Biological molecules: Proteins

General structure of amino acid

What is an amine group

NH2

Carboxylic acid group

COOH

What is the central C atom bonded to in an amino acid

Amine group, carboxylic acid group, H atom, R group

How do amino acids differ

R group

Functional groups of an amino acid

Amine, carboxyl

What bonds are formed between amino acids

Peptide bonds

What kind of bonds are peptide bonds

Covalent

What kind of reaction forms a peptide bond

Covalent

How many water molecules are released when 2 amino acids bond together

1

Draw the formation of a peptide bond

How can peptide bonds be broken down

Hydrolysis reaction

Which groups between amino acids interact to form the peptide bond

OH of COOH; H of NH2

Examples of how can R group affect amino acids properties

Polarity; acidic/basic

What is the primary structure of a protein

Sequence of amino acids

What determines primary structure of a protein

DNA of cell

Is primary structure specific for each protein

Yes

How many amino acids are there commonly found in cells

20

What is secondary structure

Shape of the polypeptide chain due to h bonds forming between amino group and carboxyl group

What creates the secondary structure of a protein

Weak -ve nitrogen/oxygen atoms form H-bonds with weak +ve hydrogen atoms

2 shapes of secondary structure

α-helix or β-pleated sheet

Describe α-helix secondary structure

Hydrogen bonds form between every 4th peptide bond; O of hydroxyl group, H of amine group

Describe β-pleated sheet secondary structure

2 parts of polypeptide chain are parallel; H-bonds form betw parallel peptide bonds; folds into pleated sheet

What is the protein backbone and what affects it

Hydrogen bonds between amino group and carboxyl group; secondary structure

What may break the hydrogen bonds which create the secondary structure

High temperatures; pH changes

What is tertiary structure

Additional bonds formed between R groups

What kind of bonds can be formed to create tertiary structure

Hydrogen; disulphide; ionic; hydrophobic interactions

Describe H bonds in tertiary structure Vs in secondary

Secondary: between carboxyl and amine group; tertiary: between R groups

Describe disulphide bonds in tertiary structure

Strong covalent bonds between sulfur atoms of 2 cysteine amino acids

How can disulphide bonds be broken

Oxidation

Describe H bonds in tertiary structure

Form between strongly polar R-groups

Which are the strongest bonds within a protein

Disulphide bonds - help stabilise proteins

Describe ionic bonds in tertiary structure

Ionic bonds form between oppositely charged R groups

Describe hydrophobic interactions in tertiary structure

Weak hydrophobic interactions between non-polar hydrophobic R groups within interior of protein

Where is secondary structure commonly found

Most fibrous proteins

Most common tertiary structure bond

H bonds

Where is tertiary structure commonly found

Globular proteins

Are ionic bonds or H bonds stronger

Ionic

Are ionic bonds common within proteins (tertiary structure)

No

What does tertiary structure determine

(Shape and) function of protein

Why are there a vast range of protein configurations (tertiary structure)

Each amino acid has unique R group; many dif interactions can occur; therefore proteins fold differently

What is quaternary structure

How different polypeptide chains (subunits) are arranged into a larger functional macromolecule

Example of a protein with quaternary structure

Haemoglobin

What is a protein subunit

Each polypeptide chain in quaternary structure

Describe a globular protein

Compact, roughly spherical, soluble protein

Are globular proteins soluble or insoluble in water

Soluble

Why do globular proteins form a spherical shape when folding into tertiary structure

Non-polar hydrophobic R groups orientated towards centre of protein (away from aqueous surroundings); polar hydrophilic R groups orientate themselves on outside of protein

What aspect of structure is the spherical shape of a globular protein

Tertiary structure

Why are globular proteins generally soluble in water

Water molecules can surround the polar hydrophilic R groups on protein’s exterior

How does solubility of globular proteins affect function

Can easily be transported around organisms and be involved in metabolic reactions

