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BIOSCI 107 > L14 - Protein Structure & Function > Flashcards

L14 - Protein Structure & Function Flashcards

1
Q

Cells and protein

A

Cells jam packed with all kinds of protein (and other things)
- human cell ~1-3 billion

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2
Q

Protein function

A 
Drive (almost) everything in the cell
- DNA replication
- Cell division
- Synthesis of the cell membrane
- Metabolism
- Transport of molecules
- Generating energy
- Structure
And much more…
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3
Q

Roles of proteins

A
  • digestive enzyme/catalytic
  • transport
  • structural
  • hormone signalling
  • immunological
  • contractile
  • storage
  • toxins: used by pathogens
  • regulatory: physiological processes
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4
Q

Peptides

A

Short (approx. < 50 aa) polypeptides

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5
Q

___peptide

A

Very short peptides

- dipeptide, tripeptide, tetrapeptide

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6
Q

Residue

A

Individual amino acid

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7
Q

Protein composition

A

A polypeptide: chain of amino acids linked by peptide bonds

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8
Q

Amino acid forms

A
  • unionised form
  • ionised form (protonated to NH3+ and deprotonated to COO-): more prevalent as present at physiological/normal pH (~7.4)
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9
Q

Glycine

A

Simplest amino acid

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10
Q

Proline

A

Commonly seen at sharp turns of protein structure

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11
Q

Amino acids with S

A

Cysteine and methionine

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12
Q

Peptide (amide) bond formation

A

Condensation/dehydration synthesis reaction (release of H2O)

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13
Q

Peptide bond rotation

A
  • rotation at single bonds between alpha carbon and its neighbouring atoms
  • no rotation at peptide bonds due to resonance (O-C N-H of bonds are essentially co-planar)
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14
Q

Peptide bond configuration

A
  • typically in trans orientation with alternating side chains
  • very rarely in cis as less stable due to steric repulsion of side chains
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15
Q

Protein structure

A
  • complex structure to facilitate varied functions as shape critical to its function
  • shape driven by chemical properties and sequences of amino acids in protein
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16
Q

Enzymes

A
  • Long ridged interconnecting structural proteins
  • Active site
  • Binding causes conformational change
  • provide function or strengthen interaction
  • lock & key vs induce fit
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17
Q

Primary structure

A
  • unique sequence of amino acids of protein
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18
Q

Primary structure driven by

A

DNA sequence of gene coding protein

= structure can be deduced from known DNA sequence

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19
Q

Secondary structure

A

Localised folding of polypeptide

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20
Q

Secondary structure driven by

A

Hydrogen bonding interactions within polypeptide backbone

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21
Q

Alpha helices

A
  • right handed helix
  • normally each turn is 3.6aa with pitch of 5.4 (0.54nm)
  • H-bond between N-H and C=O 3 or 4 residues earlier
  • tightly packed; almost no free space within
  • side chains protrude out from helix
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22
Q

Amino acids in alpha helix

A

Ethiosine, alanine, leucine, glutamine, lysine

NOT proline, glycine

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23
Q

Beta pleated sheets

A

H-bond between N-H on one strand and C=O on another strand

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24
Q

Type of beta pleated sheet structures

A

Parallel, anti parallel

- alternating R groups

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25
Q

Amino acids in beta pleated sheets

A
  • large aromatic residues: tryrosine, phenylalanine, tryptophan
  • beta-branche amino acids: threonine, valine, isoleucine
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26
Q

Secondary structure prediction

A

Different amino acids have propensity to favour structures

= can fairly accurately predict regions from sequence

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27
Q

Tertiary structure

A

3D shape of protein

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28
Q

Tertiary structure driven by

A

Chemistry of side chains and interactions between them

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29
Q

Tertiary noncovalent interactions

A
  • ionic bonds
  • hydrophobic interactions
  • hydrophilic interactions
  • dipole-dipole interactions
  • Van der Waals forces
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30
Q

Tertiary covalent bonds

A

Disulphide bond

  • formed by cystines
  • thiol oxidised, H removed, covalent linkage formed between two sulphur atoms
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31
Q

Tertiary interaction strengths

A

Disulphide > ionic > hydrogen > Van der Waals

32
Q

Cofactors

A

Aka prosthetic groups

  • Within protein and coordinated in some proteins (particularly enzymes) using R groups
  • may be essential for structure and/or function of protein
  • metal ions (Mg, Mn, Zn, Fe, Ca), organic molecules (heme), or vitamins
33
Q

Quarternary structure

A

Multiple polypeptide chains - multiple folded protein subunits
- may be dynamic: come together to perform function then separate when not needed or to release something

34
Q

Quarternary structure driven by

A

Ionic interactions, H-bonding, hydrophobic interactions (Disulphide possible but uncommon)

35
Q

Quarternary structure types

A
  • homooligomer: 2 of the same subunits

- heterooligomer: 2 different subunits

36
Q

Types of proteins

A

Globular, fibrous, membrane

37
Q

Globular solubility

A

Typically soluble in water

38
Q

Globular function

A

Functional; metabolic functions (enzyme, transport, immune)

39
Q

Globular structure

A
  • spherical/globular in shape

- irregular sequence and secondary structure

40
Q

Globular repetition

A

Not many repeating elements (structure, sequence within primary or secondary sequence)

41
Q

Globular and quarternary structures

A

Moderate to none

42
Q

Globular stability

A

Lower stability

43
Q

Globular example

A

Enzymes, hemoglobin, antibodies

44
Q

Fibrous solubility

A

Typically insoluble in water

45
Q

Fibrous function

A

Structural

46
Q

Fibrous repetition

A

Often repetitive primary and secondary structure (repeated alpha helices)

47
Q

Fibrous and quarternary structures

A

High level

48
Q

Fibrous stability

A

Highly stable (to heat, pH etc.)

