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biology module 2 > biological molecules - amino acids, proteins and enzymes > Flashcards

biological molecules - amino acids, proteins and enzymes Flashcards

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1
Q

how many types of amino acids are there

A

20 common types

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2
Q

what is the structure of an amino acid

A

NH2 - CHR - COOH

NH2 = amine group
COOH = carboxylic acid group
R - variable group

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3
Q

what is the R group on an amino acid

A

the variable group

this is what determines the characteristics of an amino acid

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4
Q

amino acids are amphoteric - what does this mean and why is this the case

A

amphoteric - molecules which can act as both an acid and a base in water

NH2 can act as a base as it can accept a proton
COOH can act as an acid as it can donate a proton

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5
Q

what type of bonds do amino acids form

A

peptide bonds
- CO - NH -
formed in condensation reactions
broken by hydrolysis reactions

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6
Q

where do we get amino acids

A

diet - protein

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7
Q

how do we extract amino acids from protein

A
  • amino acids are extracted by enzymes in the intestine
  • they absorb into blood through gut wall
  • then they travel through tissue fluid and into cells, where they can be used for protein synthesis in ribosomes
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8
Q

what is the NH2 end of a polypeptide chain called

A

N-terminus

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9
Q

what is the COOH end of a polypeptide chain called

A

C-terminus

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10
Q

what are the monomer units of protein

A

amino acids

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11
Q

outline the structural levels in protein molecules

A
  • primary - the amino acid sequence
  • secondary - they way the primary structure folds, a-helix or b-pleated sheets, these are held together by hydrogen bonds
  • tertiary - the way secondary structure folds, due to interactions between R groups, e.g. ionic bonds, disulphide bridges, hydrogen bonds, hydrophobic/philic interactions
  • quarternary - optional, refers to the modifications to already folded proteins, such as the addition of side chains or prosthetic groups by the golgi body
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12
Q

what is a prosthetic group

A

an inorganic non-protein component of a conjugated protein

these are permanently attached to the protein/enzyme

they increase enzyme functionality

e.g. Fe2+ in haemoglobin
Zn2+ in carbonic anhydrase

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13
Q

what is a cofactor

A

an inorganic molecule or ion that binds to an area of an enzyme to increase functionality by changing shape or charge of enzyme

e.g. Cl- for amylase

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14
Q

what is a coenzyme

A

an organic non-protein component, which is able to bind to the enzyme for a short period of time and changes the shape of the active site, allowing substrate to bind - often binds directly to active site

this increases enzyme functionality

e.g. coenzyme A, FAD, NAD

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15
Q

2 types of protein

A

globular and fibrous

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16
Q

what is the structure of globular proteins

A

round spherical shapes

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17
Q

what are the properties of globular proteins

A

water soluble - due to arrangement of hydrophobic/hydrophilic R groups
compact

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18
Q

what are 5 functions of globular proteins

A
  • peptide hormones - as soluble in blood, e.g. glucagon, adrenaline and insulin
  • haemoglobin - as soluble in blood
  • enzymes e.g. amylase in starch breakdown
  • antibodies
  • carrier/channel proteins
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19
Q

what is the structure of fibrous proteins

A

linearly shapes, like rods

20
Q

what are the properties of fibrous proteins

A

insoluble in water
very strong

21
Q

what are 3 functions of fibrous proteins

A
  • formation of barriers and fibres - due to high strength, e.g. collagen in skin
  • protection e.g. keratin in hair and nails
  • provides elasticity e.g. elastin in blood vessel walls
22
Q

what are conjugated proteins

A

proteins with a non-protein prosthetic group

23
Q

what is an example of a conjugated protein and its prosthetic group

A

haemoglobin, prosthetic group is iron - this forms the haem group which can reversibly bind with O2 molecules

24
Q

one amino acid is cysteine
- what molecule is found in its R group
- what protein is it commonly found in
- what types of bonds are forms by this R group
- how does this affect properties of the protein

A
  • sulfur
  • found in keratin, a fibrous protein
  • disulphide bonding
  • this makes keratin strong and inflexible
25
Q

one amino acid is glycine
- what molecule makes up its R group
- what protein is it commonly found in
- how does this affect the properties of this protein

