B.1.2

Question 1

Amino Acids

What is a peptide bond?

Answer 1

• The covalent bond between two amino acids which are the monomers (building block molecules) of protiens.
• A bond between the carbon of the carboxyl end of the amino acid and the nitrogen of the amino group.
• This bond is formed through a condensation reaction.

Question 2

Amino Acids

What is a polypeptide?

Answer 2

• A chain of amino acids.
• The polymer formed from the condensation reactions.
• A polypetide will then, be folded and further bonds formed, to turn it into a functional protein.
• It is the PRECURSOR to a protien (following translation during protein synthesis forms polypetides.)

Question 3

Amino Acids

What does the term ‘denature’ mean?

Answer 3

The loss of a proteins shape leading to the loss of its function, is called denaturation.
- Can occurr when proteins are exposed to harsh environments, due to weaker bonds breaking.
- If the shape of a protein changes, it will decrease/ compeltely lose its function.

Question 4

Amino Acids

Making a Dipeptide

(A peptide bond between TWO amino acids)

Answer 4

Formed by condensation reactions.

• The hydroxyl is removed from the carboxyl end of the first amino acid and a hydrogen is removed from the amine end of the second amino acid.
• The Carbon from the carboxyl forms a peptide bond to the nitrgoen of the amine group.
• THe OH and H combine to form water.

Question 5

Amino Acids

What makes an amino acid essential?

Answer 5

There are 9, out of the 20, amino acids that we must eat in their exact form, as we have no ability to construct them from parts.

• These are called essential amino acids –> we cannot synthesise them in the body.
• Thus, we must have a diet full of protein so we get the essential amino acids needed to make functional proteins.

Question 6

Amino Acids

Important Proteins in the body

Answer 6

• Hemoglobin –> transports oxegyn on RBCs
• Digestive enzymes –> to break down food.
• Collagen (ligaments and tendons) + Keratin (hair and nails) are structural proteins.
• Histones –> that DNA is wrapped around
• Hormones –> like insulin.

Question 7

Amino Acids

Impact of High Temperatures and atypical pH levels.

Answer 7

• Globular proteins are folded, rather than straight chains. –> fold done through many types of bonds including weaker bonds (including H bonds)
• At high temps/ acidic or alkaline environments –> the weak bonds break and the protein denatures.
• The protein can renature/ rebond when conditions return to normal –> therefore denaturation is often temporary.

Question 8

Protein Strcture

What is an R group?

Answer 8

Every amino acid has a carboxyl group branched off a central carbon.
- The additional chain of elements also coming down from the central carbon is unique to each amino acid –> The R-group is what makes amino acids unique and gives it its chemical properties.

Question 9

Protein Structure

What are hydrophobic interactions?

Answer 9

• If amino acids are NON-POLAR, they interact in the presence of water.
• Non-polar R groups are not inherently attracted to each other but they move inwards away from the polar water molecules.
• When they pull inwards –> R groups move towards each other which is called a hydrophobic interaction.

Question 10

Protein Structure

What is a Disulfide bond?

Answer 10

• The amino acid cysteine has an R-group that is a SULFUR atom bonded to a hydrogen.
• If two cysteine molecules are near each other –> hydrogens can be removed and the two sulfur molecules can covalently bond to one another.
• This covalent bondis called a disulfide bond (VERY STRONG.) –> the strongest bond in the tertiary bonding/protein structure.

Question 11

Protein Structure

Levels of Protein Structure: Primary Structure.

Answer 11

The specific SEQUENCE of amino acids that are bonded together to create a straight linear chain of amino acids.
- The protein structure is determined by the DNA CODE in the gene that codes for the protein.
- Based on the DNA triplets, the specific amino acids are added –> which give the protein its primary structure.
- THE PRIMARY STRUCTURE IS ALTERED BY MUTATIONS (as they change the DNA)

Question 12

Protein Structure

Levels of Protein Structure: Secondary Structure.

Answer 12

After the polpetide CHAIN is complete, the protein begins folding.
- All amino acids have some charge – the amine group has a slight positive charge and the carboxyl a slight negative charge.
- These charges cause hydrogen bonds to form between the amino acids in the chain.
- It comes from the carboxyl and amine groups it is consistent and forms a pattern throughout –> either an alpha helix or a beta pleated sheet.

Question 13

Protein Structure

Levels of Protein Structure: Tertiary Structure.