Do globular proteins have specific shapes

Yes

Why do globular proteins have specific shapes

Folding due to interactions between R groups

How does specific shape of globular proteins affect function

Can play important physiological roles e..g catalyse specific reactions, respond to specific antigens

What is a conjugated protein

A protein containing a non-protein chemical group e.g. prosthetic group

What is a simple protein

Protein containing only amino acids

What is a prosthetic group

A permanent, non-protein part of a protein molecule

What kind of protein is haemoglobin

Globular

What is haemoglobin

Globular protein; oxygen-carrying pigment; many in RBCs

Subunits of haemoglobin

Globin proteins; 2 α-globins, 2 β-globins; each has a prosthetic haem group

Describe quaternary structure of haemoglobin

4 globin subunits; held together by disulphide bonds; hydrophobic R groups face inwards; hydrophilic outwards => 3D spherical, soluble

What is a haem group

Prosthetic group containing an Fe2+ ion

How is haemoglobin able to bind to oxygen

Fe2+ ion of haem group can reversible bind to oxygen

How many oxygen molecules can each haemoglobin carry

4 bc/ 4 subunits each w 1 haem group

Uses of haemoglobin

Binds to oxygen in lung; transport to tissue for aerobic metabolic pathways; better bc oxygen not very soluble but haemoglobin is

What kind of protein are enzymes

Globular

Use of enzymes

Biological catalyst; control metabolic pathways; catalyse basically all metabolic reactions

How does quaternary structure affect enzyme

Determines shape of active site where substrate binds

Example of extracellular enzyme

Amylase

Where is amylase secreted

Salivary glands; pancreas

Amylase function

Catalyse hydrolysis of starch

Name an intracellular enzyme

Catalase

Catalase function

Convert harmful hydrogen peroxide into water and oxygen to prevent damage

What is insulin

Globular protein; hormone

What does insulin do

Control blood glucose concentration

Insulin quaternary structure

2 polypeptide chains held together by 3 disulphide bridges

What is a fibrous protein

Long strands of polypeptide chains w cross-linkages due to hydrogen bonds

Fibrous proteins tertiary structure

Little to no tertiary structure

Fibrous proteins insoluble or soluble and why

Insoluble due to large proportion of hydrophobic R groups

3 examples of fibrous proteins

Keratin, elastin, collagen

Fibrous proteins amino acids

Limited number; usually v repetitive sequence

How do properties of fibrous proteins make them strong structurally/suitable for structural roles

Highly repetitive amino acid sequence = v organised, strong structures; insoluble

Keratin

Tough fibrous protein; hair, nails, horns, feathers

Elastin

Elastic fibrous protein; connective tissue, tendons, skin

Collagen

Fibrous protein; skin, tendons, ligaments, cartilage

Microfibrils/fibrils

Many molecules of collagen arrange in staggered formation

How does staggered formation of collagen make it strong

No weak spots

Why does collagen have great tensile strength (can be pulled a lot without stretching/breakign)

Many hydrogen bonds within triple helix structure

Test for proteins Name

Biuret test

Why are collagen molecules insoluble in water

Long molecules

Globular proteins amino acids different or same

Irregular, wide range of R groups

Key inorganic Cations involved in biological processes

Ca2+, Na+, K+, H+, NH4+ (ammonium)

Key inorganic anions involved in biological processes

NO3-, HCO3- (hydrogen carbonate), Cl-, PO43- (phosphate), OH-

Hydrogen carbonate ion formula

HCO3-

Phosphate ion formula

PO4 3-

Describe biuret test

Add biuret reagent (sodium hydroxide + copper (ii) sulfate); observe colour change on white tile

Positive result biuret test

Blue to purple

What is sodium hydroxide for in biuret reagent

Make sample alkaline; alkali and copper (ii) sulfate react in presence of peptide bonds

Limit of biuret test

Qualitative; don’t know how much protein present; if sample contains amino acids/dipeptides, result is -ve due to lack of peptide bonds