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proteins Flashcards

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Biology 101 flashcards
1
Q

what are the functions of proteins

A

Transport - of haemaglobin
Catalysis - as enzymes for this which are made of proteins
Structure – as ligamons and tendons have proteins
Locomotion’s – such as muscle protein
Storgae- of oxygen in the muscle
Hormones – ex = ones that store protein in body

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2
Q

what are peptides and proteins made up of

A

amino acids joined together by peptide bonds.

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3
Q

why is 1 amino acid got an SP3 carbon

A

as the carbon in middle is joined to 4 things

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4
Q

how many amino acids are there in nature

A

20

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5
Q

what is the configuration of amino acids

A

often refer to amino acids as being L or D in a similar way to glyceraldehyde.
D and L configuration both occur but most naturally occurring amino acids have L-configuration.

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6
Q

explain solubility of amino acids due to their functional groups

A

Carbonyl and amino groups are charged. So are polar so can dissolve in body

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7
Q

whats the name given to amino acids since they have both basic and acidic groups

A

amphoteric

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8
Q

what are the characteristics of zwitterion and what is zwitterions charge

A

colourless
crystalline solids
high melting point & decompose on melting
varying solubility in water

Zwitterion is neutral
Basic -1
Acidic + 1

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9
Q

what does the structure of the R group determine in an amino acid

A

whether its polar or non polar

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10
Q

what does shape of amino acid determine

A

its function

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11
Q

what are polar amino acid groups, involve EX

A

Groups contain electronegative atoms that give rise to unequally sharing of the electrons in covalent bonds.
e.g. oxygen sucks electrons away from carbon, so carbonyl group is polar

e.g. Hydroxyl -OH
Sulfhydryl -CH2-SH
Carbonyl >C=O
Amino -NH3+
Carboxyl -COO-

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12
Q

what does the polarity of amino acids allow to happen due to its charge attraction

A

allows hydrogen bonding with other polar groups like water

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13
Q

where are polar side chains often found

A

on surface of proteins

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14
Q

what happens to electrons in non polar groups, and provide EX of polar groups

A

Groups where electrons are shared equally in all covalent bonds.

e.g. Aliphatic - CH2CH3
Aromatic (full circle chains)

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15
Q

where are non polar / hydrophobic side chains often found

A

buried in the protein’s core, away from the aqueous environment.

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16
Q

what affect does PH have on the amino acid side groups

A

Neutral/basic solutions (groups lose H):

COOH -> COO-
NH3+ -> NH2

Neutral/acid solutions (groups gain H):

NH2 -> NH3+
COO- -> COOH

In neutral put in basic solutions they lose protons
In neutral put in acidic solutions they gain protons

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17
Q

when do groups lose their H+

A

at different PH’s

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18
Q

in neutral amino acids what happens to the side chain charges when PH changes

A

doesnt change with PH

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19
Q

are the 2 different carboxyl groups are protonated at different pH’s.

A

yes

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20
Q

why do ionising groups each have a different pKa value.

A

pKa is another way to express the strength of an acid. The pKa for COOH and NH3+ groups depend on the structure of the amino acids.

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21
Q

what is PKa

A

another way to express the strength of an acid.

Pka, where the hydrogen is bound, and PH affect which hydrogen is lost first

If Pka is low or high it doesn’t tell you if its an acid or base

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22
Q

whats the general rule for Pka

A

if pH of a solution is less than the pKa, the H+ is on. If pH is higher than the pKa the H+ is off.

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23
Q

what does Knowing the pKa values of particular groups allows us to predict

A

its form at particular pH’s

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24
Q

how do amino acids form peptides

A

Amino acids can be linked together by an amide bond between the carboxylic group of one amino acid and the a-amino group of another amino acid to form peptides and proteins.

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25
Q

explain cell signalling peptide function

A

Enkephalin - a pentapeptide endorphin, a natural brain opioid, can bind to the body’s opioid receptors affect pain perception.

