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Biochemistry > molecular building blocks of life > Flashcards

molecular building blocks of life Flashcards

1
Q

n terminus

A

start of protein molecule

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2
Q

zwitterion

A

core has both positive and negative parts but overall no net charge

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3
Q

asymmetric molecule

A

all 4 sites are different

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4
Q

peptide bond

A

form between amino acids creating a polypeptide chain, rigid as has a partial double bond character
covalent bond
electrons shared between bonded atoms

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5
Q

trans peptide bond

A

oxygen and hydrogen face in opposite directions

1000x more common than cis

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6
Q

cis peptide bond

A

o and h face same direction

1000x less common than trans

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7
Q

chloramphenicol (eye infection treatment)

A

prevents peptide bond formation, binds to ribosome where peptide bonds are made
resistant bacteria use enzyme CAT that stops chloramphenicol from binding to the ribosome

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8
Q

thalidomide

A
  1. good at preventing morning sickness

2. enantiomer causes leg shortness

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9
Q

enantiomer

A

pair of molecules that are a mirror image of each other

2 enantiomers can be formed around the alpha carbon

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10
Q

positively charged amino acids

A

lysine, arginine, histidine

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11
Q

negatively charged amino acids

A

aspartic acid, glutamic acid

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12
Q

carboxylates

A

side chains of negatively charged amino acids

o=c-o-

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13
Q

primary amino groups

A

side chains of positively charged amino acids

n bonded to 2H and 1H+

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14
Q

isomer

A

molecules with the same molecular formula but different arrangements
e.g. D and L form

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15
Q

glycine

A

no D or L form
flexible as small side chain
neurotransmitter

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16
Q

aromatic molecule

A

a molecule that has special properties due to a closed ring of electrons

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17
Q

cysteine

A

thiol group
can bond to other cysteines by a disulphide bond
binds to metals in proteins

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18
Q

disulfide bond

A

covalent bond that forms between side chains of cysteine residues

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19
Q

peptide backbone

A

line of rigid peptide bonds with flexible links that allow folding

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20
Q

carbonyl oxygen

A

slightly negatively charged

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21
Q

amide proton

A

slightly positively charged

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22
Q

alpha helix

A

2nd structure
not made of DNA
peptide bond provides H bonds

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23
Q

prion protein transformation

A

alpha helix is stable but exposed H bonds on beta structure cause sticky velcro ends
single atom changes can cause prion disease

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24
Q

insulin and insulin receptors

A

insulin is a small peptide that acts as a hormone and influences glucose metabolism
transported in the blood, only certain tissues respond
these tissues have insulin specific receptors in their membrane

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25
Q

insulin hexamer

A

storage molecule of 6 insulin molecules attached
found in pancreas
injected into diabetics

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26
Q

type 1 diabetes

A

insulin secreting cells destroyed by autoimmune disease

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27
Q

kinesins

A

motor proteins that provide power to move microtubules

28
Q

titin

A

longest protein known

stops muscles from stretching too far

29
Q

silk beta pleated sheet design

A

interlocking Ala and Gly residues - rigid spider silk rigid sections alternate with stretchy sections to makethem strong but elastic

30
Q

alpha keratin

A

stretchy and flexible (hair) unless there are a lot of disulfide bridges (nails)

31
Q

amino acid residue

A

amino acid once it has become part of a protein - it is a residue of the free amino acid
same side chain but its alpha amino and carboxyl groups are now part of peptide bonds

32
Q

myoglobin

A

subunit of haemoglobin

33
Q

haemoglobin structure

A

4 units of myoglobin
2 alpha and 2 beta
myoglobin binds to haem group that contains an iron ion, which binds to o2 and gives the molecule its red appearance

34
Q

myoglobin saturation

A

increased sat. at normal tissue conc.

decreased sat. when o2 supply to tissue is low

35
Q

haemoglobin saturation

A

increased sat. when in lungs

decreased sat. when in tissues

36
Q

sickle cell anaemia

A

low o2 structure polymerises Hb.

many diseases result from misfolding of proteins, some lead to unwanted polymerisation

