Proteins L1 - NEEDS EDITING Flashcards
Hierarchy of protein structure: Primary
Primary … sequence of amino acids
Hierarchy of protein structure: Secondary
Secondary … small folded repeating patterns
Hierarchy of protein structure: Tertiary
Tertiary … overall fold
Hierarchy of protein structure: Quaternary
Quaternary … interaction between subunits
Hierarchy of protein structure All in order…
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
understanding ….Linear Polymer Coding..
the process of DNA to Protein. (5)
- 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
- DNA - linear polymers of nucleotides
- TRANSCRIPTION
- mRNA - linear polymer of nucleotides
- TRANSLATION
- Protein - linear polymer of amino acids
- Has amino terminus (N-terminus)
- Carboxyl terminus (C-terminus)
What is Protein primary structure?
Structure?
Represented?
- The primary structure of a protein is the sequence of amino acids in the
polypeptide chain. - has amino terminus
- carboxy (l) terminus
- Amino acids in a polypeptide chain are NUMBERED STARTING FROM THE AMINO TERMINUS
- In protein sequence DATABASES the sequences of AMINO ACIDS in
proteins are always given using the ONE-LETTER CODE for the amino
acids.
Protein Structure and Function
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.
Two main types of organised secondary structure: WHAT ARE THEY?
- a-Helix
EXAMPLE: a-keratin (structural protein in hair)
- b-Pleated Sheets
- Antiparallel b-pleated sheet & turn
-Parallel b-sheet & loop
How do a-helix secondary structure forms?
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
- Leads to the formation of a dipole moment.
- 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. - 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.
What are the 2 types of B-pleated Sheets?
- Antiparallel
b-pleated sheet & turn - Parallel
b-sheet & loop
What is usually seen as B-turns and why?
(see page 1 of proteins)
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
What are torsion angles?
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)
Orientation of Adjacent Peptide Bonds: -
F (Phi) and Y (Psi)
Some Combinations of F (Phi) and Y (Psi)
Produce Steric Clashes and Are Disallowed
look at page 2
What is the Ramachandran plot?
Ramachandran plot: phi vs psi for every amino acid in a protein
Explain the Structure of the Ramachandran plot…
See page 3
Explain the Tertiary structure: how formed?
Units of secondary structure can combine to form motifs that then combine to
form the tertiary structure of the protein.
Tertiary Structure - Structural Motifs: 5
- BaB motif
- B-hairpin motif
- aa motif
- B barrels
- a/B barrel
see page 3
Quaternary Structure -
Many Proteins Exist As Polymers of Several
Polypeptide Chains (Subunits)
Examples of proteins with quaternary structure:
- Alcohol Dehydrogenase
2 subunits
a2 (2 identical subunits) - Aldolase
3 subunits
a3 (3 identical subunits) - Pyruvate carboxylase
4 subunits
a4 (4 identical subunits) - Hemoglobin
4 subunits
a2b2 (2 sets of 2 different subunits) - Insulin
6 subunits
a6 (6 identical subunits) - Aspartate Transcarbamoylase
12 subunits
a6b6 (6 sets of 2 different subunits) - Coat of tomato bushy stunt virus
180 subunits
a180 (180 identical subunits)
Subunits bind to each other via non-covalent
interactions such as: 4
- hydrophobic interactions,
- van der Waals interactions
- hydrogen bonds
- electrostatic (ionic) bonds.
How is Quaternary Structure formed?
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
An a2b2
heterotetramer -
human hemoglobin -
the subunits are
similar but not
identical
Levels of Protein structure
- Amino acids
- Primary structure
- Secondary structure (α-helices, b-sheets and b- bends)
- Tertiary structure
- Quaternary structure: 4 monomers combine to form hemoglobin
How are alpha-helices stabilized in proteins?
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.
What are phi (Φ) and psi (Ψ) angles in proteins, and why do they have restricted values?
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.
How do secondary structure motifs relate to the tertiary structure of a protein?
Groups of secondary structures can form motifs, which are subdivisions of the final tertiary structure of the protein.
How are protein structures typically determined, and how are they represented graphically?
Protein structures are often determined by
X-ray crystallography and
represented graphically using various models, such as ball-and-stick, ribbon, or surface models.
What are the different levels of protein structure, from primary to quaternary? 6
the levels of protein structure are:
- Primary structure (amino acid sequence)
- Local secondary structure (alpha-helices and beta-sheets)
- Motifs (groups of secondary structures)
- Domains (functional units)
- Tertiary structure (completely folded polypeptide chain)
- Quaternary structure (binding of multiple polypeptide chains)
What are beta-turns, and why are Pro and Gly commonly found in them?
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.
Describe the structure of beta-pleated sheets in proteins.
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.
How are alpha-helices stabilized in proteins?
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.
What is the significance of the dipole moment in alpha-helices?
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.
Describe the graphical representations of protein structures.
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.
Explain the concept of quaternary protein structure and the role of subunits.
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.
How do secondary structures combine to form motifs, and what is their role in tertiary protein structure?
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.
Describe the structural characteristics of an alpha-helix (α-helix).
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.