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26
Q

explain hormones peptide function

A

Produced by many organs and tissues.

eg. insulin – 51 amino acid residues

Causes cells to take up glucose from the blood

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27
Q

explain antibiotic fungal peptides function

A

Cyclic decapeptides.
Active against gram positive bacteria

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28
Q

explain venoms (snake, scorpion and conesnail) peptide functions

A

Some of these toxins are only 13-50 residue peptides in length.

Induce paralysis by interfering with acetyolcholine receptors in nerves.

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29
Q

explain synthetic peptides functions

A

Variety of applications eg. the dipeptide Aspartame (Nutrasweet)

This is a sweetener in drinks

30
Q

what are the 4 levels of protein structure

A

primary
secondary
tertiary
quaternary - this has 4 subunits that are similar or different

31
Q

describe the primary level of structure

A

Amino acid sequence and chain length/size (in daltons)

Primary structure is a sequence of amino acid residues

it determines the physiological, structural, and biological properties and functions of a protein.

Involves the covalent peptide bonds in a protein.

32
Q

what is the cause of sickle cell anaemia

A

Caused by a mutation in the gene that instructs the body to produce haemoglobin.

The sixth position in the normal b chain of haemoglobin ( which usually transports oxygen I and co2 out) has glutamic acid, while a sickle b chain has valine.

Blocked blood vessels can cause pain, serious infections, and organ damage.

33
Q

what happens during the secondary structure of protein formation

A

The secondary level of structure is the arrangement in space of the atoms in the backbone of the protein.

The shape depends on the geometry of the peptide bond and local hydrogen bonding (Between the H on the N of one amide in a peptide bond with the carbonyl O of another amide in a second peptide bond).

Long chains of amino acids will commonly fold or curl into a regular, repeating structure:
- as well as sections of “random coil” or “irregular” structure
- alpha helix
- beta sheets

34
Q

what properties does the secondary structure add to the protein

A

strength, flexibility

35
Q

what is the alpha helix

A

The helix is stabilised by hydrogen bonds formed between the amide hydrogen of one peptide bond and the carbonyl oxygen above it which is located in the next turn of the helix.

Side-chain (R group) are directed outwards.

Large amounts of a-helix results in a strong, insoluble, fibrous, flexible product.

36
Q

what are beta sheets

A

Peptide chain adopt the conformation of a sheet of paper and the structure is stabilized by hydrogen bonds between peptide bonds.

Some of the strands are parallel and some are antiparallel depending on the relative directions of the peptide chains. The hydrogen bonding is different between parallel and anti parallel structures

37
Q

explain tertiary level structure

A

Further folding of the secondary structure gives the overall 3 dimensional shape - involves side chain interaction.

Protein function e.g. enzyme activity, is derived from the 3D structure (conformation)

38
Q

what bonding types are involved in tertiary level structure

A

Disulphide crosslinks – covalent bonds between cysteine residues

Hydrophobic attractions - attractions between R groups of non-polar amino acids

Hydrogen bonding - interaction between polar amino acid R groups

Ionic bonding - bonding between oppositely charged amino acid R groups.

39
Q

when can disulphide bridges form
and what are they important for

A

If there is cysteine present, strong disulphide bridges may form between them.

Important in structural proteins and gluten , therefore bread texture

40
Q

explain quaternary structure of proteins

A

Many proteins are not single peptide strands but are combinations of several polypeptides.

These may exist as dimers, trimers, tetramers etc.

Subunits are usually identical

41
Q

what are fibrous proteins

A

Water insoluble structural materials in animals eg. keratins, collagens (cartilage & tendons).

42
Q

examples of fibrous proteins

A

tendons and cartilage
horn/hoof/nail/shell
hair/feathers/wool/fur
skin

43
Q

what does the primary structure tend to lack

A

chemically-reactive side groups

44
Q

what is alpha keratin a major component of

A

of hair, nails and skin

45
Q

explain alpha keratin proteins

A

Rope-like structure - based on the alpha helix, cross-linked into bundles.

Can be very extensible - a wool fibre can be stretched to twice its length as hydrogen bonds between turns of the a-helix are broken.

In hair a-helices are held together by disulphide crosslinks.

S-S bonds help resist the stretch and restore a stretched fibre to its original length.

