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BIOSCI 107 Part One > Special Topics: Protein Structure and Function > Flashcards

Special Topics: Protein Structure and Function Flashcards

1
Q

What is the central Dogma

A

DNA (genes) >RNA > Amino Acids > Polypeptide (proteins)

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2
Q

How many proteins in a bacteria cell?

A

~2 million

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3
Q

How many proteins in a human cell

A

~1-3 billion

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4
Q

What is a protein/polypeptide?

A

A chain/polymer of amino acids linked by peptide bonds (Polypeptide)

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5
Q

What is a peptide?

A

Short polypeptides (approx. less than 50 aa)

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6
Q

What is a dipeptides, tripeptides, or tetrapeptides?

A

Very short peptides (2,3,4 amino acids in length)

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7
Q

What is a residue?

A

Individual amino acids in a polypeptide/protein

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8
Q

What are proteins made of?

A

amino acids

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9
Q

What is the term given to the the central carbon of an amino acid

A

Alpha carbon

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10
Q

What are the parts of an amino acid

A

They have an amino, carboxyl group, central alpha carbon and a side chain
They can also have an ionised form

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11
Q

How is a peptide bond formed?

A

Amino group targets carbonyl group fo the second amino acid, it releases water and they join together in a condensation/dehydration reaction

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12
Q

What are the main properties of a peptide bond

A

Rigid (cannot rotate), O-C-N-H of the Peptide bonds are coplanar

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13
Q

Where can rotation occur in amino acids?

A

Rotation can occur at the single bonds between the α-carbon and is neighbouring atoms

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14
Q

What is the more stable R-group orientation in an amino acid?

A

Trans (side chains alternate)

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15
Q

What is the least stable R-group orientation in an amino acid?

A

Cis (due to repulsion of side chains)

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16
Q

What direction are proteins drawn?

A

from N (amino) terminus to the C (carboxyl) terminus

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17
Q

What determines the behaviour of a amino acid in a protein?

A

Its side chain (hydrophobic, polar, hydrophilic, nonpolar, positive and negative charged)

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18
Q

What is the shape of a protein important for?

A

Its function

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19
Q

Where does the shape of an active site in a protein/enzyme come from?

A

This shape is driven by the chemical properties and sequences of the amino acids in the protein

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20
Q

What proteins have an active site?

A

Enzymes to allow substrates to bind

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21
Q

How do enzymes interact with substrates?

A

A substrate binds to an active site can cause conformational changes which provide a function or strengthen the interaction

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22
Q

What are the two types of models for proteins?

A

Induced fit (has conformational change) and “lock and key” model

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23
Q

What is the induced fit model?

A

The model of the enzyme that shows the substrate binding to the active site and the active site altering slightly

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24
Q

What is the lock and key model?

A

The model of the enzyme that shows the substrate fitting perfectly into the active site

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25
Q

What is the primary structure of a protein

A

The unique sequence of amino acids of a protein

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26
Q

How can we know what the primary structure of a protein is?

A

Looking at the DNA sequence of genes

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27
Q

What is a secondary structure

A

Localised folding of the polypeptide driven by hydrogen bonding interactions within the polypeptide backbone

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28
Q

What is NOT involved in secondary structures

A

R groups

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29
Q

What are the two types of secondary structures?

A

β sheet (aka β pleated sheet) and the α helix

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30
Q

What are the large aromatic residues favoured in β strands

A

tyrosine, phenylalanine, tryptophan

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31
Q

What are the β-branched amino acids favoured in β strands

A

threonine, valine, isoleucine

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32
Q

What are the residues favoured in α helices?

A

Methionine, alanine, leucine, glutamate, and lysine

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33
Q

What residues are NOT favoured in α helices?

A

Proline and glycine

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34
Q

Can we predict the secondary structure of a protein from its DNA sequence?

A

Yes (due to favoured residues)

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35
Q

How can β sheets be arranged?

A

They can be parallel (both strands going from N Terminus to C) or going in opposite directions

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36
Q

What causes β sheets to be formed

A

H bonding between a backbone Amine (N-H) group on one strand, and a backbone Carbonyl (C=O) group on another strand

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37
Q

What direction are α helices

A

right handed

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38
Q

Number of amino acids in one turn of the helix

A

3.6

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39
Q

Pitch of an alpha helix

A

5.4 Å (Angstroms)(0.54 nm)

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40
Q

What causes α helices to form?

A

Driven by H bonding between a backbone Amine (N-H) group a backbone Carbonyl (C=O) group 3 or 4 residues earlier.

41
Q

Which type of secondary structure is tightly packed?

A

α helices

42
Q

Which type of secondary structure has side chains protruding outwards?

A

α helices

43
Q

What is the tertiary structure of a protein?

A

The three dimensional shape of a protein

44
Q

What causes a tertiary structure?

A

the chemistry of the side chains (R groups) and interactions between them

45
Q

What is the general type of bond in a tertiary structure?

A

Non covalent

46
Q

What is an ionic bond in a tertiary structure?

A

Opposite charged R groups attract. Like charges can repel

47
Q

What is a hydrophobic bond in a tertiary structure?

A

Hydrophobic R groups of non-polar amino acids cluster in the interior of the protein

48
Q

What is a hydrophilic bond in a tertiary structure?

A

Hydrophilic R groups lie on the outside surface of the protein to interact with water

49
Q

How do hydrophobic R groups work in membrane spanning proteins

A

Hydrophobic R groups may be outside interacting with the lipid tails

50
Q

What is a disulfide bond in a tertiary structure?

