new protein structure -LEARN

Question 1

GLYCINE

Answer 1

R group= H -adds flexibility to protein chain since other side chains are too bulky -alpha carbon shows no chirality

Question 2

ALANINE

Answer 2

R group-CH3 -biosynthesis -non-polar

Question 3

PROLINE

Answer 3

side chain bonds to the amine (CH2CH2CH2) group –> imposes tight restraints on the conformation of a protein -both CIS and TRANS bonds -found in rigid proteins e.g. collagen

Question 4

HISTIDINE

Answer 4

-only aa with a pKa of a side chain of near neutral pH -found in AS -side chain can alter its charge at physiological pH -chaegre modulated by other amino acids surrounding it

Question 5

CYSTEINE

Answer 5

R group -SH (free thiol group) -can form disulphide bridges -only covalent bond found to hold protein in tis correct for -side chain has pKa of 8.4 -found in AS

Question 6

hierarchy of protein structure

Answer 6

primary- amino acid sequence secondary: beta and alpha and turn and loops tertiary- overall fold of protein quaternary: when several proteins fold together

Question 7

peptide bond

Answer 7

partial double bond character

Question 8

length of peptide bond

Answer 8

1.32A

Question 9

Phi

Answer 9

angle of rotation about the bond between the nitrogen and carbon

Question 10

Psi

Answer 10

angle of rotation about the bond between alpha carbon and carbonyl carbon

Question 11

both Phi and Psi determine

Answer 11

the path of the polypeptide chain

Question 12

why are many combinations of Phi and Psi

Answer 12

STERIC collisions between atoms

Question 13

allowed values of Phi and Psi can be visualised on a

Answer 13

Ramachandron Plot

Question 14

Phi and Psi restrict

Answer 14

angles therefore limit the number of structures available to the unfolded form

Question 15

secondary structures

Answer 15

alpha helix beta sheet turns and loops

Question 16

who discovered Alpha helices and Beta sheets and when

Answer 16

Linus Paul and Robert Corey 1951

Question 17

why do alpha helices arise

Answer 17

due to H bonding capacity of NH backbone and CO groups

Question 18

properties of alpha helices

Answer 18

right handed, 3.6 residues

Question 19

R groups of alpha helices always point

Answer 19

outwards

Question 20

how hydrogen bonds form in aloha helices

Answer 20

the Co group of residue n forms a hydrogen bond with the NH group of residue n+4

Question 21

helical wheel

Answer 21

amino acid residues facing outwards are ion contact with water- hydrophilic -those inside are hydrophobic

Question 22

alpha helical content can range from

Answer 22

0-100%

Question 23

ferritin

Answer 23

75% of residues are in alpha helices

Question 24

25% of all soluble proteins are composed of

Answer 24

alpha helices connected by loops and turns

Question 25

Beta sheet found by

Answer 25

linus Pauling and Robert Corey in 1951

Question 26

Beta sheets are mad cup of

Answer 26

at least two polypeptide chains (typically 4/5, but can be up to 10)

Question 27

Beta sheets are

Answer 27

parallel or antiparallel

Question 28

parallel

Answer 28

.

Question 29

antiparallel

Answer 29

.

Question 30

Bonding in Beta sheets

Answer 30

H bonding b/w c=o of one chain to N-H of another chain

Question 31

in globule proteins beta sheets are ... residues long

Answer 31

15 residues long

Question 32

beta proteins can be

Answer 32

purely parallel, purely antiparallel or mixed

Question 33

reverse turn also known as

Answer 33

hairpin turn

Question 34

what do reverse turns do

Answer 34

interaction stabilised abrupt changes in direction of the poly-peptide chain

Question 35

loops don't have

Answer 35

a regular structure like alpha and beta

Question 36

loops are

Answer 36

right and well defined

Question 37

loops lie

Answer 37

on the surface of proteins and interact with other proteins or olecules

Question 38

loops are present in

Answer 38

antibodies

Question 39

super secondary structure

Answer 39

elements of secondary structure link together into combination that are very common

Question 40

what to super secondary structures form

Answer 40

mini-domains -formed early in the process of making the whole protein structure

Question 41

tertiary

Answer 41

overall fold of the protein

Question 42

tertiary structures are any

Answer 42

combination of alpha-helices, B-sheets or loops

Question 43

myoglobin

Answer 43

all alpha helix protein -binds heme, a prostethic group -

Question 44

how much of myoglobin is alpha helices

Answer 44

70% folded into 8 alpha helices, the rest are turns and loops

Question 45

Dimensions of myoglobin

Answer 45

45 x 35 x 25 a

Question 46

first protein sturcutr to be determined

Answer 46

myoglobin by watson and Kindred in 1950

Question 47

myoglobin is made up of

Answer 47

1 polypeptide chain and 153 amino acids

Question 48

all B sheet protein

Answer 48

concavalin A

Question 49

concavalin a

Answer 49

all beta sheet -14 beta strands

Question 50

concavalin a is a

Answer 50

lectin (carbohydrate binding protein)

Question 51

most proteins have a mixture of

Answer 51

alpha and beta

Question 52

B barrel

Answer 52

alpha on outside -beta on inside

Question 53

Domains

Answer 53

section which can fold independently -each protein has at least on domain but can be more than 10

Question 54

quaternary structure

Answer 54

many proteins form in a group of 2 or more protein chains

Question 55

homomultimers

Answer 55

same protein, 2 or more copies

Question 56

heteromultimers

Answer 56

several diff proteins come together to make a mature protein

Question 57

haemoglobin is made up of

Answer 57

2 alpha subunits 2 beta subunits and 4 heme groups

Question 58

fibrous proteins are either

Answer 58

alpha or B

Question 59

examples of alpha helix fibrous protein

Answer 59

hair

Question 60

examples of B sheet protein

Answer 60

insect silk

Question 61

hair

Answer 61

2 helices -non-polar -cys residues cross link adjacent chains (broken and reformed when you have permanent wave)

Question 62

B-silk

Answer 62

made up of repeating hexapeptide -antiparallel B sheets -Gly extents from one surface and Ala from the other

Question 63

collagen

Answer 63

-200A lon and 15 A wide -fibrous component of skin, bone, tendon, cartilage and teeth -has a hydroxyl group in place of H atom -2 helices and 1000 residues long -no H bonding -eveyr 3rd residue is glycine -made up of three helix (wound around each other) -polypropine helix

Question 64

in collagen H group is replaced by

Answer 64

OH group

Question 65

residues in collagen

Answer 65

1000 residues long and every 3rd residue is glycine