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BIOC192 > Proteins > Flashcards

Proteins Flashcards

1
Q

T or F: Proteins are branching (non-linear)

A

False: proteins are non-branching polymers (linear chain)

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2
Q

What does the aa sequence determine?

A

structure and .: function

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3
Q

What do proteins begin and end with?

A

Start with amino group, carboxylate group at the end

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4
Q

Name 3 ways of depicting chemical structure in proteins

A
  • skeletal
  • ball and stick
  • space filling
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5
Q

What example protein is involved in cell signalling?

A

Insulin

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6
Q

What example proteins are involved in digestion? (2)

A

trypsin, amylase

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7
Q

What does HIV protease do?

A
  • Breaks down proteins, effective in building up HIV virus
  • HIV treated with protease inhibitor, blocks active site
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8
Q

What does insulin do (in terms of cell signalling)?

A

Binds to insulin receptors and signals cells to take up glucose

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9
Q

What does trypsin do?

A

Breaks down protein (protease) during digestion (in pancreas)

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10
Q

What does amylase do? Where is it found?

A
  • Breaks down starch into sugars
    • In saliva and pancreatic juices
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11
Q

What example proteins are involved in metabolism? (2)

A

Alcohol dehydrogenase
Hexokinase

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12
Q

What does Alcohol dehydrogenase do?

A

Helps metabolise ethanol (the alcohol you drink)

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13
Q

What is the role of a kinase?

A

adds phosphate

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14
Q

What example protein is involved in O2 transport?

A

hemoglobin

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15
Q

What example protein is involved in immune protection?

A

antibody

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16
Q

How does the SARS-CoV2 spike protein interact with our cells?

A

Binds to ACE2, unfolds a little and binds leaflet that sticks out

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17
Q

How can we block the interaction between the SARS-CoV2 spike protein and our cell? (2)

A

Need something that blocks interaction between leaflet and ACE2, or an antibody that inhibits the interaction

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18
Q

Which chiral form is generally chosen for by nature?

A

L form

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19
Q

What does the 2nd letter in a 3 digit mutation code (L#L) represent?

A

the new/mutated residue

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20
Q

Where are non-polar sidechains found within a folded protein? Why?

A

Proteins have to be soluble, so hydrophobic side chains tend to be buried within the protein

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21
Q

Which 2 aa are the odd ones out?

A

Glycine (G) and Proline (P)

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22
Q

Why is glycine special?

A
  • R group is another H so not chiral
    • No bulky R group, very flexible, used where a large side chain cannot be accommodated
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23
Q

Why is proline special?

A
  • Technically an iminoacid
    • Because side chain bonded back around to imine group = very stiff/rigid
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24
Q

Negatively charged (acidic) aa have what chemical feature?

A

2nd carboxylate group on side chain

25
Q

How are negatively charged (acidic) aa found in solution?

A

as conj base

26
Q

Positively charged (basic) aa tend to have what chemical feature?

A

Additional -NH2 group(s)

27
Q

What is Phosphorylation? What is its biological function?

A

Phosphorylation: adding a phosphate group
· Used to control enzyme activity
· A chemical on/off switch

28
Q

What is Hydroxylation? What is its biological function? What aa involved?

A

Hydroxylation: adding a hydroxyl group
· Needed to prevent connective tissue diseases, scurvy
· Often proline and lysine involved

29
Q

What is Carboxylation? What is its biological function? What aa involved?

A

Carboxylation: adding a carboxyl group
· Needed for blood clotting
· Often glutamate involved

30
Q

What is Glycosylation? What is its biological function? What aa involved?

A

Glycosylation: attaching elements of sugar molecule
· Asparagine, threonine often
· Glycosylated hemoglobin can be used to diagnose diabetes

31
Q

How much double bond character does the peptide bond have? What property of a peptide bond does this lead to?

A

40% -> planar

32
Q

What are the 3 characteristics of a peptide bond?

A
  1. PLANAR
  2. predominantly TRANS
  3. permanent DIPOLE
33
Q

Why are aa in a protein referred to as residues?

A

b/c not complete/independent (don’t have the water part)

34
Q

What makes up super secondary structure?

A

Elements of secondary structure (helices and strands) connected by turns or regions of less order structure called loops or coils

35
Q

What are 4 common motifs of super secondary structure?

A
  • helix-turn-helix
  • B hairpin
  • Greek key
  • strand -helix-strand
36
Q

What super 2ndary theme is found in Ca binding proteins? Where is the Ca atom held?

A

helix-turn-helix: EF hand arrangement where Ca atom held in turn, coordinated by C=O oxygens

37
Q

Is the b hairpin parallel or anti-parallel?

A

anti-parallel (One strand up, one strand down)

38
Q

how is a b-hairpin stabilised?

A

by H bonding across the strand

39
Q

What is the greek key made up of?

A

4 antiparallel beta strands

40
Q

In the strand, helix, strand, are the beta sheets parallel or antiparallel?

A

parallel, because of intervening helix

41
Q

What is a protein domain?

A
  • combination of super secondary elements
  • independently folded regions which possess a specific function within the protein
  • typically has a hydroPHOBIC core with hydroPHILIC parts on the surface near solvent.
42
Q

Why do protein domains typically have a hydrophobic core?

A

for stability

43
Q

T or F, small proteins contain as many protein domains as larger ones?

A

F - smaller proteins (<250bp) usually have 1 domain, larger proteins have multiple

44
Q

What are the 3 families of proteins?

A

a domain family
a/B domain family
antiparallel B family

45
Q

describe features of the alpha domain family

A
  • mostly helical
  • side chains of helices packed closely together
  • hydrophobic core
46
Q

describe the arrangement of helices in a 4 helix bindle

A

Cylinders have 20* tilt relative to binding protein so side chains pack better

47
Q

the 3º structure of the globin fold fits within which family

A

alpha domain family

48
Q

in the globin fold, packing occurs between non-adjacent helices. What does this mean?

A
  • helices are not in order of when the chain comes out of the ribosome
  • brings together elements widely separated in sequence
49
Q

a/B family proteins are made up of…

A

a mix of a and B structures

50
Q

antiparallel family proteins are made up of…

A

antiparallel b strands (no intervening helices)

51
Q

What amino acids create protein turns?

A

proline and glycine

52
Q

Describe the method of the Anfinsen Experiment.

A
  • urea and alcohol used to open chain (break non covalent bonds)
  • reacted -> didn’t react
  • urea and alcohol removed, air oxidised
  • protein refold and is functiona;
53
Q

What does the Anfinsen Experiment show?

A

the instructions for protein folding is contained in the sequence

54
Q

Outline the sequence of events for protein folding

A
  1. short 2º segments form
  2. subdomains form
  3. subdomains come together to make a partly folded domain - this is flexible and can be rearranged to minimize energy and maximize stability
  4. final domain emerges
55
Q

What gives stability to a protein?

A

Non-covalent interactions, particularly the hydrophobic core

56
Q

name and describe the 3 types of protein folding in regard to chaperones

A
  1. chaperone independent
  2. chaperone dependent - peptide has bits that tend to bond, chaperones keep this from happening
  3. chaperonin-dependent - need lots of help so go into special chamber with lid, needs ATP
57
Q

What are prion diseases caused by?

A

PrP - a protein that changes shape (misfolded) then forms aggregates which cause brain damage

a -> B transformation

58
Q

What are 3 examples of prion diseases?

A

Bovine spongiform encephalopathy (BSE)
Creutzfeldt-Jacob Disease (CJD)
Kuru

BIOC192 (11 decks)

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