Protein Structure Flashcards
Central Dogma of Molecular Biology
Amino Acids: the building blocks of proteins
The side chain R gives amino acid their unique characteristic
The 20 Common Amino Acids Found in Proteins
The charge of an amino acid is pH dependent
The 20 Common Amino Acids Found in Proteins
- Nonpolar Side Chains
The 20 Common Amino Acids Found in Proteins
- Uncharged Polar Side Chains
Peptide Bonds form the Backbone of a Polypeptide Chain
The 20 Common Amino Acids Found in Proteins
- Acidic and Basic side chains
Net charge of a protein
Polypeptides are Flexible Molecules
Noncovalent Interactions restrict the Conformation a Polypeptide can take
Disulphide bonds stabilise the conformation of some proteins
Secondary (2°) protein structures
Common folding motifs found in proteins: B-sheets
- 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
Secondary (2°) protein structures
Common folding motifs found in proteins: B-sheets photo
ß-strands can form parallel and antiparallel ß-sheets
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)
ß-strands can form parallel and antiparallel ß-sheets photo
Secondary (2°) protein structures
Common folding motifs found in proteins:
a-helix
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
Secondary (2°) protein structures
Common folding motifs found in proteins:
a-helix photo
Secondary (2°) protein structures
Common folding motifs found in proteins:
Random Coil
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).
Transmembrane proteins contain
a-helical regions
Secondary (2°) protein structures
Common folding motifs found in proteins:
Random Coil photo
Protein Domain
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
Examples of Quaternary protein structures:
homo- and heteromeric proteins
Quaternary (4°) structure:
* Homodimer: made up of two identical protein subunits.
* Heterodimer: made up of two different protein subunits.
* Also trimer, tetramer etc
Domains in Evolutionary Related Proteins often have similar function
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
Higher Orders of Protein Structure
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.
Examples of Quaternary protein structures:
homo- and heteromeric proteins photo
Can you …
- 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?
