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PHAY0003 > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

1
Q

What is the fundamental role of amino acids?

A

To act as monomers from which proteins are made

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2
Q

Describe the basic structure of amino acids

A

A central carbon atom (alpha carbon) that is bonded to an amino group, carboxylic acid, H atom and a variable side chain

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3
Q

How many different amino acids are involved in making proteins?

A

20

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4
Q

When is the amino group on amino acids ionised?

A

At low pHs it gains a proton making the overall charge positive

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5
Q

When is the carboxylic acid group on an amino acid ionised?

A

At high pHs it becomes deprotonated making the molecule negatively charged

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6
Q

What is a zwitterion?

A

When a molecule contains both a positive and negative atom making it dipolar and therefore has ionic properties.

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7
Q

When are amino acids zwitterions?

A

Around neutrality at the isoelectric point halfway between the ionisation of the amino group and the carboxyl group

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8
Q

What is the isoelectric point (pI)?

A

When a molecule has no net charge as it contains equal negative and positive charges.

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9
Q

What is the equation for the isoelectric point?

A

pK1+pK2/2

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10
Q

What is the only amino acid that doesn’t contain a chiral centre?

A

Glycine

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11
Q

What form of optical isomer of the alpha carbon atom are all amino acids in proteins found as?

A

L form

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12
Q

In biology, what optical isomerism system do we use and why?

A

Relative configuration, it impacts the shape of the molecule

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13
Q

If a molecule is L or D configuration, what is the configuration of the molecules the same as?

A

L-glyceraldehyde and D-glyceraldehyde

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14
Q

Which group on the amino acid gives the 20 amino acids?

A

The different R groups/ side chain

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15
Q

Which group on amino acids is responsible for its chemical and physical characteristics?

A

The different R groups/ side chain

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16
Q

When do amino acids have 3 pK values and what is responsible for them?

A

If the side chain is also able to be ionised.

Carboxyl group, amino group, side chain

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17
Q

What types of polymers are proteins?

A

Condensation polymers

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18
Q

What is eliminated when the alpha amino group and the alpha carboxylic acid of another amino acid are joined together?

A

Water

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19
Q

What is the bond called that forms between amino acids when a protein is being made?

A

Peptide bond (amide bond)

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20
Q

What is a chain of amino acids called?

A

Polypeptide

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21
Q

What type of bond is a peptide bond?

A

Strong covalent bond, extreme conditions are required to break it

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22
Q

Why is geometric isomerism possible in a polypeptide?

A

There is partial double bond character between the carbon and nitrogen peptide bond. This also adds rigidity

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23
Q

Describe the shape in terms of atoms lying in the plane for a polypeptide

A

The 6 atoms closest to the double bond all lie in the same plane. The peptide units alternate up and down with the R groups pointing in and out

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24
Q

What is the primary structure of proteins?

A

The linear sequence of amino acids joined together to form a polymer (polypeptide)

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25
Q

What are 3 important features of protein primary structure?

A

Amino acids are joined together by strong covalent peptide bonds
The type and number of amino acids present
The sequence that amino acids are joined will determine the shape of the protein

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26
Q

What is the important property of proteins that allows for its function?

A

The shape

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27
Q

What determines the N-terminus an the C-terminus?

A

The N-terminus of the polypeptide is the amino acid that has a free NH2 group.
The C-terminus is the end that has a free COOH group

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28
Q

Which direction are amino acids numbered in in a polypeptide chain?

A

From N-terminus to C-terminus

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29
Q

What is the secondary structure of a protein?

A

The three dimensional structure that is only determined by H bonds formed between the carbonyl oxygen of a peptide bond and the H bonded to the nitrogen atom of another peptide bond

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30
Q

What are the 3 secondary structures?structures of

A

Alpha helix
Beta pleated sheet - parallel
Beta pleated sheet - antiparallel

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31
Q

What are the 4 characteristics of the alpha helix secondary structure of proteins?

A

Right handed
The atoms involved in the H bond are 4 residues apart
All main chain c=O and NH are H bonded
The R groups point outwards

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32
Q

What type of secondary protein structure is often part of the integral protein membrane that passes through the membrane?

A

Alpha helix

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33
Q

Describe parallel beta pleated sheets

A

The H-bonds are formed between 2 chains running in the same direction and are pleated.

34
Q

Describe the anti-parallel beta pleated sheets

A

The H-bonds are formed between 2 chains running in opposite directions either as a loop or U turn

35
Q

Describe the tertiary structure of proteins

A

The three dimensional shape of a protein formed by non-covalent bonding between the chemical group in the side chains

36
Q

What are the 4 bonds involved in the tertiary structure of a protein?

A

Ionic bonds, H bonds, Hydrophobic bonds and VDW forces

37
Q

How does the tertiary structure of spherical proteins allow the protein to be soluble in aqueous environments?

A

The hydrophilic (charged and polar) part will face outwards and the hydrophobic (non-polar) parts will be on the inside

38
Q

Is it primary, secondary or tertiary structure that affects the shape of the active site of an enzyme

A

Tertiary

39
Q

What are disulphide bridges?

A

The covalent bond formed between the side chain of 3 cysteine amino acids to form cystine, part of its tertiary structure

40
Q

What is the difference between intermolecular and intramolecular in terms of tertiary structure of proteins?

A 
Intermolecular = Between 2 different polypeptide chains
Intramolecular = Between the same polypeptide chain
41
Q

What is the requirement for a protein to have quaternary structure?

