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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
What is a polypeptide
Many amino acids bonded by peptide bonds
26
What is the only part of the amino acid that makes them differ from each other
R group
27
What are the two configurations that the R side chains of the two amino acids bonded by a peptide bond can be in
Cis and trans
28
Is the cis orientation stable or unstable, and why
Unstable: increased steric interactions between the R groups on the same side
29
Is trans orientation stable or unstable, and why
Stable: decreased steric interaction between R groups on opposing sides
30
Can peptide bonds rotate, and why
No, peptide bonds are rigid and can't rotate due to resonance.
31
What part of the peptide bonds are co-planar
O-C-N-H
32
Where can rotation occur in polypeptides
At the single bonds between the alpha carbon and its neighbouring atoms
33
What does variation in structure and shape of proteins allow?
Allows them to carry out diverse functions
34
What does the unique shape of a protein allow?
Allows it to interact with other molecules to carry out specific functions
35
What is the shape of a protein determined by?
The sequence of amino acids in the protein and its chemical properties
36
What shape does the active site of an enzyme have?
Complementary shape to the substrate
37
What is the shape of the active site of an enzyme driven by?
The chemical properties and amino acids of the protein
38
What occurs at the enzyme-substrate complex?
The enzyme catalyses the reaction and transforms the substrates into products
39
What occurs after the product of an enzyme-substrate complex reaction is released?
The enzyme returns to its initial state and is therefore unchanged by the reaction so can go on to catalyse more reactions
40
What does the unique 3D shape with a specific surface configuration of enzymes allow them to do?
Allows them to recognise and bind to specific substrates
41
What is the active site of an enzyme?
The part of an enzyme that catalyses reactions
42
What does the induced fit hypothesis state?
The shape of the active site and substrate can change slightly to ensure a better fit
43
Order of protein structures
Primary, secondary, tertiary, and quaternary structures
44
What is the primary structure
The unique sequence of amino acids that make up a protein encoded by DNA
45
What are the two sides to a polypeptide
N terminus (end with amino acid) C terminus (end with carbonyl group)
46
How are amino acids read (of N and C terminus)
Amino acids read from N to C terminus
47
How can we deduce the primary structure of a protein?
By looking at the DNA sequence of the gene coding for it
48
What are secondary structures
Amino acids sequence fold together (localised) to form two things - alpha and beta helix.
49
What type of bonds between polypeptide bonding in secondary structures
Weak hydrogen bonding
50
What is an alpha helix
Backbone forms spiral shape with 3 or 4 amino acids per turn. Normally all r groups point on outside of helix.
51
What is a beta sheet?
The backbone extends one way and does a U-turn in the opposite direction to line up with each.
52
How does beta-sheet form
Hydrogen bonding between a backbone amine group on one strand, and a backbone carbonyl group on another strand
53
What is the hydrophobic effect
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
How are alpha helix and beta sheets formed and what binds hold it together
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
What is a tertiary structure
Folded 3D shape of the polypeptide chain (fold even further than before)
56
What drives the formation of tertiary structures
The chemistry of the R side groups and the interactions between them
57
Is the folding process in tertiary structures random and why
Not random, because have a specific primary structure sequence. DNA tends to fold the same way and give same shape.
58
What are the two types of beta sheets
Parallel (both going N to C) or antiparallel (one strand going from C to N, the other going N to C)
59
How does the hydrophobic effect occur
When proteins fold, hydrophobic residues want to go inside. For the hydrophilic residues, surface of the protein interacts with the H2O molecules.
60
What are the two shapes of proteins
Globular and Fibrous
61
Describe shape of globular proteins
When proteins are highly folded
62
Describe the shape of fibrous proteins
When proteins are long and spindly
63
What is the structure of fibrous proteins
Repeated amino acid sequences from long polypeptide chain, and twists together
64
Are globular proteins insoluble or soluble in water?
Soluble
65
What functions do most globular proteins have?
Metabolic functions - transport, enzymes, immunity
66
What are examples of globular proteins?
Enzymes, antibodies, haemoglobin
67
Are fibrous proteins stable or unstable?
Extremely stable when subject to changes in temperature or pH for example
68
Are fibrous proteins soluble or insoluble in water?
Insoluble
69
What functions do most fibrous proteins have?
Structural
70
What are examples of fibrous proteins?
Keratin and collagen
71
What are quaternary structures
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
What is hydrogen bonding
Theorces involved in maintaining protein structures
73
What are hydrogen bonding held together by
Weak interactions
74
What are electrostatic interactions
Forces involved in maintaining protein structures
75
What are hydrophobic interactions
Forces involved in maintaining protein structures. Clustering of polar/hydrophobic side chains away from H2O.
76
How strong are hydrophobic interactions
Weakest of ionic and hydrogen, but there are strength in numbers
77
How strong are covalent bonds
Strongest bond, aside from peptide backbones
78
How do covalent bonds form
Bonds occur spontaneously under mild oxidising conditions.
79
Which amino acid forms disulphide bonds?
Cysteine
80
What causes a protein to denature
Change in: pH Salt concentration Temperature

biosci (28 decks)

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