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chapter 4 - enzymes and proteins Flashcards

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1
Q

what are the four structures of forming a protein?
How is this done?
and what bonds are involved?

A
  1. primary - amino acid chain held together by peptide bonds
  2. secondary - amino acid sequences interact folding into either an alpha helix or a beta pleated sheet. held together by hydrogen bonds
  3. tertiary - further folding of secondary structure, interactions between R-groups, forming a specific 3D structure. consistsof hydrophobic and hydrophilic regions, hydrogen bonds, ionic bonds and disulfide bridges
  4. quaternary - made up of multiple tertiary subunits.
    same interactions as tertiary (except between different protein molecules rather than within one molecule.
    some quaternary proteins have a prosthetic group, eg. haemoglobin has a “HAEM” group made of Fe ions.
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2
Q

describe the types of bonding in tertiary and quaternary structures

A
  1. hydrophobic and hydrophilic regions - weak interactions between polar and non-polar R groups
  2. hydrogen bonds - (weakest of the bonds) between lone pairs of electrons around oxygen and a positive hydrogen ion.
  3. ionic bonds - (stronger than hydrogen bonds) form between oppositely charged R groups
  4. disulfide bridges - (strongest covalent bond) but only form between the R groups that contain Sulfur atoms
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3
Q

what are the four main roles of proteins (give examples of each)

A

structural - muscle, skin, ligaments and hair

catalytic - enzymes

cell signalling - hormones and receptors

immunological - antibodies

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4
Q

what is the smallest amino acid and what is the chemical formula?

A

Glycine C2 H5 NO2

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5
Q

what is the general formula for an amino acid

A

H2 N C H R COOH

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6
Q

what part of the amino acid is the amine group and which part is the carboxylic acid group

A

amine = H2N

carboxylic acid = COOH

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7
Q

how are amino acids bonded together?

A

via a condensation reaction, water is produced when the peptide bond is formed between the C of one amino acid and the N of another bond together as the OH of one and the H of the other is broken off.
when 2 amino acids bond it is called a dipeptide

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8
Q

how are amino acids broken apart?

A

via a hydrolysis reaction, water is used to break the peptide bond between the C and the N returning the two amino acids to their original structures.

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9
Q

how do you calculate the total number of possible “R-groups” in a protein?

A

multiply the number of possibilities (20) by the number of amino acids in the protein.

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10
Q

what is important about the hydrophobic and hydrophilic regions of a tertiary protein

A

proteins are assembled in the aqueous cytoplasm. how the proteins fold depends on whether the R-groups are hydrophobic or hydrophilic.
hydrophilic groups are on the outside of the protein and hydrophobic groups are inside, shielded from the water in the cytoplasm

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11
Q

why does haemoglobin have prosthetic (haem) groups?

A

so it can deliver oxygen around the body

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12
Q

what types of proteins contain prosthetic groups? and what are the 2 main types of this protein?

A

conjugated proteins
haemoglobin, catalase

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13
Q

what are simple proteins

A

proteins that do not contain a non-protein component called a prosthetic group

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14
Q

what are the 3 main types of proteins and what are their structures like?

A

globular - compact, water soluble and usually roughly spherical shaped

conjugated - globular proteins that contain a non-protein prosthetic group

fibrous - formed from long, insoluble molecules

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15
Q

why do globular proteins water soluble?
why is the solubility necessary?
give an example of a globular protein

A

the tertiary structure has the hydrophobic R-groups kept away from the aqueous cytoplasm and the hydrophilic R-groups are on the outside of the proteins
needs to be soluble for regulating processes such as: chemical reactions, immunity, muscle contraction and many more.

insulin is a type of globular protein that regulated blood glucose concentration.

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16
Q

what are the different types of prosthetic groups?
what are HAEM groups?
list 2 proteins that have haem groups?

A

lipids and carbohydrates bond with proteins forming lipoproteins glycoproteins and metal ions or minerals (from vitamins)

HAEM groups are a prosthetic group that consists of Iron II
catalase and haemoglobin both have haem groups

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17
Q

what are three examples of fibrous proteins?
where are they found?
and what are their functions?

A

Keratin - present in hair, skin and nails. contains a large proportion of sulfur-containing amino acids resulting in strong disulfide bridges.

elastin - present in the walls of blood vessels and alveoli in the lungs - give structures the flexibility to expand and return to their normal size

Collagen - connective tissue found in skin, tendons, ligaments and the nervous system. provide structure, strength and support in the body.

