3.1.4 proteins Flashcards

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1
Q

what are amino acids?

A

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

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2
Q

structure of an amino acid

A

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

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3
Q

describe a proteins function

A

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

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4
Q

what are proteins?

A

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)

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5
Q

describe a basic molecule of amino acids

A

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

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6
Q

what is a carboxylic amino acid?

A

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

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7
Q

describe an alanine protein

A

alanine = posses a CH3 group as its R group

posses a acidic and base group

amino acid is a neutral molecule

diagram on notes

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8
Q

what do simple amino acids possess?

A

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

amino acid = glyciene

diagram on notes

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9
Q

what are individual amino acids?

A

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

diagram on notes

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10
Q

describe a protein structure

A

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

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11
Q

describe the formation of a dipeptide

A

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

to form a peptide bond

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12
Q

what are dipeptides?

A

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

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13
Q

describe the quaternary structure of proteins

A

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

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14
Q

describe the tertiary structure of proteins

A

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
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15
Q

describe the secondary structure of proteins

A

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

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16
Q

describe the primary structure of proteins

A

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

17
Q

what are globular proteins?

A

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

18
Q

what are fibrous proteins?

A

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

19
Q

what is a calibration curve?

A

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

20
Q

how would you conduct a biuret test?

A
  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)
21
Q

what is the structure of haemoglobin?

A

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

22
Q

what does a HAEM group contain?

A

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

23
Q

describe the function of haemoglobin

A

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

24
Q

what is the structure and function of enzymes?

A

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

25
Q

how to enzymes catalyse reactions?

A

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

26
Q

what is the structure of enzymes?

A

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

27
Q

describe the induced fit model of enzyme action

A

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

28
Q

how do you measure enzyme catalysed reactions?

A
  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
29
Q

list factors affecting the rate of enzyme action

A

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

30
Q

what is the relationship between temperature and enzymes?

A

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

31
Q

what is the relationship between pH and enzymes?

A

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

32
Q

what happens to the enzyme with a low substrate conc?

A

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

33
Q

what happens to the enzyme with a intermediate substrate conc?

A

all the active sites are occupied at one time

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

34
Q

what happens to the enzyme with a high substrate conc?

A

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

no increase in rate of reaction

35
Q

what is the maximum rate of reaction known as?

A

Vmax

36
Q

name the type of peptidase that will hydrolyse polypeptide bonds

A

endopeptidase