37
Q

proteins propagating diseases

A

beta sheets can stick together

alpha helix is stable but exposed h bonds on beta structure can form sticky velcro ends

38
Q

tamiflu and relenza

A

anti influenza drugs
inhibit neuraminidase
neuraminidase removes neuramic acid residues from surface of host cells to ease virus lifecycle

39
Q

penicillin

A

binds to enzymes that make the bacterial cell wall, stops bacteria from growing

40
Q

Keq

A

equilibrium constant

ratio of product conc./reactant conc. = Eq

41
Q

gibbs free energy

A

energy associated with a chemical reaction that can do work

42
Q

transition state/intermediates

A

intermediate transition states in reactants have higher energy levels than reactants
energy is required to generate the intermediate/transition state = activation energy

43
Q

enzyme basic theory

A

enzymes = biological catalysts
enzymes form a complex with the substrate before catalysing its conversion to a product
formation of this complex leads to alternative transition state

44
Q

enzyme and Keq

A

enzymes increase the speed at which Eq is reached, NOT the concentration of products and substrates at Eq

45
Q

catalysis mechanisms

A 
proximity
orientation
strain/distortion, binding puts strain on bond making it easier for reaction to occur
acid/base catalysis
covalent catalysis
46
Q

specificity

A

only binds to CERTAIN substrates

interaction takes place at active site

47
Q

lock and key model

A

substrate has a complementary shape to the enzyme active site

48
Q

induced fit model

A

active site provides strain on the substrate to convert it into the product

49
Q

absolute specificity

A

the substrate is broken down into 2 absolute molecules

50
Q

bond specificity

A

the substrate is changed because the enzyme changes a bond within its structure

51
Q

group specificity

A

a group is added onto the molecule

52
Q

kCat

A

turnover number

number of substrate molecules that can be converted to product by 1 enzyme in 1 second

53
Q

ways of measuring enzyme activity

A

substrate disappearance
product appearance
if coloured using spectrometer

54
Q

km

A

affinity of enzyme for its substrate
stability of enzyme substrate complex
high km = low affinity
low km = high affinity

55
Q

vmax

A

fastest rate an enzyme cn catalyse a reaction

only occurs when there is an infinite supply of substrate

56
Q

types of reversible enzyme inhibitors

A

competitive
non competitive
uncompetitive

57
Q

types of irreversible enzyme inhibitors

A

bind by covalent bond
bind to a.a. side chain at active site
binding permanently inactivates a.s.
usually prevents susbtrate binding

58
Q

DFP

A

sarin
nerve gas
covalently binds to Ser residue in acetylcholinesterase
prevents breakdown of acetylcholine

59
Q

irreversible inhibitors - aspirin

A

blocks action of prostaglandin H2 synthase by transferring an acetyl group to serine 530

60
Q

penicillin

A

beta lactam antibiotic
covalently binds to Ser residue in penicillin binding protein
prevents synthesis of bacterial cell wall peptidoglycan

61
Q

penicillin as an enzyme inhibitor

A

binds to and irreversibly inhibits bacterial cell wall enzymes
covalent bond inhibits cell wall building enzymes

62
Q

bacteria becoming resistant to penicillin

A

resistant bacteria produces beta latamase

beta lactamase breaks down penicillin

63
Q

augmentin

A

contains potassium clavulanate which is a beta lactamase irreversible inhibitor

64
Q

competitive inhibitors

A

competes with substrate for active site
often has structure similar to substrate
when bound to enzyme prevents binding of substrate
can be overcome by increasing substrate until this outcompetes inhibitor

65
Q

non competitive inhibition

A 
inhibitor binds away from active site 
modifies reaction rate 
still binds substrate with same affinity
Km is unaltered
vmax decreases
66
Q

uncompetitive inhibition

A

occurs with multisubstrate reactions
km decreases
vmax decreases
binds only to ES complex

67
Q

pH reduces enzyme activity if…

A

overall 3D structure of a.s. is altered

group involved in substrate binding or catalytic event changes charge

Biochemistry (8 decks)

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