49
Q

Fibrous examples

A

Keratin, actin, collagen, silk, cytoskeleton proteins

50
Q

Membrane location

A

Transverse through lipid bilayer

51
Q

Membrane function

A

Transport, receptors, signalling, adhesion

52
Q

Membrane structure by region

A
  • transmembrane region: single alpha helix or alpha helical bundle
  • mitochondria and gram negative bacterial: beta barrel transmembrane proteins
53
Q

Beta barrel

A

Lots of beta sheets that stack around to form barrel (like sheet of paper)

54
Q

Membrane polarity

A
  • high degree of non-polar (hydrophobic) amino acids where side chains face out towards membrane
  • polar (hydrophilic) side chains face inwards except at top or bottom where no farting membrane and towards soluble environment
55
Q

Resolution

A

Distance corresponding to smallest observable feature

- closer than this = one combine blob not two separate objects

56
Q

ABBE’s diffraction limit

A

Can only resolve objects that are about half the wavelength of imaging light

57
Q

ABBE’s diffraction limit visual light example

A

Visual light: 400-700 nm
= theoretically can only see/resolve items 200-300 nm apart under perfect optical microscope (but this is not common too)

58
Q

Studying protein structure

A

Experimental lab determination

  • very time consuming
  • often ‘impossible’
59
Q

Ways of studying protein structure

A

1) X-ray crystallography/diffraction
2) electron microscopy
- single particle cryogenic electron microscopy

60
Q

X-ray crystallography/diffraction

A

Very pure protein crystallised into lattice (left in condition where evaporation will take place very slowly)

61
Q

X-ray crystallography/diffraction calculations

A

Short wavelength X-rays and basic principles of diffraction to deduce atomic structure of protein

  • Bragg’s law (2dsinø = n.wavelength) and some complex math
  • use predictable diffractions and back-calculate
62
Q

X-ray crystallography/diffraction usage

A

Most common/widely used

- used for ~50 years; revolutionised understanding of biology

63
Q

X-ray crystallography/diffraction resolution

A

Atomic resolution: generally highest resolution

64
Q

X-ray crystallography/diffraction limitations

A
  • slow crystallisation; may take years
  • prone to failure; most proteins don’t crystallise, crystallisation may damage protein structure
  • doesn’t tell much about how protein moves (somewhat artificial state - not same as when in human body)
65
Q

X-ray crystallography/diffraction protein

A
  • any size macromolecule

- good for soluble proteins (and SOME membrane proteins)

66
Q

Electron microscopy radiation

A

Illuminating radiation type with smaller wavelength

- wavelength of accelerated electron beam ~2.5 pm (>150,000 shorter than light)

67
Q

Electron microscopy resolution

A

Theoretical ~1.5 pm (C atom ~ 70 pm)
Practical ~ 0.5 nm
- electron optics complex and hard to control

68
Q

Electron microscopy images

A

Inherently noisy thus thousands of images must be combined to increase S/N (signal:noise ratio)

69
Q

Single particle cryogenic electron microscopy

A

Freeze suspension of particles in thin layer of virtuous ice in native state
- rapidly emerging technique

70
Q

Single particle cryogenic electron microscopy advantages over X-ray crystallography/diffraction

A
  • Fast determination (early as a week)
  • insight to protein dynamics/movements
    • tease out multiple conformations in one sample
    • extract active/inactive state or ligand-bound/unbound separately, freeze individually and treat separately
  • big protein complexes with lots of subunits (and symmetry) that would never crystallise
71
Q

Single particle cryogenic electron microscopy proteins

A

Soluble proteins, MEMBRANE PROTEINS, large protein complexes, dynamic proteins

72
Q

Levinthal’s paradox

A
  • very large number of degrees of freedom in unfolded polypeptide chain
  • 100 aa protein will have 3^198 different conformations
  • Require time longer than age of universe to sample all conformations; simple computational prediction of structures under same basis is infeasible
73
Q

Protein folding time taken

A

Most correctly fold in ms-µs scale (instantaneously) - how is not known

74
Q

Influences on protein folding

A
  • Environment: solute, salt conc., pH, temp., macromolecular crowding etc.
  • Temporal: co-translational folding as polypeptide is coming off ribosome (N folds before C term)
  • Chaperones: other proteins which bind to/prevent misfolding of parts of protein
75
Q

Protein folding current technology

A

G enerally quite bad at predicting (historically)
- constantly improving
- if structure of related protein known, better
Computational de novo prediction of tertiary protein structure is improving rapidly
- Google DeepMind - AlphaFold
improving but not accurate enough so typically still need to experimentally investigate structure

BIOSCI 107 (15 decks)

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