1.4 Proteins

general structure of an amino acid and what each represents

describe how to test for proteins in a sample

Biuret test. biuret reagenet colour change from blue to purple indicates presence of peptide bonds

which monomers make proteins

amino acids

how many amino acids are there and how do they differ from one another?

20

differ only by side R group

how do dipeptides and polypeptides form?

condensation reaction forming peptide bond between the carboxyl group of one amino acid and amine group of another. water molecule is eliminated.

dipeptide- 2 amino acids

polypeptide- many/3 or more amino acids

what does it mean by a functional protein may contain one or more polypeptide

some working proteins consist of a single chain of amino acids, others require multiple, separate polypeptide chains to assemble together to form a fully working 3D structure

how many levels of protein structure are there

4

define primary structure of a protein

sequence of amino acids in a polypeptide forming peptide bond.

determined by the sequence of codons on mRNA.

define secondary structure of a protein

hydrogen bond form between slightly negative oxygen of C=O and slightly positive H of amine group

describe 2 types of secondary protein structure

alpha helix and beta pleated sheets

define the tertiary structure of a protein and name the bond presents

3D structure formed by further folding of the polypeptide

held by disulfide bridges ionic and hydrogen bonds

describe each type of bond in the tertiary structure of proteins. name them from strongest to weakest

Disulfide bridges: strong covalent S-S bonds between molecules of amino acid- cysteine

ionic bonds: between charged R groups

Hydrogen bonds: numerous and easily broken

name the amino acid which has disulphide bridges

cysteine

Define quaternary structure of a protein

functional protein consist of more than one polypeptide chain

describe the structure and function of globular proteins give 3 examples.

enzymes, hormones and antibodies

spherical and compact

hydrophilic R groups face outwards and hydrophobic R groups face inwards= easily water soluble

involved in metabolic processes

describe the structure and function of fibrous proteins

keratin and collagen

form long chains or fibers

insoluble in water

useful for structure and support

outline how chromatography could be used to identify the amino acids in a mixture

use capillary tube to spot the mixture onto pencil origin line and place the paper in solvent

allow solvent to run until it almost touches other end of paper. Amino acids move different distances based solubility in solvent

use UV light to see spots

calculate RF values and match to database

what are enzymes

Biological catalysts that speed up rate of reaction by lowering activation energy of the reaction.

specific tertiary structure determines shape of active site which is complementary to a specific substrate

forms ES complexes.

explain the induced fir model of enzyme action

shape of active site is not directly complementary to substrate as its flexible

conformational change enables ES complex to form

puts strain on substrate bonds which lowers activation energy.

explain the lock and key model

rigid shape of active site complementary to one substrate

what does the current induced fit model suggest

explains why binding at allosteric sites can change shape of active site

how could a student identify the activation energy of a metabolic reaction from an energy level diagram

difference between free energy of substrate and peak of curve

name 5 factors that affect the rate of an enzyme controlled reaction

enzyme concentration

substrate concentration

concentration of inhibitors

pH

temperature

How does substrate concentration affect rate of reaction imagine/draw diagram

given that enzyme concentration is fixed the rate increases proportional to substrate concentration.

Rate levels off when maximum number of ES complexes form at any given time

How does enzyme concentration affect rate of reaction imagine/draw diagram

given that substrate is in excess rate increases proportionally to enzyme concentration rate levels off when maximum number of ES complexes form at any given time.

how does temperature affect rate of reaction imagine/draw diagram

rate increases as kinetic energy increases ad peaks at optimum temperature

above optimum the ionic and hydrogen bonds in tertiary structure break= active site no longer complementary to substrate- denaturation.

How does pH affect rate of reaction imagine/draw diagram

enzymes have narrow optimum pH range

outside range H/OH ions interact with H-bonds and ionic bonds holding the tertiary structure= denaturation

contrast competitive and non competitive inhibitors

competitive:

similar shape to substrate= bind to active site

do not stop reaction, ES complex forms when inhibitor is released

increasing substrate concentration deceases their effect

Non competitive:

bind at allosteric site

stop reaction as active site change shape

increase substrate concentration has no impact.

outline how to calculate rate of reaction from a graph

calculate gradient by drawing tangent

initial rate: draw tangent at t=0

outline how to calculate rate of reaction from raw data

change in concentration of product or reactant/time

why is it advantageous to calculate initial rate

represents maximum rate of reaction before concentration of reactants decreases

state formula for pH

pH= -log10[H+]