Proteins (Edexcel A Level Biology (A) SNAB): Flashcards

To carry the genetic code from the DNA in the nucleus to the ribosomes in the cytoplasm, where translation occurs.

In the 3' to 5' direction.

This means the mRNA molecule grows in the 5' to 3' direction.

Translation is the second stage of protein synthesis, in which the base sequence of mRNA is used to assemble a chain of amino acids.

In the cytoplasm, on a ribosome.

An anticodon is the triplet of unpaired bases on a tRNA molecule that pairs with a complementary codon on the mRNA.

It carries a specific amino acid to the ribosome.

Its anticodon pairs with the complementary codon on the mRNA.

A codon is a triplet of bases on the mRNA molecule that codes for one amino acid.

The start codon is AUG.

It codes for the amino acid methionine and signals the start of translation.

Two tRNA molecules bring their amino acids side by side on the ribosome.

A peptide bond forms between the amino acids in a condensation reaction.

A stop codon on the mRNA.

At this point the polypeptide chain is complete and is released.

Its anticodon has bases complementary to the mRNA codon.

The two pair up by complementary base pairing.

During translation, the anticodon of a tRNA molecule pairs with a complementary codon on the mRNA.

False.

Translation takes place in the cytoplasm, on a ribosome — it is transcription that occurs in the nucleus.

The final polypeptide (protein).

A gene is a sequence of nucleotides in DNA that codes for the production of a specific polypeptide.

Each sequence of three bases in a gene codes for one amino acid.

Each base is read only once.

No base is part of more than one codon, so adjacent codons do not overlap.

More than one codon can code for the same amino acid.

There are 64 possible codons but only 20 amino acids.

A base change may still produce a codon for the same amino acid.

So the resulting protein may be unchanged.

Almost every organism uses the same code.

The same triplet codes for the same amino acid in all living things.

A gene transferred from one species is read the same way in another.

So it produces the same protein, allowing genes to be transferred between species.

There are four bases, and each codon is three bases long.

4³ = 64 possible combinations.

Each triplet of three bases in a gene codes for one amino acid.

False.

The code is non-overlapping — each base is read only once and belongs to only one codon.

A gene determines the exact sequence of amino acids joined together during protein synthesis.

This sequence determines the protein's shape and function.

An amino acid is the monomer of proteins — there are 20 that occur in the proteins of living organisms.

A central carbon bonded to:

• An amine group (-NH₂)

• A carboxylic acid group (-COOH)

• A hydrogen atom

• An R group (variable side chain)

The R group (side chain).

It determines properties such as whether the amino acid is acidic, basic, polar or non-polar.

Twenty.

A peptide bond is the covalent bond formed between two amino acids during a condensation reaction.

A hydroxyl (-OH) is lost from the carboxylic acid group of one amino acid and a hydrogen from the amine group of another.

The carbon of the first bonds to the nitrogen of the second, releasing water.

A condensation reaction, which releases a molecule of water.

A dipeptide forms from two amino acids.

A polypeptide forms from many (three or more) amino acids.

By hydrolysis — the addition of water.

This breaks a polypeptide back down into amino acids.

A peptide bond forms by a condensation reaction, which releases a molecule of water.

False.

The peptide bond forms between the amine and carboxylic acid groups — the R group is not involved.

Examples include:

• Enzymes — biological catalysts

• Haemoglobin — transport

• Keratin or collagen — structural

Primary, secondary, tertiary and quaternary.

The primary structure is the sequence of amino acids in a polypeptide chain, joined by peptide bonds.

The DNA of the cell.

It determines the exact sequence of amino acids, which affects the protein's shape and function.

The folding of the chain into an α-helix or β-pleated sheet.

It is held together by hydrogen bonds between the amino and carboxyl groups of the backbone.

The α-helix and the β-pleated sheet.

The overall 3D shape of a polypeptide.

It forms from bonds between the R groups, and is common in globular proteins.

Between R groups:

• Hydrogen bonds

• Disulfide bonds (between cysteines)

• Ionic bonds

• Hydrophobic interactions

The arrangement of two or more polypeptide chains (subunits) working together as one functional protein, for example haemoglobin.

In secondary structure they form between the amino and carboxyl groups of the backbone.

In tertiary structure they form between the R groups.

Disulfide bonds in the tertiary structure of a protein form only between cysteine amino acids.

False.

Only proteins with more than one polypeptide chain have a quaternary structure.

The amino acid sequence determines how the protein folds.

A change can alter its 3D shape, and therefore its function.

A globular protein is a compact, roughly spherical protein, generally soluble in water, with physiological roles such as enzymes and haemoglobin.

The non-polar (hydrophobic) R groups point inwards, away from water.

The polar (hydrophilic) R groups point outwards, towards the water.

Their hydrophilic R groups face outwards.

Water molecules can surround these groups, allowing the protein to dissolve.

It allows them to be transported around the organism.

This lets them take part in metabolic reactions, such as enzymes catalysing reactions.

It is made of four polypeptide chains (subunits).

These are two α-globins and two β-globins, each with a haem group.

Each haem group contains an iron(II) ion (Fe²⁺).

This reversibly binds an oxygen molecule, forming oxyhaemoglobin.

Four — one at each of its four haem groups.

