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BIOC 192 > lectures 1-6 > Flashcards

lectures 1-6 Flashcards

1
Q

what are the methods of protein research

A

Protein crystallography, Cryo-electron microscopy, NMR spectroscopy

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2
Q

whats the weird amino acid that can fit into two categories

A

cystine

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3
Q

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

A

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

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4
Q

what are the amino acid groups based off of

A

their charge state in an environment PH of 7

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5
Q

how do we name the amino acid residue mutations

A

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

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6
Q

define PKa

A

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

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7
Q

define PI, isoelectric point

A

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

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8
Q

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

A

amino acid residues or residues

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9
Q

whats a post-translational modification

A

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

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10
Q

how are PTMs added

A

Added via covalent attachment (usually enzyme-mediated)

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11
Q

what do PTMs do

A

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

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12
Q

what type of reaction is the formation of a peptide bond

A

a dehydration or condensation

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13
Q

what does it mean to be a globular protein?

A

a protein which is roughly circular in shape

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14
Q

define secondary structure

A

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

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15
Q

whats the phi bond?

A

the bond between the alpha C and the N

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16
Q

whats the psi bond

A

the bond between the alpha C and the carbonyl carbon

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17
Q

what values can the phi and psi bonds take on

A

anywhere from 0 to +-180 degrees

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18
Q

whats the omega bond and what values can it take on

A

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

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19
Q

can phi and psi be any value at any point?

A

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

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20
Q

over phi and psi rotation can lead to what

A

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

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21
Q

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

A

most are trans at 180 degree rotation

22
Q

what the value of rotation for cis peptide bonds

A

0 degrees

23
Q

beta strand vs beta sheet

A

a beta sheet is a collection of beta strands

24
Q

what are alpha helices stabilised by and where are they

A

stabilised between H bonds at N and N+4

25
Q

what are the key features of the alpha helix

A

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

26
Q

key features of the beta sheet

A

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,

27
Q

in alpha helix each amino acid is separated by how much

A

100 degrees turn

28
Q

describe antiparallel beta sheets

A

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

29
Q

describe parallel beta sheets

A

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

30
Q

key features of turns

A

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

31
Q

why is glycine good for turns

A

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

32
Q

why is proline good for turns

A

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

33
Q

what is super secondary structure?

A

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

34
Q

what is a domain

A

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

35
Q

what makes up domains

A

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

36
Q

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

A

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

37
Q

combinations of what can be used to make different functioning proteins

A

combinations of different domains

38
Q

what drives protein folding

A

the sequence of amino acids more specifically the hydrophobic amino acids

39
Q

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

A

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

40
Q

whats the likely sequence of events for protein folding

A

(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

41
Q

whats the most important contributor to protein stability

A

The hydrophobic core

42
Q

what are some common super secondary structures

A

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

43
Q

what collectively makes strong contribution to the conformational stability of protein

A

non covalent interactions

44
Q

what are the non-covalent interactions in proteins

A

metal ion coordination, hydrophobic interactions, electrostatic attraction,

45
Q

what covalent bond can proteins do

A

disulphite bridges

46
Q

whats an aggregate

A

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

47
Q

what are chaperones

A

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

48
Q

what are the 3 folding methods of proteins

A

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

49
Q

different between chaperone and chaperonin

A

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

50
Q

what are prions

A

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

51
Q

examples of prion related disease

A

mad cow disease, alzheimers

BIOC 192 (15 decks)

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