The degree of S-S bridging determines the properties of the keratin

46
Q

explain the degree of disulphide bridging on keratin properties

A

Hard Keratins - high sulphur e.g. horn (less flexible, less extensible)

Soft Keratins flexible, extensible –
low sulphur e.g. skin

47
Q

what is collagen a major component of

A

cartilage, skin, blood vessels and bone

48
Q

explain collagen proteins

A

Collagen protein occurs in the form of a triple helix (3 left-handed helices) (known as “Tropocollagen”).

The triple helix tightens under tension, resisting stretching, making collagen inextensible.

Most abundant protein in mammals

Secreted by the cells of connective tissue

49
Q

describe the repetitive primary structure

A

Bulky Proline and Hydroxyproline side chain rings point outwards and are responsible for the tendency to form left-handed helices.

Glycine at every third position sits in the interior of the helix, where there is little space.

Collagen fibres are stabilised by extensive inter-chain hydrogen bonding and some covalent S-S cross-links.

Fibres have stability, tensile strength and rigidity

50
Q

explain silk in terms of structure

A

Extensible & very strong (large no. of H bonds)

Primary level - highly repetitive glycine and alanine blocks

51
Q

what are globular protein examples

A

enzymes, hormones, transport, and storage, etc

52
Q

describe the solubility and shape of globular proteins

A

are water soluble and roughly spherical in shape.

53
Q

how are globular proteins folded

A

Intricately folded so that hydrophobic side chains are tucked inside - away from water.

54
Q

what is myoglobin

A

Is the oxygen-holding protein in muscle tissue.

55
Q

what does the myoglobin structure consist of

A

Consists of one polypeptide unit, of which 75% is an a-helix, which is further folded.

56
Q

what are prosthetic groups

A

Myoglobin also has a non-protein group called a haem which holds the oxygen molecule.

57
Q

describe haemoglobins structure

A

Quaternary structure: 4 polypeptide molecules (Globins).

58
Q

how are subunits in haemoglobin held together

A

Sub units are held together by hydrophobic interactions, electrostatic (ionic) attraction and hydrogen bonds.

59
Q

what affect on proteins does high temperature and extream PH have

A

cause denaturation

Beyond the ‘normal’ range of pH and at high temperatures weak bonds (e.g. H. bonds) break, dramatically altering the 3-D shape of the protein (secondary and tertiary level of structure ) thus affecting their function.

Strong peptide bonds remain intact.

60
Q

what happens to denatured proteins in solution

A

clump together – coagulate/precipitate.

61
Q

what happens beyond denaturation (hydrolysis)

A

Heating in acid conditions can result in the protein being reduced to simpler peptides and amino acids i.e. breakage of peptide linkages.

62
Q

what does altering PH change in proteins

A

alter the overall charge on protein which alters their solubility and possibly their shape.

63
Q

what is isoelectric point

A

Is the pH at which the total charge on the protein molecule is zero (no net electric charge)

This pH varies between proteins.

64
Q

what charge do proteins have at PH below isoelectric point

A

+ve charge overall

65
Q

what charge do proteins have at PH above isoelectric point

A

–ve charge overall.

66
Q

at isoelectric point charged proteins repulsing each other prevents

A

aggregation

67
Q

At the isoelectric point proteins tend to aggregate and are in their what

A

least soluble undenatured form.

68
Q

how are proteins separated by electrophoresis

A

Usually, proteins are loaded on a gel and given a negative charge using a buffer (pH above their isoelectric point).

A potential difference is applied.

Large proteins move slowly, smaller ones move more quickly.

The gel is then stained e.g. with Coomassie blue.

69
Q

name 3 complex proteins

A

lipoproteins
glycoproteins,
nucleoproteins

70
Q

what the function of the complex protein lipoprotein

A

e.g.carry fats around the body in the blood

71
Q

explain the complex protein glycoproteins and give ex

A

(proteins with oligosaccharides covalently attached) e.g. antibodies, cell surface proteins (receptors), hormones

72
Q

what are examples of nucleoproteins

A

ribosomes, some virus particles

biomolecular science (6 decks)

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