Proteins L1 - NEEDS EDITING

Question 1

Hierarchy of protein structure: Primary

Answer 1

Primary … sequence of amino acids

Question 2

Hierarchy of protein structure: Secondary

Answer 2

Secondary … small folded repeating patterns

Question 3

Hierarchy of protein structure: Tertiary

Answer 3

Tertiary … overall fold

Question 4

Hierarchy of protein structure: Quaternary

Answer 4

Quaternary … interaction between subunits

Question 5

Hierarchy of protein structure All in order…

Answer 5

Primary … sequence of amino acids
- amino acid residues

Secondary … small folded repeating patterns
- alpha helix

Tertiary … overall fold
- polypeptide chain

Quaternary … interaction between subunits
- Assembled subunits

Question 6

understanding ….Linear Polymer Coding..

the process of DNA to Protein. (5)

Answer 6

1. Genes are linear sequences of nucleotide bases in the coding strand of DNA that code for the sequence of amino acids in the polypeptide chain of a protein
2. DNA - linear polymers of nucleotides
3. TRANSCRIPTION
4. mRNA - linear polymer of nucleotides
5. TRANSLATION
6. Protein - linear polymer of amino acids
   - Has amino terminus (N-terminus)
   - Carboxyl terminus (C-terminus)

Question 7

What is Protein primary structure?

Structure?
Represented?

Answer 7

1. The primary structure of a protein is the sequence of amino acids in the
   polypeptide chain.
2. has amino terminus
3. carboxy (l) terminus
4. Amino acids in a polypeptide chain are NUMBERED STARTING FROM THE AMINO TERMINUS
5. In protein sequence DATABASES the sequences of AMINO ACIDS in
   proteins are always given using the ONE-LETTER CODE for the amino
   acids.

Question 8

Protein Structure and Function

Answer 8

Although a PROTEIN = LINEAR POLYMER of amino acids (polypeptide chain)

it is ONLY FUNCTIONAL when thePOLYPEPTIDE CHAINS FOLDS in a DEFINED WAY TO GIVE AN INDIVIDUAL 3-D STRUCTURE.

Question 9

Two main types of organised secondary structure: WHAT ARE THEY?

Answer 9

1. a-Helix

EXAMPLE: a-keratin (structural protein in hair)

2. b-Pleated Sheets
   - Antiparallel b-pleated sheet & turn

-Parallel b-sheet & loop

Question 10

How do a-helix secondary structure forms?

Answer 10

Hydrogen Bonds Give a-Helices Dipoles.

1 - The partial negative charge on the carbonyl
oxygen
- partial positive charge on the amino nitrogen in the peptide bond

2. Leads to the formation of a dipole moment.
3. The dipole moment across each peptide bond accumulates in the a-helix
   - because of the
   regular arrangement of the residues resulting in
   the creation of a dipole moment across the whole
   helix.
4. This can affect the binding of charged ligands
   to proteins e.g. negatively charged ligands often bind
   close to the N-terminus of an a-helix.

Look at Protein page.

Question 11

What are the 2 types of B-pleated Sheets?

Answer 11

1. Antiparallel
   b-pleated sheet & turn
2. Parallel
   b-sheet & loop

Question 12

What is usually seen as B-turns and why?

(see page 1 of proteins)

Answer 12

Beta-turns are tight turns that link adjacent sections of antiparallel beta-sheets, involving a 180° turn in the space of 4 amino acids.

Glycine is found in beta-turns because of its small side chain, reducing steric hindrance.

Proline is also common in beta-turns due to its ring structure and cis configuration of the peptide bond, causing a natural turn in the polypeptide chain.

Owing to sterically constricted nature of b-turns

Gly -Owing to sterically constricted nature of b-turns

Pro - owing to the direction
change forced on a polypeptide chain by its rigid, ring side-chain when the N-terminal peptide bond is in the cis configuration

Question 13

What are torsion angles?

Answer 13

Torsion angles are where a molecule is twisted around a bond.

This is NOT the same a bond angle, which is relatively fixed.

(SEE page 2 of proteins)

Question 14

Orientation of Adjacent Peptide Bonds: -

Answer 14

F (Phi) and Y (Psi)

Question 15

Some Combinations of F (Phi) and Y (Psi)
Produce Steric Clashes and Are Disallowed

Answer 15

look at page 2

Question 16

What is the Ramachandran plot?

Answer 16

Ramachandran plot: phi vs psi for every amino acid in a protein

Question 17

Explain the Structure of the Ramachandran plot…

Answer 17

See page 3

Question 18

Explain the Tertiary structure: how formed?

Answer 18

Units of secondary structure can combine to form motifs that then combine to
form the tertiary structure of the protein.

