Protein Structure

Question 1

Central Dogma of Molecular Biology

Answer 1

Question 2

Amino Acids: the building blocks of proteins

Answer 2

Question 2

The side chain R gives amino acid their unique characteristic

Answer 2

Question 3

The 20 Common Amino Acids Found in Proteins

Answer 3

Question 3

The charge of an amino acid is pH dependent

Answer 3

Question 4

The 20 Common Amino Acids Found in Proteins
- Nonpolar Side Chains

Answer 4

Question 5

The 20 Common Amino Acids Found in Proteins
- Uncharged Polar Side Chains

Answer 5

Question 5

Peptide Bonds form the Backbone of a Polypeptide Chain

Answer 5

Question 6

The 20 Common Amino Acids Found in Proteins
- Acidic and Basic side chains

Answer 6

Question 7

Net charge of a protein

Answer 7

Question 8

Polypeptides are Flexible Molecules

Answer 8

Question 9

Noncovalent Interactions restrict the Conformation a Polypeptide can take

Answer 9

Question 9

Disulphide bonds stabilise the conformation of some proteins

Answer 9

Question 10

Secondary (2°) protein structures
Common folding motifs found in proteins: B-sheets

Answer 10

• Many proteins have rigid cores formed by B-
  sheets
• The carbonyl oxygens on the polypeptide backbone in one B-strand form hydrogen bonds
  with hydrogen on nitrogen group of a second ß-
  strand to form a ß-sheet.
• The hydrogen bonds keep the ß-strands
  together
• R-aroup stick outwards from the sheets. thev are not involved in holding sheets together
• B-sheets can form with ß-strands in same protein/polypeptide or between ß-strands in
  different polypeptide chains

Question 11

Secondary (2°) protein structures
Common folding motifs found in proteins: B-sheets photo

Answer 11

Question 12

ß-strands can form parallel and antiparallel ß-sheets

Answer 12

Anti-parallel B-sheet:
* neighboring B-strands run in opposite orientation (one
from N to C terminus the other from C to N terminus)
Parallel B-sheet
* neighboring ß-strands run in same orientation (both
from N to C terminus or both from C to N terminus)

Question 13

ß-strands can form parallel and antiparallel ß-sheets photo

Answer 13

Question 13

Secondary (2°) protein structures
Common folding motifs found in proteins:
a-helix

Answer 13

Hydrogen bonds between the carbonyl
oxygen atom of a peptide bond and
the amide hydrogen atom of the amino
acid four residues away stabilizes the
helical structure
R-group stick outwards they are not involved in forming the a-helix

Question 14

Secondary (2°) protein structures
Common folding motifs found in proteins:
a-helix photo

Answer 14

Question 15

Secondary (2°) protein structures
Common folding motifs found in proteins:
Random Coil

Answer 15

Few proteins have only a-helices or B-
sneersi
*Manv nave unstructured unis called randomi
enils
Random coils do not form regular secondary structure and are not characterized by any
regular hydrogen bonding pattern.
* They are found in two locations in proteins:
> Terminal ends - both at the N-
rerminis 2netne prminis 0p
protein;
> Loops - found between regular
secondary structure elements (-
helices, ß-sheets).

Question 15

Transmembrane proteins contain
a-helical regions

Answer 15

Question 16

Secondary (2°) protein structures
Common folding motifs found in proteins:
Random Coil photo

Answer 16

Question 17

Protein Domain

Answer 17

A protein domain or motif is a region of a polypeptide that can fold independently into a
compact, stable structure
(A) a domain made up of 4 alpha helices.
(B) a domain made up of alpha helices and
beta strands.
(C)a domain only consisting of beta strands
forming a beta sheet

Question 17

Examples of Quaternary protein structures:
homo- and heteromeric proteins

Answer 17

Quaternary (4°) structure:
* Homodimer: made up of two identical protein subunits.
* Heterodimer: made up of two different protein subunits.
* Also trimer, tetramer etc

Question 18

Domains in Evolutionary Related Proteins often have similar function

Answer 18

A domain can occur in different proteins with the rest of the amino acids in the proteins
completely different → domain are recognisable listed in databases
similar domains are found in proteins with similar functions in evolutionarily distant
organisms
as organism complexity increases, so does
the number of domains

Question 18

Higher Orders of Protein Structure

Answer 18

Primary (1 °) Structure: Amino acid sequence
Secondary (2 °) Structure: Local folded structures (a-helix, B-sheet, random coils)
Tertiary (3°) structure: full 3-dimensional conformation ALL «-helices, B-sheets, random coils, loops of a polypeptide
Chain
Quaternary (4°) structure: 3-dimensional relationship of polypeptides in a protein made up of more than one protein.
Each of the proteins is referred to as a subunit → quaternary structure refers to multisubunit proteins.

Question 19

Examples of Quaternary protein structures:
homo- and heteromeric proteins photo

Answer 19

Question 20

Can you …

Answer 20

• draw and explain the general structure of an amino acid?
• explain the terms L- and D- stereoisomer of an amino acid?
• explain the relationship of pH and amino acid charge and how this relates to the overall charge of a protein?
• remember the twenty amino acids found in proteins and classify those according to their side chains as having a positive (basic),negative (acidic) or uncharged polar (hydroxyl or amide) side chain and those
  with a non-polar side chain and which of those contain sulfur?
• remember the three letter abbreviations for the 20 amino acids and use those when reading a protein sequence?
• explain how peptide bonds are formed and which of the bonds in a peptide allow free rotation?
• relate non-covalent bonds and covalent bonds to conformations of a protein?
• explain what happens during denaturation and renaturation of proteins?
• name and explain secondary structures found in proteins?
• explain what a protein domain is and how they can help us to understand the evolution of proteins?
• explain the terms primary, secondary, tertiary and quaternary structure of proteins and homo and
  heterodimers?