A
  • a single H group
  • every 3rd amino acid in collagen, a fibrous protein
  • it is the smallest amino acid so the protein can pack together tightly
26
Q

what are proteins

A

complex macromolecules made of one or more polypeptide chains

27
Q

outline the process of protein synthesis

A
  • transcription of DNA into mRNA takes place in the nucleolus
  • mRNA travels to ribosomes on RER where DNA code is translated by tRNA molecules
  • tRNA reads base triplet codons and builds up polypeptide chain with amino acids
  • polypeptide chain moves through the RER where is gets folded into proteins
  • proteins get packaged into vesicles and travel to golgi body
  • proteins are modified by golgi body and packaged into secretory vesicles UNLESS protein is a hydrolytic enzyme, in which case it will be packaged into a lysosome and it doesn’t leave the cell, floats around until needed
28
Q

what is the model used to describe enzyme action

A

induced fit hypothesis

29
Q

outline the induced fit hypothesis

A

this model suggests that when an enzyme binds to a substrate, the enzyme undergoes a conformational change for a tighter fit
this helps it selectively bind and catalyse reactions with specific substrates, thus increasing reaction rate

30
Q

what is formed when an enzyme binds to a substrate

A

enzyme-substrate complex

31
Q

what are the 3 types of enzyme inhibition

A

competitive , non-competitive , end product

32
Q

what is competitive inhibition

A

inhibitor competes with the substrate for the active site and blocks it so the enzyme cannot be used

this means the inhibitor has a similar shape to the substrate

decreases number of successful collisions, so decreases number of enzyme substrate complexes formed, so decreases reaction rate

33
Q

how can competitive inhibition be overcome?

A

by increasing substrate concentration

34
Q

what is non-competitive inhibition

A

inhibitor binds to another area of the enzyme - allosteric site - which changes the tertiary structure, therefore changing shape so active site is deformed and enzyme cannot bind to substrate

decreases number of successful collisions, so decreases number of enzyme substrate complexes formed, so decreases reaction rate

35
Q

can non-competitive inhibition be overcome by increasing concentration

A

no

36
Q

what is end product inhibition

A

the end product of a reaction or chain of reactions acts as an inhibitor by binding to starting enzymes and preventing the reaction from continuing

this is a control mechanism for reactions to ensure no excess products are made or wasted

an example of a reaction where this occurs is during the formation of ATP

this is an example of negative feedback

37
Q

what allows a substrate to bind to an active site

A

complementary shapes or opposite charges to active site

38
Q

how does a change in pH alter the rate of an enzyme catalysed reaction

A

electric charges of both the enzyme and substrate are neutralised by the presence of + or - ions
therefore no enzyme-substrate complexes can be formed

39
Q

why are heavy metals such as lead poisonous

A

they have such strong affinities for -SH groups and so they destroy catalytic activity

40
Q

how is enzyme inhibition used to our advantage in industry

A

it can be used to control disease
e.g. penicillin inhibits enzymes that some pathogens use in order to survive

41
Q

what are the 2 types of enzymes

A
  • intracellular e.g. catalase, others in human body
  • extracellular e.g. digestive enzymes secreted by fungi
42
Q

what 4 factors affect the rate of an enzyme controlled reaction

A
  • temperature
  • pH
  • enzyme concentration
  • substrate concentration
43
Q

effects of pH on enzymes

A

enzymes denature at extreme pH
H+ ions that cause acidity affect interactions between polar and charged are groups therefore altering tertiary structure

44
Q

effects of temperature on enzymes

A

at low temps, there is less kinetic energy so less movement of molecules, so less enzyme substrate complexes formed therefore a lower reaction rate

at high temps, the peptide bonds that hold enzymes together begin to denature, changing the shape of the enzyme and causing the active site to be deformed, so no more enzyme-substrate complexes can be formed therefore a lower reaction rate

45
Q

how does enzyme or substrate concentration affect enzymes

A

as concentration increases, rate of reaction increases

both factors are limited by the other, e.g. at high substrate conc reaction rate is still limited by lower enzyme conc. and vice versa

biology module 2 (10 decks)

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