Oxygen itself is not very soluble in water.

Bound to soluble haemoglobin, oxygen can be carried efficiently around the body.

A base substitution changes one amino acid, so valine (non-polar) replaces glutamic acid (polar).

This makes the haemoglobin less soluble.

The haem group of haemoglobin contains an iron ion that binds reversibly to oxygen.

False.

Globular proteins are generally soluble because their hydrophilic R groups face outwards.

A prosthetic group is a non-protein component permanently bound to a protein, such as the haem group in haemoglobin.

A fibrous protein is a long, strand-like protein with a highly repetitive amino acid sequence, making it strong and insoluble — suited to structural roles.

They have a large number of hydrophobic R groups.

This means they do not interact well with water.

They are strong and insoluble.

Their highly repetitive sequences create very organised, stable structures.

Examples include:

• Keratin — hair, nails and horns

• Elastin — connective tissue, skin and tendons

• Collagen — skin, tendons and ligaments

Three polypeptide chains wound together into a triple helix.

They are held together by hydrogen bonds.

Glycine is the smallest amino acid, with only a hydrogen atom as its R group.

It fits on the inside of the chains, letting them wind into a tight triple helix.

Covalent cross-links form between the R groups of parallel triple helices.

Molecules with staggered ends join into fibrils, and many fibrils form fibres.

Its triple helix contains many hydrogen bonds, and covalent cross-links join the molecules.

The staggered ends of molecules within fibrils add further strength.

It has a high proportion of proline and hydroxyproline.

The R groups of these amino acids repel each other, adding stability.

Collagen is formed from three polypeptide chains wound together into a triple helix.

False.

Fibrous proteins have little or no tertiary structure — they are long, organised strands.

In connective tissue throughout the body.

Examples include tendons, ligaments, cartilage, bones, skin and blood vessel walls.

An enzyme is a biological catalyst — a globular protein that speeds up the rate of a reaction without being used up.

They lower the activation energy of the reaction.

They provide an alternative pathway that needs less energy.

Activation energy is the minimum energy needed by the substrate to become unstable enough for a reaction to occur.

They speed up the rate of chemical reactions.

They are not used up and undergo no permanent change, so they can be reused.

Intracellular enzymes are produced and act inside the cell.

Extracellular enzymes are secreted to act outside the cell, such as digestive enzymes.

Almost every metabolic reaction in an organism is catalysed by an enzyme.

Without them, reactions would be far too slow to sustain life.

Very high temperatures or pressures would be needed to reach the activation energy.

These conditions would kill cells, so enzymes avoid the need for them.

A globular protein with a complex tertiary structure.

Enzymes speed up reactions by lowering the activation energy needed for the reaction to occur.

False.

Enzymes are not used up — they undergo no permanent change and can be reused.

False.

Enzymes lower the activation energy, not the overall energy change of the reaction.

The enzyme destabilises the bonds in the substrate.

This makes the substrate more likely to react.

The active site is the region of an enzyme with a specific shape where the substrate binds, forming an enzyme-substrate complex.

An enzyme-substrate complex is the structure formed when a substrate binds to the active site of an enzyme.

The active site has a specific shape.

Only a substrate with a complementary shape can fit and bind to it.

The tertiary structure of the protein.

This in turn depends on the sequence of amino acids in its primary structure.

Denaturation is the change in shape of an enzyme's active site, caused by extremes of heat or pH, so the substrate can no longer bind.

The enzyme and substrate are rigid structures.

The substrate fits precisely into the active site like a key into a lock.

The active site changes shape slightly as the substrate enters.

This conformational change gives an ideal binding arrangement that maximises catalysis.

In lock-and-key the active site is rigid.

In induced fit the active site is flexible and moulds around the substrate.

The shape of the active site changes.

The substrate can no longer bind, so no enzyme-substrate complex forms and the enzyme cannot function.

The active site of an enzyme is complementary in shape to its specific substrate.

True.

The lock-and-key model was modified into the induced-fit model as molecular techniques advanced.

Only a correctly oriented collision allows the substrate to fit the active site.

Otherwise no enzyme-substrate complex forms and no reaction occurs.

Measure how fast the product is made.

Measure how fast the substrate is used up.

Draw a tangent to the curve through the origin.

Calculate the gradient of that tangent.

The rate increases linearly, provided substrate is plentiful.

More enzyme means more active sites and more enzyme-substrate complexes.

If substrate is limited, it becomes the limiting factor.

Adding more enzyme then has no further effect.

The rate increases at first, as more collisions occur between enzyme and substrate.

At the saturation point all active sites are occupied and the rate levels off.

The saturation point is the substrate concentration at which all active sites are occupied, so adding more substrate does not increase the rate.

Catalase breaks down hydrogen peroxide into water and oxygen.

The volume of oxygen collected over time is measured for different catalase concentrations.

To keep the pH constant.

This stops pH from affecting enzyme activity and confounding the results.

Iodine gives starch a blue-black colour.

A colorimeter measures how the absorbance falls over time as the starch is broken down.

pH and temperature.

Both affect enzyme activity, so they must be kept constant.

The initial rate of reaction is found by calculating the gradient of a tangent drawn through the origin.

True.

The initial rate is fastest, because substrate concentration is highest and falls as it is used up.