lectures 1-6

Question 1

what are the methods of protein research

Answer 1

Protein crystallography, Cryo-electron microscopy, NMR spectroscopy

Question 2

whats the weird amino acid that can fit into two categories

Answer 2

cystine

Question 3

how do we determine the amino acid grouping from the amino acid

Answer 3

non polar has only hydrocarbons at their end of their sidechains or rings
polar uncharged: have an OH NH2 or O at end of the R side chain.
polar charged: tell by charge

Question 4

what are the amino acid groups based off of

Answer 4

their charge state in an environment PH of 7

Question 5

how do we name the amino acid residue mutations

Answer 5

First letter – original or native amino acid
- Number – location of mutation in the protein
- Second letter – new or mutated residue
for example E6V

Question 6

define PKa

Answer 6

pKa value for an ionisable group on an amino
acid or protein is the pH at which the group is 50% ionised

Question 7

define PI, isoelectric point

Answer 7

The pI, or isoelectric point is the pH at which the
net charge on an amino acid (or protein) is zero

Question 8

what do we call amino acids once they are in a polpeptide

Answer 8

amino acid residues or residues

Question 9

whats a post-translational modification

Answer 9

A chemical group can added to an amino acid residue after translation has occurred → PTM!

Question 10

how are PTMs added

Answer 10

Added via covalent attachment (usually enzyme-mediated)

Question 11

what do PTMs do

Answer 11

Modify the protein is a way that switches it on or off, directs cellular
location, targets for degradation etc

Question 12

what type of reaction is the formation of a peptide bond

Answer 12

a dehydration or condensation

Question 13

what does it mean to be a globular protein?

Answer 13

a protein which is roughly circular in shape

Question 14

define secondary structure

Answer 14

The three-dimensional arrangement of a protein chain over a short stretch of adjacent amino acid residues. Includes -helices and -sheets

Question 15

whats the phi bond?

Answer 15

the bond between the alpha C and the N

Question 16

whats the psi bond

Answer 16

the bond between the alpha C and the carbonyl carbon

Question 17

what values can the phi and psi bonds take on

Answer 17

anywhere from 0 to +-180 degrees

Question 18

whats the omega bond and what values can it take on

Answer 18

the peptide bond is the omega bond, it is either 0 or 180 degrees

Question 19

can phi and psi be any value at any point?

Answer 19

no they cannot, they have limited accessible values due to steric hindrance

Question 20

over phi and psi rotation can lead to what

Answer 20

over phi can lead to O-O collisions
over Psi can lead to NH-NH

Question 21

whats peptide bonds are what and whats the bond angle for this

Answer 21

most are trans at 180 degree rotation

Question 22

what the value of rotation for cis peptide bonds

Answer 22

0 degrees

Question 23

beta strand vs beta sheet

Answer 23

a beta sheet is a collection of beta strands

Question 24

what are alpha helices stabilised by and where are they

Answer 24

stabilised between H bonds at N and N+4

Question 25

what are the key features of the alpha helix

Answer 25

3.6 residues, right handed turn, side chains point out from the centre, don't have glycine and proline in them as they interupt the helix, altnerates between polar and non polar side chains

Question 26

key features of the beta sheet

Answer 26

2-10 strands per sheet, stabilised between hydrogen bonds, each strand approximately 6-15 residues long, the side chains alternate between point up and pointing down,

Question 27

in alpha helix each amino acid is separated by how much

Answer 27

100 degrees turn

Question 28

describe antiparallel beta sheets

Answer 28

Strands run in the opposite direction. Hydrogen bonding pattern is optimal. usually a turn between each strand

Question 29

describe parallel beta sheets

Answer 29

Strands run in the same direction, less optimal H bonds, usually an alpha helix between each stand, or a loop/coil

Question 30

key features of turns

Answer 30

involve 3-4 residues, lots of glycine and proline, type 1 and type 2 very common

Question 31

why is glycine good for turns

Answer 31

Small side chains make glycine very flexible. It has a lot of conformational freedom.

Question 32

why is proline good for turns

Answer 32

Proline is too rigid for helices but has a built-in turn because of the bonding between the R-group and the amino group.

Question 33

what is super secondary structure?

Answer 33

helices and beta strands connected by loops or turns to make local regions of secondary structures

Question 34

what is a domain

Answer 34

independently folded regions that often possess a specific function within the protein.

Question 35

what makes up domains

Answer 35

super secondary structures combine to form domains and the domain has a hydrophobic core normally.

Question 36

proteins can be grouped into families based on what? examples please

Answer 36

s based on tertiary structure – three examples… alpha domain family alpha/beta family antiparallel beta family

Question 37

combinations of what can be used to make different functioning proteins

Answer 37

combinations of different domains

Question 38

what drives protein folding

Answer 38

the sequence of amino acids more specifically the hydrophobic amino acids

Question 39

who was the guy who solved protein folding and what was his test

Answer 39

The Anfinsen Experiment. he took a protein and denatured it with urea and mercaptoethanol. he then removed these things and then the protein folded back to exactly how it was before. showing that the information to fold is in the amino acid sequence it self

Question 40

whats the likely sequence of events for protein folding

Answer 40

(i) Formation of short secondary structure segments (ii) Subdomains form (iii) Subdomains come together to form a partly folded domain; a “molten globule” that can rearrange, (tertiary structure still partly disordered) (iv) Final domain structure emerges, small conformational adjustments to give final compact native structure

Question 41

whats the most important contributor to protein stability

Answer 41

The hydrophobic core

Question 42

what are some common super secondary structures

Answer 42

beta hairpin, greek key, helix-turn-helix, EF hand proteins

Question 43

what collectively makes strong contribution to the conformational stability of protein

Answer 43

non covalent interactions

Question 44

what are the non-covalent interactions in proteins

Answer 44

metal ion coordination, hydrophobic interactions, electrostatic attraction,

Question 45

what covalent bond can proteins do

Answer 45

disulphite bridges

Question 46

whats an aggregate

Answer 46

when proteins fold improperly and the hydrophobic regions bind to hydrophobic regions of another protein to form a mishapen protein aggregate

Question 47

what are chaperones

Answer 47

Sometimes the protein may not fold itself completely correctly. Chaperones can be used. these are proteins which help the protein to fold correctly and not form aggregates

Question 48

what are the 3 folding methods of proteins

Answer 48

Chaperone-independent b) Chaperone-dependent e.g., Hsp70 c) Chaperonin-dependent e.g., GroEL-GroES

Question 49

different between chaperone and chaperonin

Answer 49

chaperonins which are like a bin, they insert the protein making a favourable environment for folding on the interior of the chaperonin. chaperones fold the protein sequence whilst still in solution

Question 50

what are prions

Answer 50

prion is a misfolded protein that can transmit its misfoldedness to normal variants of the same protein and trigger cellular death. these prions form aggregates with other proteins, inducing them to become prions

Question 51

examples of prion related disease

Answer 51

mad cow disease, alzheimers