3.1.4 proteins

Question 1

what are amino acids?

Answer 1

proteins are huge three dimensional molecules

building blocks of monomers are the 20different amino acids found in nature

these amino acids combine to form a polymer called a polypeptide

Question 2

structure of an amino acid

Answer 2

amino group (-NH2) = basic group from which the amino name is formed

carboxyl group (-COOH)

hydrogen atom

R side = each amino acid has a different R group

Question 3

describe a proteins function

Answer 3

type of protein, function, example
structural, support, collagen, keratin
transport, transport, haemoglobin
hormonal, coordination, insulin
receptor, chemical stimuli, CD4
contractile, movement, actin, mysin
enzymatic, action of chemical response, digestive enzymes
defensive, protection against defensive, anitbodies

Question 4

what are proteins?

Answer 4

polymers of amino acids are called polypeptides

a protein consists of one or more foiled and coiled polypeptides

conformation: thousands of different kinds of protein, each with a unique 3D structure

proteins always contain = nitrogen, hydrogen, oxygen
(sulfur and phosphorous are sometimes present)

Question 5

describe a basic molecule of amino acids

Answer 5

amino acid has an amino (basic) group in the R group

2 basic groups and 1 acidic group

amino acid = basic molecule

diagram on notes

Question 6

what is a carboxylic amino acid?

Answer 6

amino acid has a carboxylic acid group in its R group

2 acid groups and 1 base group

amino acid = acidic molecule

diagram on notes

Question 7

describe an alanine protein

Answer 7

alanine = posses a CH3 group as its R group

posses a acidic and base group

amino acid is a neutral molecule

diagram on notes

Question 8

what do simple amino acids possess?

Answer 8

simplest of amino acids = posses a hydrogen atom for its R group

amino acid = glyciene

diagram on notes

Question 9

what are individual amino acids?

Answer 9

individual amino acids display a terrahedral shape due to the angle of bonds between the atoms

diagram on notes

Question 10

describe a protein structure

Answer 10

protein is more or one polypeptides, precisely twisted and coiled into a molecule of unique shape

proteins must be globular (roughly spherical) or fibrous (rope like)

non protein elements may be incorparated into protein structure = prosthetic groups eg haemoglobin contains iron

4 levels of protein structure are frequently cleted with respect to protein structure

Question 11

describe the formation of a dipeptide

Answer 11

hydroxyl group is lost from one’s carboxylic group and H from the others amino acid

to form a peptide bond

Question 12

what are dipeptides?

Answer 12

two linked amino acids = dipeptide

joined by peptide bonds (covalent bond)

any number of extra amino acids can be added by further condensation reactions

molecule of many amino acids = polypeptides (polymer and macromolecule)
happes in a process called polymerisation

Question 13

describe the quaternary structure of proteins

Answer 13

secondary and tertiary structure are all still single polypeptides

quarternary structure is the way in which 2 polypeptides may join together to form larger proteins

held by the same 3 bonds in tertiary structure: hydrogen, ionic and disulphide bridges

Question 14

describe the tertiary structure of proteins

Answer 14

secondary structure can be twisted and folded even more to give a complex precise 3D structure

held in shape by bonds between amino acids side groups in different parts of the chain

1. hydrogen bonds = can form between a range of R groups. numerous but easily broken
2. disulphide bonds = between two cysteine residues. strong covalent bonds, not easily broken
3. ionic bonds = between R groups that have amino acids and carboxyl groups
   weaker than disulphide bonds, easily broken by changes in pH

Question 15

describe the secondary structure of proteins

Answer 15

polypeptide chains often coil or fold in a regular pattern to make 3D shapes

often coil into a shape called an ALPHA HELIX, this is due to the attraction between the oxygen on the -CO group on one aa and the -NH on a 4 places ahead

hydrogen bonding

sections of alpha helix can be linked to areas of polypeptide chain with no regular arrangements

Question 16

describe the primary structure of proteins

Answer 16

sequence of a chain of amino acids as a result of their covalent bonds

huge number of possible primary structure

just one change in the amino acids sequence may lead to a completely different property for protein
can lead to a change in shape and prevent the function

Question 17

what are globular proteins?

Answer 17

proteins that curl into a ball eg haemoglobin

found in all cells, tissue fluid, and fluids being transported

all these environments contain water

globular proteins curl up so that non-polar hydrophobic R groups part in the centre AWAY FROM THE WATER

soluable = water molecules cluster

Question 18

what are fibrous proteins?