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18
Q

how does haemoglobin transport oxygen around the body?

A

oxygen binds to the iron (Fe^2+) in the haem (prosthetic group), haemoglobin has 4 haem groups therefore, 4 oxygens can bind

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19
Q

describe what type of protein haemoglobin is and its structure?

A

globular protein
4 poly-peptide chains - 2 alpha helix, 2 beta pleated sheet
haem/ prosthetic groups imbedded in sub-units

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20
Q

why is haemoglobin water soluble?

A

the hydrophilic amino acids are on the outside of the structure so interact with water

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21
Q

describe the type of and structure of COLLAGEN

A

structural protein
-fibrous protein made up of 3 polypeptide chains (like a rope)
-provides mechanical strength
-each chain is 1000’s of amino acids
hydrogen bonds form between the chains, increasing strength

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22
Q

why is collagen so strong?

A

each collagen molecule forms covalent bonds (cross links) with collagen molecules next to it

eg. peptide chains -> fibrils -> many fibrils = collagen fibres

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23
Q

state and describe the 5 functions of collagen

A

walls of arteries - prevents walls from bursting under high pressure

tendons from skeletal muscle to bones - strong connection, allowing muscles to pull bones for movement

bones - spongy layer in the middle, reinforced with materials such as calcium phosphate to make them hard

cartilage & connective tissue - made of collagen

cosmetic treatments - used to inject into lips to make them “fuller”

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24
Q

what are the differences between globular and fibrous proteins?

A

GLOBULAR FIBROUS
quaternary& tertiary secondary
spherical/ globular shape long parallel chains
soluble insoluble
can have prosthetic group no prosthetic group
blood, tissue fluid etc structural
eg. haemoglobin & insulin eg. collagen

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25
Q

how does temperature affect enzyme activity

A

increasing temp increases kinetic energy so more collisions with substrate - higher activity

too high temp - bonds holding protein together vibrate until they break, denaturing enzyme as no longer fits substrate

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26
Q

define temperature coefficient

A

measure of how much the rate of reaction increases with a 10degrees rise in temperature

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27
Q

what are the optimum temperatures of enzymes in…
1. human body
2. thermophilic bacteria
3. psychrophilic organisms (arctic regions)

A
  1. around 40 degrees
  2. around 70 degrees
  3. below 5 degrees
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28
Q

how do enzymes adapt to extreme high and low temperatures

A

enzymes adapted to cold have more FLEXIBLE structures
thermophiles adapted to extreme heat have more enzymes due to increased number of bonds in tertiary structure

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29
Q

how can pH affect enzyme activity

A

when the pH changes from the optimum, the structure of the enzyme changes

however, if the pH returns to optimum then protein can resume its shape and catalyse again - RENATURATION

significant pH change causes irreversibly altered structure - DENATURED

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30
Q

what are enzyme inhibitors?

A

molecules that prevent enzymes from carrying out their function of catalysing reactions, or slow them down

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31
Q

what are the two types of enzyme inhibitors?

A

competitive and non-competitive

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32
Q

how do competitive enzyme inhibitors work?

A
  • molecule with a similar shape to substrate fits into active site of enzyme
  • blocking substrate from entering active site, enzyme cannot carry out function

substrate and inhibitors COMPETE to bind to enzyme active site

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33
Q

define degree of inhibition

A

how much the enzymes are inhibited depends on the concentration of the substrate, inhibitors and enzymes

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34
Q

how do non-competitive enzyme inhibitors work?

A
  • inhibitor binds to location on enzyme other than active site, allosteric site
  • binding causes tertiary structure to change, changing the active site
  • enzyme no longer has complimentary shape to substrate
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35
Q

what is end product inhibition

A

when the product of a reaction acts as an inhibitor to the enzyme that produces it - negative feedback control mechanism

36
Q

outline the function of enzyme inhibitors in respiration?
is it competitive or non-competitive?

A
  • when ATP is high, more ATP binds to the allosteric site on PFK, preventing addition of second phosphate group to glucose - glucose not broken down, ATP not produced
  • when ATP is low, less binds to PFK, enzyme is able to catalyse addition of 2nd phosphate group, respiration resumes, producing more ATP

non-competitive

37
Q

what are catabolic and anabolic reactions?