Answer 13

Proteins that are globular have different bodns between the R-groups of their amino acids.
- This causes a non-uniform and unique set of FOLDS that give the protein its trademark shape.
- The bonds that contribute to tertiary structure include: IONIC bonds between CHARGED R-groups, HYDROPHOBIC interactions between NON-POLAR R-groups, H-Bonds between polar R-groups and disulfide bridges between cystienes.

Question 14

Protein Structure

Levels of Protein Structure: Quaternary Structure.

Answer 14

Multiple polypetides join together to make one protein.
- The polypeptide bond to one another using the same type of bonds as for tertiary structure but between R-groups of different polypeptides.

Question 15

Protein Structure

Alpha Helix vs Beta Pleated Sheets.

Answer 15

Secondary structure consists of consistent hydrogen bonds between the amine group of one amino acid and the carbozyl of another.
1.) IN ALPHA HELIX:
- the polypeptide is wound into a helix shape and hydrogen bonds form between the turns of the helix.
2.) IN EBTA-PLEATED SHEET:
- Sections of the polypeptide are run in opposite directions and hydrogen bonds form between the lines giving a pleated (FOLDED) shape because of the bond angles.

Question 16

Protein Structure

Amino Acid polarity and structure.

Answer 16

The R-group properties give amino acids their reactive properties.
- The polarity of the R-group determines the teriary structure of the protein. –> Often the hydrophobic amino acids comprise the centre of the protein while apolar amino acids surround the outside.
- This is an effective strategy for placement in cell membranes and other uses.

Question 17

Protein Shape and Function

What is a globular protein?

(Haemoglobin)

Answer 17

• Globular proteins are HIGHLY FOLDED proteins that end up with a spherical shape.
• Often have HYDROPHOBIC amino acids in their centre with POLAR acids on the outside, making the PROTEIN HYDROPHILLIC.
• Globular proteins are more DIVERSE IN SHAPE –> and function.
• Act as enzymes, hormones, anitbiodies and cell membrane transport + communication.

Question 18

Protein Shape and Function

What is a fibrous protein?

Collagen, for example.

Answer 18

• Fiborous proteins have LONG POLYPEPTIDES that LACK TERTIARY BONDS AND FOLDING and typically DO NOT HAVE consistent secondary structure either.
• They often have quaternary structure –> multiple polypeptides are linked together with fibres/ filaments and held together with H-bonds.
• Fiborous proteins are generally structural in function.

Question 19

Protein Shape and Function

Conjugated vs
Non-conjugated protein.

Answer 19

• Distinction between types of proteins is based on whether they also contain non-protein components.
• Non-conjugated proteins contain ONLY POLYPEPTIDES SUBUNITS.
• Conjugated proteins consist polypeptide subunit, AND A NON-POLYPEPTIDE subunit.

Question 20

Protein Shape and Function

Role of cryogenic electron microscopy.

Answer 20

Cyro-electron microscopy involves flash freezing proteins in liquid ethane.

• Proteins are way too small and can’t be observed by the light from microscopes.
• The images of the protein trapped in ice from cyro-eelctron microspy technology can be obtained using a beam of electrons.
• Software then develops the image –> to wheer individual atoms of a protein can be seen.

(How we understand proteins specific structure.)

Question 21

Protein Shape and Function

Structure and Function of:
COLLAGEN

Answer 21

• A fiborous protein with S quaternary structure of three polypeptides held together.
• Made of repeating amino acid sequence of glycine-hydroxyproline -X, whereby X-amino acid varies for the part of the body found.
• The structure creates a strong and elastic fibre that is useful for building body tissue including tendons, ligaments, cartilage and facial structure.

Question 22

Protein Shape and Function

Structure and Function of:
INSULIN

Globular, NON-conjugated (contrast with Haemoglobin)

Answer 22

Made up of two polypeptide chains: one contains 30 amino acids while the other 21 amino acids.

• Two chains are held together by R-bonds interactions, including multiple DISULFUDE BRIDGES.
• The specific shape of insulin is crucial for its ability to bind to an insulin receptor for its functiona s a hormone involved in glucose uptake.

Question 23

Protein Shape and Function

Structure and Function of:
HAEMOGLOBIN.

Answer 23

• A protein found on the surface of RED BLOOD CELLS.
• Contains two different types of polypeptides: ALPHA HELIX CHAIN AND BETA CHAIN.
• Sections of alpha helices are seen in the chains.
• Each chain has a complex tertiary structure and then are held together by bonds to form a quanternary structure.
• Also contains four Heme groups that faciliate the binding of oxygen to each.