Answer 18

have a primary structure of regular, repetitive sequences eg collagen

predominant secondary structure > tertiary structure being less important

form large fibrous sheets or fibres, which are stable, tough and generally insoluable in water

STRUCTURAL PROTEINS

collagen molecules are made up of three polypeptide chains wound into a helix
each fibre contains numerous collagen molecules

Question 19

what is a calibration curve?

Answer 19

use a colourimeter to determine the absorbance of known concentrations of proteins

with this information, a graph can be drawn that can hel you to work out the concentration of a unknown protein

Question 20

how would you conduct a biuret test?

Answer 20

1. sample solution in a test tube and add an equal volume of sodium hydroxide at room temperature
2. add a few drops of dilute copper II sulphate solution and mix gently
3. a purple colouration indicates the prescence of peptide bonds (a protein)

Question 21

what is the structure of haemoglobin?

Answer 21

oxygen carrying protein found in red blood cells

made up of 4 polypeptide chains

two are identical alpha chains and the other two are identical beta chains

nearly spherical molecule - interactions between R group hold it’s shape

Question 22

what does a HAEM group contain?

Answer 22

each polypeptide chain contains a HAEM group

permanent part of the molecule = prosthetic group

contains a iron ion -Fe2+

an a oxygen molecule can bind with each iron ion

Question 23

describe the function of haemoglobin

Answer 23

complete haemoglobin molecule has four haem groups that can carry four oxygen molecules at a time

HAEM group is responsible for the colour

colour change is dependant on iron ions being combined with oxygen

oxyhaemoglobin is bright red

Question 24

what is the structure and function of enzymes?

Answer 24

enzymes are globular proteins

found in tissues, bodily fluid and blood

specific tertiary structure so each enzyme has its own unique shape

catalysts and speed up chemical reactions without a permanent change

can be used repeatedly in small amounts

Question 25

how to enzymes catalyse reactions?

Answer 25

each reaction has an activation energy, which must be overcome before a reaction can proceed

enzymes lower activation energy
allows metabolic reactions to occur at certain temperatures

Question 26

what is the structure of enzymes?

Answer 26

active site forms a depression in the much larger enzyme molecule

substrate is held within the active site that form briefly with R groups of active site amino acids

enzyme-substrate complex = combination of enzyme and substrate

substrate is complimentary in shape to active site

Question 27

describe the induced fit model of enzyme action

Answer 27

functional active sites found when substrate binds to the enzyme

shape of the active site is flexible and moulds itself around the substance

puts a strain on bonds in the substrate, which lowers activation energy needed to break bonds

Question 28

how do you measure enzyme catalysed reactions?

Answer 28

1. formation of product over time (sketch and explain graph)
2. disappearance of substrate over time (sketch and explain graph)
   initial rate of reaction is determined and used as an indicator of the rate of an enzyme catalysed reaction

Question 29

list factors affecting the rate of enzyme action

Answer 29

temperature
pH
substrate concentration
inhibitors (competitors and non-competitors)
enzyme concentration

Question 30

what is the relationship between temperature and enzymes?

Answer 30

increasing the temperature increases the kinetic energy of the substrate and enzyme molecules
collide more frequently and with more energy making an enzyme-substrate complex and effective collisions are more frequent

above a certain high temp, structure of enzyme vibrates to such a degree that hydrogen bonds start to break
enzymes active site starts to lose shape
rate of reaction decreases
active site is no longer complimentary

if temp continues the enzyme denatures

Question 31

what is the relationship between pH and enzymes?

Answer 31

enzymes have an optimum pH of 7
low pH = high H+ concentration

if pH is to far from optimum, the change in the concentration of these ions affect the bonds between aa chains, breaking hydrogen and ionic bonds that maintain the tertiary structure of the enzyme and the enzyme is denatured

Question 32

what happens to the enzyme with a low substrate conc?

Answer 32

too few substrate molecules to occupy all available sites

rate of reaction is therefore only half the maximum possible for the number of enzyme molecules available

Question 33

what happens to the enzyme with a intermediate substrate conc?

Answer 33

all the active sites are occupied at one time

rate of reaction has doubled to its maximum as all active sites are filled

Question 34

what happens to the enzyme with a high substrate conc?

Answer 34

addition of further substrate molecules have no effect as all active sites are already occupied at one time

no increase in rate of reaction

Question 35

what is the maximum rate of reaction known as?

Answer 35

Vmax

Question 36

name the type of peptidase that will hydrolyse polypeptide bonds

Answer 36

endopeptidase