Proteins

Chemistry for Biologists

What are proteins made from?

Proteins are macromolecules made from many amino acid monomers joined together.

What elements are found in proteins?

Carbon, hydrogen, oxygen and nitrogen; some proteins also contain sulfur.

Give some functions of proteins.

Proteins form structures such as hair, skin and nails; act as enzymes and hormones; form antibodies; enable muscle contraction; and transport substances such as oxygen.

What are amino acids?

The monomers or building blocks from which proteins are made.

Approximately how many naturally occurring amino acids are used to make proteins?

About 20.

What is the general structure of an amino acid?

A central carbon atom bonded to an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom and a variable R group.

What is the amino group of an amino acid?

-NH₂.

What is the carboxyl group of an amino acid?

-COOH.

What is the R group of an amino acid?

The variable side chain that differs between amino acids.

What determines the differences between amino acids?

The structure of their R groups.

Why are R groups important in proteins?

They affect interactions between amino acids and therefore influence the folding, 3D structure and properties of the protein.

What is the R group in glycine?

A single hydrogen atom.

What is special about the R group of cysteine?

It contains sulfur and can form disulfide bonds with another cysteine.

How do two amino acids join together?

The amino group of one amino acid reacts with the carboxyl group of another in a condensation reaction.

What type of reaction joins amino acids?

A condensation reaction.

What is released when two amino acids join?

One molecule of water.

What bond forms between two amino acids?

A peptide bond.

What is a peptide bond?

A covalent bond formed by a condensation reaction between two amino acids.

What is a dipeptide?

Two amino acids joined together by a peptide bond.

What is a polypeptide?

A long chain of amino acids joined together by peptide bonds.

How is a polypeptide formed?

Many amino acids join through repeated condensation reactions, forming peptide bonds.

Approximately how many amino acids can a polypeptide contain?

From about 100 to many thousands of amino acids.

When does a polypeptide form a functional protein?

When it folds or coils into a specific 3D structure or associates with other polypeptide chains.

How can a peptide bond be broken?

By hydrolysis, which involves adding water.

What is the difference between condensation and hydrolysis in proteins?

Condensation removes water to form peptide bonds, while hydrolysis adds water to break peptide bonds.

What bonds can contribute to the 3D structure of proteins?

Hydrogen bonds, disulfide bonds and ionic bonds.

How do hydrogen bonds form in proteins?

They form through attraction between small opposite charges on groups within amino acids.

What is the role of hydrogen bonds in proteins?

They help hold polypeptide chains in their folded and coiled shapes.

Are hydrogen bonds in proteins strong or weak?

Individually they are weak, but many together help stabilise the protein.

Why can hydrogen bonds easily break?

They are relatively weak and can be disrupted by changes in temperature or pH.

What happens to hydrogen bonds after conditions return to normal?

They may reform.

How are disulfide bonds formed?

They form when two cysteine amino acids are close together and their sulfur-containing groups undergo an oxidation reaction.

What is a disulfide bond?

A strong covalent bond formed between sulfur-containing groups of two cysteine amino acids.

How do disulfide bonds compare with hydrogen bonds?

Disulfide bonds are much stronger but occur less frequently.

What is the role of disulfide bonds in proteins?

They help hold folded polypeptide chains in their correct 3D shape.

How do ionic bonds form in proteins?

They form between strongly positively and negatively charged amino acid side chains.

Where can ionic bonds occur in proteins?

They may occur deep inside protein molecules between oppositely charged R groups.

What is the primary structure of a protein?

The specific linear sequence of amino acids in a polypeptide chain.

What bonds hold together the primary structure of a protein?

Peptide bonds.

Why is the primary structure of a protein important?

The sequence of amino acids determines how the protein folds and therefore determines its final 3D structure and function.

What is the secondary structure of a protein?

The regular repeating arrangement of a polypeptide chain produced mainly by hydrogen bonding between nearby amino acids.

What are the two common types of secondary protein structure?

An α-helix and a β-pleated sheet.

What is an α-helix?

A spiral-shaped secondary structure of a polypeptide chain stabilised by hydrogen bonds.

What is a β-pleated sheet?

A folded sheet-like secondary structure stabilised by hydrogen bonds between parts of the polypeptide chain.

What bonds stabilise protein secondary structure?

Hydrogen bonds.

What is the tertiary structure of a protein?

The overall three-dimensional folding of a polypeptide chain in addition to its secondary structure.

What causes a protein to develop its tertiary structure?

Interactions between R groups, including hydrogen bonds, ionic bonds and disulfide bonds.

Which parts of amino acids interact to form tertiary structure?

The R groups.

What is the quaternary structure of a protein?

The three-dimensional arrangement of two or more polypeptide chains associated together.