Question 19

Tertiary Structure - Structural Motifs: 5

Answer 19

1. BaB motif
2. B-hairpin motif
3. aa motif
4. B barrels
5. a/B barrel

see page 3

Question 20

Quaternary Structure -
Many Proteins Exist As Polymers of Several
Polypeptide Chains (Subunits)

Examples of proteins with quaternary structure:

Answer 20

1. Alcohol Dehydrogenase
   2 subunits
   a2 (2 identical subunits)
2. Aldolase
   3 subunits
   a3 (3 identical subunits)
3. Pyruvate carboxylase
   4 subunits
   a4 (4 identical subunits)
4. Hemoglobin
   4 subunits
   a2b2 (2 sets of 2 different subunits)
5. Insulin
   6 subunits
   a6 (6 identical subunits)
6. Aspartate Transcarbamoylase
   12 subunits
   a6b6 (6 sets of 2 different subunits)
7. Coat of tomato bushy stunt virus
   180 subunits
   a180 (180 identical subunits)

Question 21

Subunits bind to each other via non-covalent
interactions such as: 4

Answer 21

• hydrophobic interactions,
• van der Waals interactions
• hydrogen bonds
• electrostatic (ionic) bonds.

Question 22

How is Quaternary Structure formed?

Answer 22

EXAMPLE: A large protein like hemoglobin is
constructed of four long
polypeptides each of 142 amino acids

It’s three dimensional
structure is stabilised by:

1 - Interactions between hydrophobic sidechains.

2 - Ionic interactions between charged sidechains.

3 - Hydrogen bonds between polar sidechains.

4 - Covalent disulfide bonds between Cysteine residues.

• Rigid amide bonds (peptide bonds) between amino acid residues

Question 23

An a2b2
heterotetramer -
human hemoglobin -

Answer 23

the subunits are
similar but not
identical

Question 24

Levels of Protein structure

Answer 24

1. Amino acids
2. Primary structure
3. Secondary structure (α-helices, b-sheets and b- bends)
4. Tertiary structure
5. Quaternary structure: 4 monomers combine to form hemoglobin

Question 25

How are alpha-helices stabilized in proteins?

Answer 25

Alpha-helices are stabilized by hydrogen bonding between the N-H and O=C of peptide bonds. They typically have a right-handed structure with amino acid side chains on the outside.

Question 26

What are phi (Φ) and psi (Ψ) angles in proteins, and why do they have restricted values?

Answer 26

Phi (Φ) and psi (Ψ) angles describe the rotation of peptide bonds. They have restricted values due to steric clashes between the amide proton and carbonyl oxygen of adjacent peptide bonds.

Question 27

How do secondary structure motifs relate to the tertiary structure of a protein?

Answer 27

Groups of secondary structures can form motifs, which are subdivisions of the final tertiary structure of the protein.

Question 28

How are protein structures typically determined, and how are they represented graphically?

Answer 28

Protein structures are often determined by
X-ray crystallography and

represented graphically using various models, such as ball-and-stick, ribbon, or surface models.

Question 29

What are the different levels of protein structure, from primary to quaternary? 6

Answer 29

the levels of protein structure are:

1. Primary structure (amino acid sequence)
2. Local secondary structure (alpha-helices and beta-sheets)
3. Motifs (groups of secondary structures)
4. Domains (functional units)
5. Tertiary structure (completely folded polypeptide chain)
6. Quaternary structure (binding of multiple polypeptide chains)

Question 30

What are beta-turns, and why are Pro and Gly commonly found in them?

Answer 30

Beta-turns are tight turns that link adjacent sections of antiparallel beta-sheets. Proline (Pro) and Glycine (Gly) are commonly found in beta-turns because Pro’s ring structure and a cis configuration of its peptide bond produce a natural turn, while Gly has a small side chain that reduces steric hindrance.

Question 31

Describe the structure of beta-pleated sheets in proteins.

Answer 31

Beta-pleated sheets comprise stretches of polypeptide chain running either parallel or antiparallel, bonded together by hydrogen bonds between carbonyl oxygens and amide protons. Amino acid side chains are located above and below the plane of the sheet.

Question 32

How are alpha-helices stabilized in proteins?

Answer 32

Alpha-helices are stabilized by hydrogen bonding between the N-H and O=C of peptide bonds. They typically have a right-handed structure with amino acid side chains on the outside.

Question 33

What is the significance of the dipole moment in alpha-helices?

Answer 33

Alpha-helices have a dipole moment, with the amino terminus being positive and the carboxy terminus being negative. This can affect the way charged ligands bind to proteins.

Question 34

Describe the graphical representations of protein structures.

Answer 34

Protein structures can be represented in various ways, including backbone models, ribbon models (for α-helices and β-sheets), ball-and-stick models, and surface models with different color-coding for acidic and basic residues.

Question 35

Explain the concept of quaternary protein structure and the role of subunits.

Answer 35

Quaternary protein structure involves multiple polypeptide chains (subunits) coming together to form a supermolecular structure. These subunits can be identical (e.g., α2) or different (e.g., αβ). Non-covalent interactions typically hold subunits together, sometimes stabilized by intermolecular disulfide bonds.

Question 36

How do secondary structures combine to form motifs, and what is their role in tertiary protein structure?

Answer 36

Secondary structures can combine to form motifs, which are subdivisions of the final tertiary structure of a protein. Motifs play a role in defining the overall 3D structure and function of the protein.

Question 37

Describe the structural characteristics of an alpha-helix (α-helix).

Answer 37

An alpha-helix is a right-handed helical structure where the polypeptide chain winds in a clockwise manner when viewed from the amino terminus. The side chains of amino acids are on the outside of the helix. It has a dipole moment with a positive amino terminus and a negative carboxy terminus.