A

catabolic - breaking down reactions

anabolic - building up reactions

38
Q

what is the main difference between cofactors and coenzymes?

A

cofactors are inorganic ions ( include prosthetic groups) - don’t have to be bound to the enzyme to work
coenzymes are organic compounds - bind to active site

39
Q

what is the main function of cofactors?

A

the inorganic ions gather around the enzyme, changing the charge of the active site to attract the substrate

40
Q

what are prosthetic groups?
how can they be removed?
give an example

A

a type of cofactor that is permanently bound to the enzyme
can only be removed by denaturing the enzyme
example = haem groups (Fe2+) in haemoglobin

41
Q

what is the function of coenzymes

A

assist biological transformations by serving as carriers to enzymes. bind temporarily to the active site

42
Q

what is an inactive precursor protein called and what is an active precursor protein called?
how are they activated?

A

inactive = apoenzyme
active = haloenzyme
activated by a cofactor which can cause a change in tertiary structure making it complimentary to the substrate

43
Q

how are coenzymes bound to the enzyme and what do they do?

A

loosely bound to active site.
assist biological transformations.
serve as carriers to enzymes.

44
Q

how are prosthetic groups bonded to the enzyme and what do they do?

A

covalently bonded to enzymes.
increase rate of catalysis.
aid the function of a relative enzyme

45
Q

what is precursor activation

A

many enzymes are produced in an inactive form, cofactors are added to change the shape and activate the enzyme

46
Q

what are enzymes called before and after cofactors are added?

A

before = apoenzyme
after = holoenzyme

47
Q

what is the series of successive enzyme activations in blood clotting called?

A

coagulation cascade

48
Q

what are enzymes?
what type of organic molecule are they?

A

biological catalysts, globular proteins that interact with substrate molecules to speed up reactions/ lower the activation energy

49
Q

why does metabolism rely on enzymes

A

metabolism is the sum of all the chemical reactions and reaction pathways in a cell or organism
- this can only happen due to the control and order imposed by enzymes

50
Q

what is Vmax

A

the maximum initial velocity or rate of the enzyme-catalysed reaction

51
Q

how does the lock and key hypothesis and the induced fit hypothesis differ?

A

lock and key suggests enzymes have a rigid active site specific to the substrate that is unchangeable unless enzyme denatures

induced fit suggests that the active site changes slightly as substrate enters. Weak interactions between enzyme and substrate induce changes to tertiary structure of the enzyme - strengthening the binding

52
Q

what type of enzymes are digestive enzymes?
why?

A

extracellular - they are released from cells to break down the molecules, rather than working within the cell

53
Q

how does digestion in multicellular organisms differ to single-celled organisms

A

single celled = enzymes released into immediate environment, the small molecules produced are then absorbed into the blood stream

multi-cellular = eat food for nutrients, enzymes released from cells into the body to break down large molecules. useful molecules absorbed into the blood stream

54
Q

how is starch digested in the body?

A

-begins in the mouth, continues to the small intestine
step 1 - amylase partially breaks down starch into maltose (disaccharide),
amylase produced in salivary glands and pancreas
step 2 - maltose broken down into glucose (monosaccharide) by the enzyme MALTASE - present in small intestine

55
Q

how are proteins digested in the body?

A

trypsin is a PROTEASE - a type of enzyme that catalyses digestion of proteins into smaller peptides
smaller peptides are broken down into amino acids by other proteases

56
Q

how is haemoglobin structured for its function?

A

contains a prosthetic haem group (Fe2+ ions) bind to oxygen, allow transport of oxygen

57
Q

how do disulfide bridges form?

A

when 2 cysteine amino acid molecules are close together and their sulfur atoms bond

58
Q

define biological catalyst

A

substances found in living organisms that speed up chemical reactions without being used up themselves

59
Q

what is an example of an intracellular enzyme
what does it catalyse the breaking down of

A

catalase
speeds up hydrolysis of hydrogen peroxide (which is toxic)

60
Q

what are 2 examples of extracellular enzymes and what do they break down

A

amylase - starch to glucose
trypsin - polypeptides to amino acid monomers

61
Q

define temperature coefficient (Q10)
how do you work it out?

