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biosci > Protein structure and function > Flashcards

Protein structure and function Flashcards

1
Q

What do different side chains of amino acids determine

A

Determine the properties and dictate protein shape at end

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2
Q

What is an example of a transport protein

A

Haemoglobin

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3
Q

What are proteins

A

Large polypeptides that are folded in such a way to carry out a specific function in the body

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4
Q

What are amino acids linked by

A

Peptide bonds

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5
Q

What are short polypeptides referred to as

A

Peptides

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6
Q

What groups do all amino acids contain?

A

C, O2 and N and H

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7
Q

What is a dehydration reaction?

A

When two amino acids are joined together and lose 2Hs and 1 O2.

A new bond (peptide) is formed between carbonyl group of one amino acid and one amino group of another amino acid.

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8
Q

What is the dehydration reaction catalysed by?

A

Ribosomes, in a hamburger structure

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9
Q

How are peptide bonds formed?

A

Through dehydration reactions

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10
Q

What is the bi-product of the formation of a peptide bond?

A

A water molecule per bond

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11
Q

What is an example of a structural protein

A

Actin

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12
Q

What is an example of a hormonal protein

A

Insulin

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13
Q

What is an example of an immune protein

A

Antibodies

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14
Q

What are examples of digestive enzyme proteins

A

Amylase, lipase, and pepsin

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15
Q

What is an example of a toxin protein

A

Cholera toxin

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16
Q

What is an example of a storage protein

A

Egg white

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17
Q

What is an example of a contractile protein

A

Myosin

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18
Q

Are polar amino acids hydrophobic or hydrophillic?

A

Hydrophillic

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19
Q

Are hydrophilic amino acids polar or non-polar

A

Polar

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20
Q

Are non-polar amino acids hydrophobic or hydrophilic

A

Hydrophobic

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21
Q

Are hydrophobic amino acids polar or non-polar

A

Non-polar

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22
Q

Are peptide bonds strong or weak? What kind of bond are they?

A

Strong, covalent bonds

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23
Q

What are peptide bonds formed between?

A

The C of the carboxyl group on one amino acid and the N of the amine group of another amino acid.

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24
Q

What is a dipeptide

A

Two amino acids bonded by a peptide bond

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25
Q

What is a polypeptide

A

Many amino acids bonded by peptide bonds

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26
Q

What is the only part of the amino acid that makes them differ from each other

A

R group

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27
Q

What are the two configurations that the R side chains of the two amino acids bonded by a peptide bond can be in

A

Cis and trans

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28
Q

Is the cis orientation stable or unstable, and why

A

Unstable: increased steric interactions between the R groups on the same side

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29
Q

Is trans orientation stable or unstable, and why

A

Stable: decreased steric interaction between R groups on opposing sides

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30
Q

Can peptide bonds rotate, and why

A

No, peptide bonds are rigid and can’t rotate due to resonance.

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31
Q

What part of the peptide bonds are co-planar

A

O-C-N-H

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32
Q

Where can rotation occur in polypeptides

A

At the single bonds between the alpha carbon and its neighbouring atoms

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33
Q

What does variation in structure and shape of proteins allow?

A

Allows them to carry out diverse functions

34
Q

What does the unique shape of a protein allow?

A

Allows it to interact with other molecules to carry out specific functions

35
Q

What is the shape of a protein determined by?

A

The sequence of amino acids in the protein and its chemical properties

36
Q

What shape does the active site of an enzyme have?

A

Complementary shape to the substrate

37
Q

What is the shape of the active site of an enzyme driven by?

A

The chemical properties and amino acids of the protein

38
Q

What occurs at the enzyme-substrate complex?

A

The enzyme catalyses the reaction and transforms the substrates into products

39
Q

What occurs after the product of an enzyme-substrate complex reaction is released?

A

The enzyme returns to its initial state and is therefore unchanged by the reaction so can go on to catalyse more reactions

40
Q

What does the unique 3D shape with a specific surface configuration of enzymes allow them to do?

A

Allows them to recognise and bind to specific substrates

41
Q

What is the active site of an enzyme?

A

The part of an enzyme that catalyses reactions

42
Q

What does the induced fit hypothesis state?