Which proteins have quaternary structure?

Proteins made from two or more polypeptide chains.

Give an example of a protein with quaternary structure.

Haemoglobin.

What is denaturation?

The loss of the specific 3D shape of a protein.

What can cause protein denaturation?

Changes in conditions such as temperature or pH.

How can changes in temperature or pH denature a protein?

They disrupt bonds maintaining the protein's 3D structure, causing its shape to change.

Why can denaturation cause a protein to stop functioning?

A protein's function depends on its specific 3D shape, so changing the shape can prevent it from working correctly.

What are the two broad structural groups of proteins?

Fibrous proteins and globular proteins.

What are fibrous proteins?

Proteins consisting of long, parallel polypeptide chains with occasional cross-links that form strong fibres.

What is the general shape of fibrous proteins?

Long and fibre-like rather than compact and spherical.

Do fibrous proteins usually have extensive tertiary structure?

No, they usually have little or no tertiary structure.

What are the properties of fibrous proteins?

They are strong, tough, insoluble in water and relatively stable.

Why are fibrous proteins suited to structural functions?

Their long parallel chains and cross-links produce strong, tough fibres.

Give examples of fibrous proteins.

Collagen, keratin and proteins found in spider silk.

What is collagen?

A strong fibrous protein with a triple-helix structure.

Where is collagen found?

Tendons, ligaments, bones and skin.

What is the function of collagen?

It provides strength and structural support to tissues.

Approximately how much of the protein in the human body is collagen?

Up to about 35%.

Why is collagen extremely strong?

Three polypeptide chains form a triple helix held together by many hydrogen bonds.

How many polypeptide chains form a collagen molecule?

Three.

Approximately how long is each collagen polypeptide chain?

Up to about 1000 amino acids.

Which amino acids occur repeatedly in collagen?

Glycine, proline and hydroxyproline.

What is the structure of collagen?

Three polypeptide α-chains wound together into a triple helix.

What holds the three chains of collagen together?

A large number of hydrogen bonds.

How do collagen molecules form collagen fibres?

Collagen molecules associate into fibrils, which combine to form strong collagen fibres.

How does collagen contribute to bone strength?

Collagen fibres combine with bone tissue to provide tensile strength, similar to steel rods reinforcing concrete.

What can happen if collagen does not develop properly in bone?

Bone may have reduced tensile strength and become brittle and break more easily.

What are globular proteins?

Proteins with complex tertiary and sometimes quaternary structures that fold into compact, roughly spherical shapes.

What is the general shape of globular proteins?

Compact and approximately spherical.

How do globular proteins differ from fibrous proteins?

Globular proteins are compact and often metabolically active, whereas fibrous proteins are long, structural and generally more stable.

Why are many globular proteins soluble in water?

Hydrophilic R groups tend to face outward where they can interact with water.

Where are hydrophobic R groups usually found in globular proteins?

On the inside of the protein away from water.

What does hydrophobic mean?

Having a tendency to repel water and not dissolve or mix with it.

What does hydrophilic mean?

Having an affinity for water and tending to dissolve or mix with it.

Why does the position of R groups affect globular protein behaviour in water?

Hydrophobic R groups tend to face inward while hydrophilic R groups face outward and interact with water.

What is a colloid?

A suspension of molecules that are not fully dissolved.

Why can globular proteins form colloids rather than true solutions?

Their molecules are very large, so they remain suspended in water rather than fully dissolving.

Why are globular proteins important in the cytoplasm?

They help hold molecules in position and perform many metabolic functions.

Give examples of globular proteins.

Enzymes, antibodies, some hormones and haemoglobin.

What is haemoglobin?

A globular protein and red pigment that transports oxygen in the blood.

How many amino acids are present in haemoglobin?

574 amino acids.

How many polypeptide chains make up haemoglobin?

Four.

What type of protein structure does haemoglobin have?

Quaternary structure.

What connects the polypeptide chains of haemoglobin?

Disulfide bonds.

What does each haemoglobin polypeptide chain contain?

An iron-containing haem group.

How many haem groups are present in one haemoglobin molecule?

Four.

How many oxygen molecules can one haemoglobin molecule transport?

Four oxygen molecules.

What is the function of the haem group in haemoglobin?

It binds oxygen reversibly.

Why can haemoglobin load and unload oxygen?

Its haem groups can bind oxygen and release it again depending on conditions.

How does haemoglobin's structure relate to its function?

Its four polypeptide chains each contain a haem group, allowing one haemoglobin molecule to transport up to four oxygen molecules.

What are conjugated proteins?

Proteins joined to another non-protein molecule called a prosthetic group.

What is a prosthetic group?

A non-protein molecule incorporated into and permanently associated with a conjugated protein.