BIOSCI 107 > L14 - Protein Structure & Function > Flashcards

L14 - Protein Structure & Function Flashcards

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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
Amino acids in beta pleated sheets
- large aromatic residues: tryrosine, phenylalanine, tryptophan - beta-branche amino acids: threonine, valine, isoleucine
26
Secondary structure prediction
Different amino acids have propensity to favour structures | = can fairly accurately predict regions from sequence
27
Tertiary structure
3D shape of protein
28
Tertiary structure driven by
Chemistry of side chains and interactions between them
29
Tertiary noncovalent interactions
- ionic bonds - hydrophobic interactions - hydrophilic interactions - dipole-dipole interactions - Van der Waals forces
30
Tertiary covalent bonds
Disulphide bond - formed by cystines - thiol oxidised, H removed, covalent linkage formed between two sulphur atoms
31
Tertiary interaction strengths
Disulphide > ionic > hydrogen > Van der Waals
32
Cofactors
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
Quarternary structure
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
Quarternary structure driven by
Ionic interactions, H-bonding, hydrophobic interactions (Disulphide possible but uncommon)
35
Quarternary structure types
- homooligomer: 2 of the same subunits | - heterooligomer: 2 different subunits
36
Types of proteins
Globular, fibrous, membrane
37
Globular solubility
Typically soluble in water
38
Globular function
Functional; metabolic functions (enzyme, transport, immune)
39
Globular structure
- spherical/globular in shape | - irregular sequence and secondary structure
40
Globular repetition
Not many repeating elements (structure, sequence within primary or secondary sequence)
41
Globular and quarternary structures
Moderate to none
42
Globular stability
Lower stability
43
Globular example
Enzymes, hemoglobin, antibodies
44
Fibrous solubility
Typically insoluble in water
45
Fibrous function
Structural
46
Fibrous repetition
Often repetitive primary and secondary structure (repeated alpha helices)
47
Fibrous and quarternary structures
High level
48
Fibrous stability
Highly stable (to heat, pH etc.)
49
Fibrous examples
Keratin, actin, collagen, silk, cytoskeleton proteins
50
Membrane location
Transverse through lipid bilayer
51
Membrane function
Transport, receptors, signalling, adhesion
52
Membrane structure by region
- transmembrane region: single alpha helix or alpha helical bundle - mitochondria and gram negative bacterial: beta barrel transmembrane proteins
53
Beta barrel
Lots of beta sheets that stack around to form barrel (like sheet of paper)
54
Membrane polarity
- 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
Resolution
Distance corresponding to smallest observable feature | - closer than this = one combine blob not two separate objects
56
ABBE’s diffraction limit
Can only resolve objects that are about half the wavelength of imaging light
57
ABBE’s diffraction limit visual light example
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
Studying protein structure
Experimental lab determination - very time consuming - often ‘impossible’
59
Ways of studying protein structure
1) X-ray crystallography/diffraction 2) electron microscopy - single particle cryogenic electron microscopy
60
X-ray crystallography/diffraction
Very pure protein crystallised into lattice (left in condition where evaporation will take place very slowly)
61
X-ray crystallography/diffraction calculations
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
X-ray crystallography/diffraction usage
Most common/widely used | - used for ~50 years; revolutionised understanding of biology
63
X-ray crystallography/diffraction resolution
Atomic resolution: generally highest resolution
64
X-ray crystallography/diffraction limitations
- 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
X-ray crystallography/diffraction protein
- any size macromolecule | - good for soluble proteins (and SOME membrane proteins)
66
Electron microscopy radiation
Illuminating radiation type with smaller wavelength | - wavelength of accelerated electron beam ~2.5 pm (>150,000 shorter than light)
67
Electron microscopy resolution
Theoretical ~1.5 pm (C atom ~ 70 pm) Practical ~ 0.5 nm - electron optics complex and hard to control
68
Electron microscopy images
Inherently noisy thus thousands of images must be combined to increase S/N (signal:noise ratio)
69
Single particle cryogenic electron microscopy
Freeze suspension of particles in thin layer of virtuous ice in native state - rapidly emerging technique
70
Single particle cryogenic electron microscopy advantages over X-ray crystallography/diffraction
- 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
Single particle cryogenic electron microscopy proteins
Soluble proteins, MEMBRANE PROTEINS, large protein complexes, dynamic proteins
72
Levinthal’s paradox
- 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
Protein folding time taken
Most correctly fold in ms-µs scale (instantaneously) - how is not known
74
Influences on protein folding
- 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
Protein folding current technology
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
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