A

The shape of the active site and substrate can change slightly to ensure a better fit

43
Q

Order of protein structures

A

Primary, secondary, tertiary, and quaternary structures

44
Q

What is the primary structure

A

The unique sequence of amino acids that make up a protein encoded by DNA

45
Q

What are the two sides to a polypeptide

A

N terminus (end with amino acid)
C terminus (end with carbonyl group)

46
Q

How are amino acids read (of N and C terminus)

A

Amino acids read from N to C terminus

47
Q

How can we deduce the primary structure of a protein?

A

By looking at the DNA sequence of the gene coding for it

48
Q

What are secondary structures

A

Amino acids sequence fold together (localised) to form two things - alpha and beta helix.

49
Q

What type of bonds between polypeptide bonding in secondary structures

A

Weak hydrogen bonding

50
Q

What is an alpha helix

A

Backbone forms spiral shape with 3 or 4 amino acids per turn.

Normally all r groups point on outside of helix.

51
Q

What is a beta sheet?

A

The backbone extends one way and does a U-turn in the opposite direction to line up with each.

52
Q

How does beta-sheet form

A

Hydrogen bonding between a backbone amine group on one strand, and a backbone carbonyl group on another strand

53
Q

What is the hydrophobic effect

A

Describes the interaction of non-polar or hydrophobic side chains with the aqueous environment, and their subsequent burial in the interior of the protein.

54
Q

How are alpha helix and beta sheets formed and what binds hold it together

A

Both shapes are held together by H bonds.
Key interactions hold proteins together and proteins rely on these weak interactions to keep their shape.

55
Q

What is a tertiary structure

A

Folded 3D shape of the polypeptide chain (fold even further than before)

56
Q

What drives the formation of tertiary structures

A

The chemistry of the R side groups and the interactions between them

57
Q

Is the folding process in tertiary structures random and why

A

Not random, because have a specific primary structure sequence. DNA tends to fold the same way and give same shape.

58
Q

What are the two types of beta sheets

A

Parallel (both going N to C) or antiparallel (one strand going from C to N, the other going N to C)

59
Q

How does the hydrophobic effect occur

A

When proteins fold, hydrophobic residues want to go inside. For the hydrophilic residues, surface of the protein interacts with the H2O molecules.

60
Q

What are the two shapes of proteins

A

Globular and Fibrous

61
Q

Describe shape of globular proteins

A

When proteins are highly folded

62
Q

Describe the shape of fibrous proteins

A

When proteins are long and spindly

63
Q

What is the structure of fibrous proteins

A

Repeated amino acid sequences from long polypeptide chain, and twists together

64
Q

Are globular proteins insoluble or soluble in water?

A

Soluble

65
Q

What functions do most globular proteins have?

A

Metabolic functions - transport, enzymes, immunity

66
Q

What are examples of globular proteins?

A

Enzymes, antibodies, haemoglobin

67
Q

Are fibrous proteins stable or unstable?

A

Extremely stable when subject to changes in temperature or pH for example

68
Q

Are fibrous proteins soluble or insoluble in water?

A

Insoluble

69
Q

What functions do most fibrous proteins have?

A

Structural

70
Q

What are examples of fibrous proteins?

A

Keratin and collagen

71
Q

What are quaternary structures

A

When two or more polypeptide chains come together to form even larger structures.

The combination of multiple polypeptide chains forming multiple folded protein subunits

72
Q

What is hydrogen bonding

A

Theorces involved in maintaining protein structures

73
Q

What are hydrogen bonding held together by

A

Weak interactions

74
Q

What are electrostatic interactions

A

Forces involved in maintaining protein structures

75
Q

What are hydrophobic interactions

A

Forces involved in maintaining protein structures.

Clustering of polar/hydrophobic side chains away from H2O.

76
Q

How strong are hydrophobic interactions

A

Weakest of ionic and hydrogen, but there are strength in numbers

77
Q

How strong are covalent bonds

A

Strongest bond, aside from peptide backbones

78
Q

How do covalent bonds form

A

Bonds occur spontaneously under mild oxidising conditions.

79
Q

Which amino acid forms disulphide bonds?

A

Cysteine

80
Q

What causes a protein to denature

A

Change in:
pH
Salt concentration
Temperature

biosci (28 decks)

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