A

shows how much the rate of reaction increases for every 10degrees increase in temperature

Q(10) = rate at higher temp/ rate at lower temp

62
Q

what are the optimum pHs of
a. pepsin
b. catalase
c. most human enzymes

A

a. pepsin = 2
b. catalase = 9
c. most human enzymes = 7/ neutral

63
Q

what is the positive result for when catalase breaks down hydrogen peroxide (dependent variable)

A

volume of oxygen gas produced

64
Q

what is an example of a hyperthermophilic bacterium
what is the enzyme for that bacterium

A

Thermus Aquaticus
T.A.C. polymerase

65
Q

what is a potential problem of using a liquid as a source of enzyme in an experiment
how can you minimise this problem?

A

different samples have different concentrations of the enzyme

thorough mixing of solution before use

66
Q

why are some foods preserved in vinegar?

A

vinegar has a low pH (acidic) so the enzymes denature and the microorganisms don’t spoil the food

67
Q

why is rate of an enzyme controlled reaction always fastest at the very start of a reaction?

A

that is when the concentration of substrates is highest, therefore more enzyme substrate complexes can be formed

68
Q

what are the two ions you need to know and what do they do?

A

Chloride (Cl-) and Calcium (Ca2+)
they act as cofactors, their presence changes the charge of the active site, attracting the substrate towards the active site.

69
Q

what are 3 differences in the PROPERTIES of globular and fibrous proteins

A

fibrous are:
strong
insoluble
unreactive

70
Q

are insulin and haemoglobin globular proteins that can change shape?

A

haemoglobin can change shape but insulin has a specific fixed shape

71
Q

why does having a more flexible structure help enzymes work faster at lower temperatures

A

easier / increased chance of substrate entering enzyme
more bonds form in enzyme, greater surface area for contact
easier for enzyme to be induced by substrate (induced fit)

72
Q

Name 3 metabolic poisons, are they competitive or non-competitive?
and what they bind to
And what reaction do they all prevent

A

Cyanide - non-competitive - binds to cytochrome-C-oxidase
Malonate - competitive - binds to succinate dehydrogenase
Arsenic - non-competitive - binds to pyruvate dehydrogenase

All inhibit respiration - causing cells to die

73
Q

What bonds are in reversible and non-reversible enzyme inhibition

A

Reversible - weak hydrogen or weak ionic bonds (easily removed)

Non-reversible - strong covalent bonds
(not easily removed)

74
Q

Explain the method of enzyme inhibition that is used to protect cells that synthesise potentially damaging enzymes

A

Enzymes sometimes synthesised as “inactive precursors”
Part of the precursor molecule inhibits its action as an enzyme
Once this part is removed, enzyme becomes active

75
Q

Describe the structure of insulin

A

Soluble - transported in the blood
Made of 2 polypeptide chains - held together by disulfide bridges
When in pancrease, 6 molecules bind together to form quaternary, globular structure
surrounding 2 zinc ions (prosthetic groups)

76
Q

when starch and amylase are mixed in iodine, the blue-black colour rapidly disappears. this is due to the formation of what molecule?

A

maltose - iodine does not stain maltose

77
Q

what enzyme group catalyses oxidation reactions?

A

dehydrogenases - catalyse reactions where hydrogen is removed by another molecule being oxidised

78
Q

which property of enzymes is responsible for its specificity?

A

the surface configuration of enzymes - active site

79
Q

what is the approximate temperature coefficient (Q10) of a enzyme controlled reaction?

A

2 - rate doubles as their temp increases by 10degrees

80
Q

what enzyme catalyses the hydrolysis of a triglyceride –> a glycerol + 3 fatty acids

A

hydrolases - adds a water molecule

81
Q

is trypsin an extracellular or intracellular enzyme?

A

extracellular - digestive enzyme secreted by the pancreas

82
Q

out of:
1. a high temp
2. an extreme pH
3. heavy metal ions
4. a low temp
which are LEAST likely to denature an enzyme?

A

a low temperature - slow down the rate of activity but unlikely to denature

83
Q

what type of enzyme catalyses the conversion of a dipeptide into two separate amino acids?

A

hydrolase

84
Q

when an enzyme denatures due to high temperatures, which bonds are first to be disrupted?

A

hydrogen

85
Q

At which levels of protein structure do hydrophobic and philic interactions occur

A

Tertiary

86
Q

What causes the gradient of a graph of maximum intracellular concentration against external concentration to plateau

A

All the active transport carriers had been operating at their maximum rate

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