terminal to C-terminal of the polypeptide q

Question 5

what do all amino acids contain (apart from proline) (3)

Answer 5

1. acidic carboxyl group
2. basic amino group
3. hydrogen

Question 6

what are the 2 ionisable protons in amino acids? (2)

Answer 6

1. carboxylic acid
2. amino group

Question 7

what does ionisation of amino acids depend on?

Answer 7

pH (usually have 0 charge at physiological pH)

Question 8

structure of amino acids

Answer 8

chiral (L isomer)

Question 9

what has a different chemical property in amino acids?

Answer 9

each ‘R’ group

Question 10

which amino acids are hydrophobic?

Answer 10

non-polar

Question 11

where are hydrophobic amino acids found?

Answer 11

inside of cytosolic globular proteins

Question 12

which amino acids are hydrophillic?

Answer 12

polar (able to form H-bonds)

Question 13

which amino acids can form electrostatic interactions and are basic (+ve charge) or acidic (-ve charge)?

Answer 13

polar amino acids with charged side groups

Question 14

which amino acid can form disulfide bonds?

Answer 14

cysteine

Question 15

describe peptide bond formation

Answer 15

carboxyl group of one amino acid bonds to amino group of another amino acid, with elimination of a molecule of water (condensation reaction)

Question 16

what is the structure of a protein dictated by? (2)

Answer 16

1. properties of amino acid side chains
2. partly by properties of the peptide bond

Question 17

where are hydrophilic/hydrophobic amino acid residues found? (2)

Answer 17

1. hydrophilic - predominantly on surface of protein
2. hydrophobic - predominantly found in interior of protein (cystolic)

Question 18

primary structure

Answer 18

linear sequence of amino acids linked by peptide bonds

Question 19

secondary structure (2)

Answer 19

1. 3D structure formed by H-bonds between peptide NH and CO groups
2. folding of polypeptide chain into a-helices or B-sheets

Question 20

tertiary structure (2)

Answer 20

1. adopt specific 3D conformation, able to fulfil specific biological function
2. achieved by numerous weak interactions between amino acid side chains

Question 21

quaternary structure

Answer 21

some functional proteins composed of more than one polypeptide (association through non-covalent interactions)

Question 22

a-helix (2)

Answer 22

1. tightly coiled, rodlike structure
2. R groups projecting out from axis of helix

Question 23

B-sheet (3)

Answer 23

1. formed by adjacent B-strands which have fully extended polypeptide (linked by H-bonds)
2. strands may be parallel, antiparallel or mixed
3. may be flat or twisted conformation

Question 24

disulfide bonds

Answer 24

oxidation reaction can generate a cystine unite with a disulfide bond (comes from thiol SH)

Question 25

globular protein domains

Answer 25

distinct 3D structural motifs

Question 26

what is a domain

Answer 26

part of polypeptide chain that is independently stable or could undergo movement as single entity

Question 27

example of a globular protein domain

Answer 27

kinase domain

Question 28

how is modular construction of proteins possible?

Answer 28

through different domain combinations

Question 29

what % of eukaryotic proteins have multiple structural domains

Answer 29

75%

Question 30

how many domains do small proteins usually have

Answer 30

1

Question 31

what are the 2 types of protein? (2)

Answer 31

1. fibrous 2. globular

Question 32

what are the 2 solubilities of proteins? (2)

Answer 32

1. water soluble 2. lipid soluble

Question 33

what is the role of fibrous proteins in nature?

Answer 33

structural

Question 34

superfamily of structural (fibrous) proteins

Answer 34

coiled-coil proteins

Question 35

give an example of a coiled-coil protein

Answer 35

a-keratin

Question 36

properties of coiled-coil proteins and why (2)

Answer 36

1. strong/flexible 2. because of intertwining design

Question 37

structure of fibrous proteins (2)

Answer 37

1. two right-handed a-helices intertwining to form left-handed super helix 2. further coiling into protofilaments and fibrils makes hair shaft

Question 38

how is the structure of fibrous proteins stabilised?

Answer 38

ionic and van der waals interactions

Question 39

globular protein structure

Answer 39

complicated and very compact 3D structure

Question 40

what do the interior/exterior of globular proteins consist of? (2)

Answer 40

1. interior - mainly hydrophobic amino acids (little/no space) 2. exterior - charged/polar amino acids

Question 41

how does hydrophobic amino acid distribution differ between fibrous/globular proteins? (2)

Answer 41

1. fibrous - hydrophobic amino acids on outside of protein 2. globular - hydrophobic amino acids inside protein

Question 42

what is the role of membrane proteins?

Answer 42

interact with lipid bilayer, have specific sequences and structures

Question 43

what type of protein are membrane proteins?

Answer 43

usually 'inside out' globular proteins (hydrophobic amino acids facing aqueous solution)

Question 44

what proteins are targeted by majority of drugs?

Answer 44

membrane proteins - particularly receptors and enzymes, but also membrane transport proteins

Question 45

GPCRs

Answer 45

G-protein-coupled receptors

Question 46

structure of GBCRs

Answer 46

seven transmembrane a-helical domains, form huge protein family

Question 47

examples of crucial protein-protein interactions (3)

Answer 47

1. antibody-antigen recognition 2. signals binding to receptors 3. enzyme/substrate reactions

Question 48

molecule (typically small) that binds to protein

Answer 48

ligand

Question 49

how does ligand bind to protein (2)

Answer 49

1. same non-covalent interactions that dictate protein structure 2. induced fit model

Question 50

enzyme role

Answer 50

catalyse making/breakdown of covalent bonds (facilitates formation of transition state)

Question 51

2 fates of misfolded proteins (2)

Answer 51

1. degraded by cellular quality control machinery 2. form aggregates

Question 52

what are various neurodegenerative diseases associated with?

Answer 52

accumulation of tau and a-Syn aggregates (taupathies and synucleinopathies)

Question 53

what could be responsible for different neurodegenerative diseases?

Answer 53

aggregates adopting different structures