Structure of Proteins 1

Question 1

what do proteins do? (5)

Answer 1

provide structure, transport molecules, defence, biological catalysts, regulation of genes

Question 2

what is the most abundant protein in mammals and what percentage of the total protein is it?

Answer 2

collagen fibres - 25-35%

Question 3

collagen fibres is…

Answer 3

the main component of connective tissue

Question 4

where is collagen found? (4)

Answer 4

skin, tendon, organs, bone

Question 5

what are erythrocytes?

Answer 5

red blood cells

Question 6

what does haemoglobin do?

Answer 6

selective delivery of O2 to metabolic tissues

Question 7

how many protein subunits per molecule is there in haemoglobin?

Answer 7

4

Question 8

give an example of a prosthetic group…

Answer 8

haem

Question 9

what is low-density lipoprotein composed of?

Answer 9

a monolayer phospholipid shell and a single molecule of apolipoprotein B

Question 10

what is low-density lipoprotein used for?

Answer 10

transportation of cholesterol between cells via the circulatory system

Question 11

what is the uptake of LDL particles mediated by?

Answer 11

the LDL receptor that binds LDL and facilitates internalisation (their uptake into cells)

Question 12

what do patients with familial hypercholesterolemia have a mutation in?

Answer 12

the LDL receptor gene

Question 13

what is atherosclerosis?

Answer 13

disease of which the arteries have fatty material on their inner walls

Question 14

what can atherosclerosis lead to? (3)

Answer 14

restricted blood flow, hypertension, blockages

Question 15

antibody structure…

Answer 15

two identical light chains covalently linked to two identical heavy chains by disulphide bonds

Question 16

where is the antigen recognition site?

Answer 16

on the tips between the heavy and light chains

Question 17

what does the antigen recognition site do?

Answer 17

highly specific and tightly binds the complementary antigen allowing recognition of foreign proteins by the immune system

Question 18

what does lysozyme do?

Answer 18

catalyses the cutting of polysaccharide chains

Question 19

how does lysozyme work?

Answer 19

it binds to the polysaccharide chain, catalyses the cleavage of a specific covalent bond and releases the cleaved product

Question 20

what does the Lac repressor do?

Answer 20

controls production (expression) of proteins metabolising lactose in bacteria

Question 21

how does the Lac repressor work?

Answer 21

the repressor binds to DNA and prevents expression of the gene in the absence of lactose

Question 22

what does binding depend on?

Answer 22

conformation

Question 23

what makes an amino acid hydrophilic?

Answer 23

if it is polar

Question 24

what makes an amino acid hydrophobic?

Answer 24

if it is non-polar - usually contains hydrocarbon or aromatic R groups

Question 25

cysteine can form...

Answer 25

disulphide bonds with other cysteine residues

Question 26

glycine is...

Answer 26

the smallest amino acid residue and can fit in tight spaces

Question 27

the side chain of proline...

Answer 27

bends around to form a covalent bond with the nitrogen atom of the amino group which creates a kink in the protein chain

Question 28

what does an acid do?

Answer 28

release a hydrogen ion

Question 29

what does a base do?

Answer 29

readily combines with a hydrogen ion

Question 30

what is the equilibrium constant?

Answer 30

Ka = [H+][A-] / [HA] (products/reactants)

Question 31

the pH can be calculated using the Henderson Hasselbach equation...

Answer 31

pH = pKa + log([A-]/[HA])

Question 32

the overall charge of an amino acid and therefore protein varies with...

Answer 32

pH

Question 33

pKa is...

Answer 33

the pH at which dissociation is 50% complete

Question 34

give an example of receptor mediated endocytosis...

Answer 34

uptake of low-density lipoprotein

Question 35

what does a reduction in the pH in the endosome cause (LDL) ?

Answer 35

a change in conformation of the LDL-receptor due to the presence of histidine residues within the protein

Question 36

what does the change in conformation of the LDL-receptor mean in receptor mediated endocytosis?

Answer 36

LDL can no longer bind and is released to the lysosome

Question 37

(receptor mediated endocytosis) patients with familial hypercholesterolemia frequently have mutations in the...

Answer 37

histidine residues of the LDL-receptor

Question 38

how do the side chains of a polypeptide arrange themselves?

Answer 38

usually the hydrophobic side chains are on one side and hydrophilic on the other and they usually alternate as the side chains can be bulky

Question 39

how is a peptide bond formed?

Answer 39

a covalent bond is formed when the carbon from the carboxylate group shares electrons with the nitrogen atom from the amino group of a second amino acid

Question 40

what is lost during the formation of a peptide bond?

Answer 40

water

Question 41

what does the peptide bond not permit?

Answer 41

rotation

Question 42

where are the only places a peptide bond can rotate?

Answer 42

on the alpha carbon

Question 43

where are bulky side group positioned and what does this limit?

Answer 43

on either side of the back bone limiting the conformations possible for a polypeptide

Question 44

what is secondary structure?

Answer 44

the initial folding pattern (periodic repeats) of the linear polypeptide

Question 45

what are the 3 main types of secondary structure?

Answer 45

alpha helix, beta sheets and bends/loops

Question 46

what bonds stabilise secondary structures?

Answer 46

hydrogen

Question 47

what is an alpha helix?

Answer 47

right handed with each turn having 3.6 amino acid residues stabilised by H bonds between the amino and carboxyl groups of every 4th amino acid

Question 48

what are beta sheets?

Answer 48

extended stretches of 5 or more amino acids organised next to each other to make beta sheets

Question 49

what is a parallel beta sheet?

Answer 49

when adjacent strands are oriented in the same direction (N-end to C-end)

Question 50

what is an anti-parallel beta sheet?

Answer 50

when adjacent strands run opposite to each other

Question 51

what is a bend/loop?

Answer 51

polypeptides can fold themselves into bends or loops with usually 4 amino acids being required to form the turn

Question 52

what residues are usually found in bends/loops?

Answer 52

proline