biological molecules - amino acids, proteins and enzymes

Question 1

how many types of amino acids are there

Answer 1

20 common types

Question 2

what is the structure of an amino acid

Answer 2

NH2 - CHR - COOH

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

Question 3

what is the R group on an amino acid

Answer 3

the variable group

this is what determines the characteristics of an amino acid

Question 4

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

Answer 4

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

Question 5

what type of bonds do amino acids form

Answer 5

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

Question 6

where do we get amino acids

Answer 6

diet - protein

Question 7

how do we extract amino acids from protein

Answer 7

• 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

Question 8

what is the NH2 end of a polypeptide chain called

Answer 8

N-terminus

Question 9

what is the COOH end of a polypeptide chain called

Answer 9

C-terminus

Question 10

what are the monomer units of protein

Answer 10

amino acids

Question 11

outline the structural levels in protein molecules

Answer 11

• 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

Question 12

what is a prosthetic group

Answer 12

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

Question 13

what is a cofactor

Answer 13

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

Question 14

what is a coenzyme

Answer 14

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

Question 15

2 types of protein

Answer 15

globular and fibrous

Question 16

what is the structure of globular proteins

Answer 16

round spherical shapes

Question 17

what are the properties of globular proteins

Answer 17

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

Question 18

what are 5 functions of globular proteins

Answer 18

• 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

Question 19

what is the structure of fibrous proteins

Answer 19

linearly shapes, like rods

Question 20

what are the properties of fibrous proteins

Answer 20

insoluble in water
very strong

Question 21

what are 3 functions of fibrous proteins

Answer 21

• 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

Question 22

what are conjugated proteins

Answer 22

proteins with a non-protein prosthetic group

Question 23

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

Answer 23

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

Question 24

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

Answer 24

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

Question 25

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

Answer 25

- 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

Question 26

what are proteins

Answer 26

complex macromolecules made of one or more polypeptide chains

Question 27

outline the process of protein synthesis

Answer 27

- 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

Question 28

what is the model used to describe enzyme action

Answer 28

induced fit hypothesis

Question 29

outline the induced fit hypothesis

Answer 29

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

Question 30

what is formed when an enzyme binds to a substrate

Answer 30

enzyme-substrate complex

Question 31

what are the 3 types of enzyme inhibition

Answer 31

competitive , non-competitive , end product

Question 32

what is competitive inhibition

Answer 32

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

Question 33

how can competitive inhibition be overcome?

Answer 33

by increasing substrate concentration

Question 34

what is non-competitive inhibition

Answer 34

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

Question 35

can non-competitive inhibition be overcome by increasing concentration

Answer 35

no

Question 36

what is end product inhibition

Answer 36

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

Question 37

what allows a substrate to bind to an active site

Answer 37

complementary shapes or opposite charges to active site

Question 38

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

Answer 38

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

Question 39

why are heavy metals such as lead poisonous

Answer 39

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

Question 40

how is enzyme inhibition used to our advantage in industry

Answer 40

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

Question 41

what are the 2 types of enzymes

Answer 41

- intracellular e.g. catalase, others in human body - extracellular e.g. digestive enzymes secreted by fungi

Question 42

what 4 factors affect the rate of an enzyme controlled reaction

Answer 42

- temperature - pH - enzyme concentration - substrate concentration

Question 43

effects of pH on enzymes

Answer 43

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

Question 44

effects of temperature on enzymes

Answer 44

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

Question 45

how does enzyme or substrate concentration affect enzymes

Answer 45

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