A

Thiol (S-H) groups are oxidized removing the H and forming a covalent linkage between the two Sulphur atoms.

51
Q

What is the amino acid capable of forming a disulphide bond?

A

Cystine

52
Q

Strength of bonds in tertiary structures from strongest to weakest

A

Disulphide > Ionic > hydrogen > Van der Waals

53
Q

What is a cofactor?

A

Non-protein helpers that may be bound to the protein

54
Q

Examples of cofactors

A

Metal ions (Mg, Mn, Zn, Fe, Ca), organic molecules (heme), or vitamins

55
Q

How and why do proteins use cofactors

A

Some proteins (particularly enzymes) can coordinate a cofactor or “prosthetic groups” within the protein using the R groups. This may be essential for the function and/or structure of the protein

56
Q

What is a quaternary structure?

A

Arrangement of two or more polypeptide chains. Because some proteins are composed of more than one polypeptide chain so they need to fold the multiple protein subunits

57
Q

What is a homooligomer

A

Quaternary structure is constructed from a single type of subunit

58
Q

What is a heterooligomer

A

Quaternary structure is constructed from different types of subunits

59
Q

What drives quaternary structures?

A

Ionic interactions, hydrogen bonding, hydrophobic interactions

60
Q

Are quaternary structures dynamic?

A

Yes

61
Q

What are the types of proteins?

A

Globular, fibrous, membrane

62
Q

Are globular or fibrous proteins soluble in water?

A

Globular

63
Q

What are the functions of globular proteins?

A

enzymes, transport, immune

64
Q

How are globular proteins arranged?

A

Irregular sequence and secondary structure

65
Q

How much quaternary structure do globular proteins have?

A

Moderate or none

66
Q

Are globular proteins stable?

A

They are not very stable

67
Q

Examples of globular proteins

A

Enzymes, hemogloblin, antibodies

68
Q

What are the functions of fibrous proteins?

A

structural

69
Q

How are fibrous proteins arranged?

A

often repetitive primary and secondary structures

70
Q

How much quaternary structure do fibrous proteins have?

A

High level

71
Q

Are fibrous proteins stable?

A

Very stable (e.g. heat, pH)

72
Q

Examples of fibrous proteins

A

Keratin, Actin, collagen, silk

73
Q

What are membrane proteins?

A

proteins that traverse through a lipid bilayer (membrane)

74
Q

What is contained in a transmembrane region?

A

single α-helix or α-helical bundle (R groups out and hydrophobic)

75
Q

What do mitochondria and Gram negative bacteria contain in their membranes?

A

β-barrel ™ proteins

76
Q

What type of amino acids are most present in membrane proteins?

A

non-polar (hydrophobic) amino acids

77
Q

Where do non-polar side chains face in membrane proteins

A

Non-polar (hydrophobic) side chains face out toward the membrane

78
Q

Where do polar side chains face in membrane proteins

A

Polar (hydrophilic) side chains face inwards

79
Q

What does Abbe’s diffraction limit mean?

A

Abbe’s diffraction limit means we cannot see anything smaller than a mitochondrion on a microscope so we cannot see proteins

80
Q

What is Abbe’s diffraction limit?

A

0.2 micrometres

81
Q

What is Levinthal’s paradox

A

It is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest-energy one is found

82
Q

What are the factors that contribute to successful protein folding

A

environment, temporality, chaperone proteins, enzymes

83
Q

What are example of a correct environment needed for protein folding?

A

solute, salt concentration, pH, temperature, macromolecular crowding (how much is being crowded in)

84
Q

What is temporality in protein folding?

A

Timing: co-translational folding as the polypeptide is coming of the ribosome (i.e. N folds before C term)

85
Q

What do chaperones do in protein folding?

A

other proteins which bind to and prevent misfolding of parts of the protein

86
Q

What do enzymes do in protein folding?

A

Enzymes form disulfide bonds

87
Q

Which way of studying protein structure is the best

A

X Ray crystallography

88
Q

What is resolution?

A

is the distance corresponding to the smallest observable feature: if two objects are closer than this
distance, they appear as one combined blob rather than two separate objects

89
Q

What are the four types of protein structure models

A

Backbone Model
Ribbon Model
Wire Model
Space filling model

90
Q

How does X-ray crystallography/diffraction occur?

A

You crystallise a pure protein and use the short wavelength of X-Rays and the basic principles of diffraction in a crystal lattice to deduce the atomic structure of a protein (using Bragg’s law and some complex math)

91
Q

What is the most common type of method used to determine protein structure?

A

X-ray crystallography/diffraction

92
Q

Which type of protein structure determining method has the best resolution?

A

X-ray crystallography/diffraction

93
Q

Advantages of X-ray crystallography

A

Molecule size unimportant, very high resolution

94
Q

Disadvantages of X-ray crystallography

A

crystallisation is slow and doesn’t always work, must be soluble

95
Q

Disadvantages of NMR

A

molecules must be <30kDa, must be tagged with heavy C/N, must be soluble

96
Q

How does Single Particle Cryogenic Electron Microscopy

work?

A

Freeze suspension of particles in thin layer of virtuous ice

97
Q

Advantages of cryo-electron microscopy

A

relatively fast, high resolution, Can gain insights in to protein dynamics/movements
Tease out multiple conformations in one sample, can look at big protein complexes and membrane proteins which would never crystallise

98
Q

Disadvantages of cryo-electron microscopy

A

molecules must be >100kDa, must be soluble

99
Q

What method of protein structure determination was used for COVID-19?

A

Single Particle Cryogenic Electron Microscopy

BIOSCI 107 Part One (12 decks)

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