A

More than one polypeptide chain

42
Q

What is an oligomeric protein?

A

When polypeptide chains or monomers (subunits) bond using noncovalent interactions, proteins that have quaternary structure

43
Q

What is a subunit (quaternary structure of protein)

A

Each protein component of the quaternary structure

44
Q

What is a domain in a protein?

A

An individual section of a protein that has a shape

45
Q

Give 3 molecules that interact with binding sites on proteins

A

Nucleic acids, lipids, carbohydrates

46
Q

What does the shape of a protein depend on?

A

The sequence of amino acids in the primary structure which then determines the protein fold up into tertiary structure that gives the 3D shape which also contains the secondary structure

47
Q

As well as the size and shape of the protein, what does the three dimensional structure of a protein also determine?

A

The function, the sequence of amino acids give the shape of the protein which gives the function of the protein

48
Q

What is an enzyme?

A

A protein that is a biological catalyst

49
Q

What is the most important group of proteins in the body?

A

Enzymes

50
Q

How doe enzymes act as catalysts?

A

They have an active site which allows for interactions with substrates which can then react easier

51
Q

What are histones?

A

Basic proteins that associate with DNA in the nucleus and help condense it into chromatin. The proteins that the DNA strands are wrapped around

52
Q

What characteristic of histones allows DNA to wrap around it tightly?

A

It is positively charged and DNA is negatively charged

53
Q

What modification of histones is required in order for the DNA to be revealed again for trasncription?

A

Acylation

54
Q

What are antibodies?

A

Proteins that are involved in the immune response of the organism to neutralise large foreign molecules that are part of an infection

55
Q

Briefly describe the quaternary structure of an antibody

A

It has 2 light chains and 2 heavy chains which are held together by disulphide bonds

56
Q

What are actin and myosin responsible for?

A

Muscular movement as well as cellular movements such as cell division

57
Q

What does myosin do?

A

Converts ATP to mechanical energy which generates force and movement (muscular contraction)

58
Q

What does actin do?

A

Allows myosin to bond to its filaments so that it can hydrolyse ATP

59
Q

What are structural proteins?

A

Proteins that maintain shape and structure of cells an tissues. E.g collagen and elastin

60
Q

What kind of shape are structural proteins?

A

Fibres

61
Q

Why are some structural proteins sometimes described to have super-secondary structure? And what does it do?

A

Some proteins such as collagen have a triple helix, like a rope of three strands. These strands are riveted together with covalent crosslinks formed from lysine side chains. This increases the strength of the molecules

62
Q

Where is collagen found?

A

Connective tissues such as bone, cartilage, skin and tendons

63
Q

What are the transport proteins that transports oxygen?

A

Haemoglobin and myoglobin

64
Q

What do transport proteins that are also integral membrane proteins allow?

A

The passage of substrates and ions across the membranes of the cell. E.g the calcium channel in the plasma membrane

65
Q

Describe the structure of haemoglobin

A

It has quaternary structure of 2 identical alpha chains and 2 identical beta chains. Each chain contains a “haem” which is an iron porphyrin molecule

66
Q

What is porphyrin?

A

A tetrapyrrole structure, the molecule part of haem consisting of an iron atom with a porphyrin ring that links 4 N atoms

67
Q

Which part of haemoglobin allows for the binding of an O2 molecule?

A

The haem pockets on the alpha subunits

68
Q

Why can O2 not bind to the beta subunits on haemoglobin?

A

It is blocked by valine (an amino acid)

69
Q

What part of haemoglobin aids its solubility?

A

The molecule contains hydrophobic amino acids inside and hydrophilic ones on the surface

70
Q

Describe the mutation to haemoglobin which results in sickle cell anaemia

A

The beta-globin subunit increases its hydrophobicity causes all the mutated haemoglobin molecules to become stuck together, making the shape of the red blood cell sickled which block narrow blood vessels.

71
Q

Give an example of a group of signalling proteins

A

Hormones

72
Q

Where are hormones secreted from and how do they reach their target tissues?

A

They are secreted by endocrine glands into the blood stream where they are carried to their target tissues

73
Q

What are hormones?

A

Proteins that are chemical messengers and allow cells and tissues to communicate

74
Q

Describe the quaternary structure of insulin

A

It is made up of one A chain and one B chain held together by disulphide bridges

75
Q

Which part of the structure of proteins is responsible for its hydrophobicity?

A

The primary structure

76
Q

What makes membrane proteins more hydrophobic?

A

They are typically alpha helices and are made up of hydrophobic amino acids

77
Q

What forms the binding site for receptors and what happens when the substrate binds?

A

The tertiary structure. The interaction between amino acid side chains form specific binding sites. When the substrate binds it causes a change in shape which is the signal for physiological changed in the cell

78
Q

What causes denaturation of proteins?

A

Processes that weaken the noncovalent bonds holding the three dimensional structure of the protein. E.g pH extremes, heat and UV

79
Q

Which parts if protein structure are affected in denaturation?

A

Secondary and tertiary

80
Q

Why is denaturation theoretically reversible (renaturation)

A

The primary structure is unaffected and so in theory the protein could fold up again

81
Q

When does denaturation become irreversible?

A

When the covalent structure of the protein is damaged, the peptide chains form new cross-linked bonds changing the shape

PHAY0003 (22 decks)

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