Lecture 6 Flashcards
Why are proteins important?
- mediate nearly all of the processes in a cell
- they have diverse structure and function
- all proteins use the same set of 20 amino acids
Name few different types of protein
- enzymes
- motor proteins
- signal proteins
- transport proteins
- structural proteins
Describe the primary structure of protein
- amino acid sequence
What are amino acids
- amino acids are building blocks of protein
- all 20 amino acids have similar structure, differing in their side chain (R) which dictates their behaviour
Amino acids can be grouped into 4 categories which are
- non polar
- polar (uncharged)
- acidic
- basic
what are the basic amino acids
- Arginine
- Lysine
what are the acidic amino acids
- aspartic acid
- glutamic acid
Name an uncharged polar amino acid
- serine
Name a non polar amino acid
- valine
What are peptides
2+ amino acids joined by peptide bonds which were formed as a result of a condensation reaction
What is each side of a peptide labelled as?
- peptides have directionality with an amino acid terminus (N-terminus) on one side and a carboxyl terminus (C-terminus) in the other
- it is written from left to right
- N terminus to C terminus
peptides bonds are found between what
- peptides bonds are found between carbonyl carbon and nitrogen
What dictates the shape of a protein
- the specific amino acid sequence
what dictates how the protein folds
- the side chain
What is the secondary structure of a protein
- stable arrangements of amino acids
Name 2 stable secondary structures
- the a helix
- the b sheet
The a helix
- peptide backbone wraps around imaginary axis
- 3.6 residues/turn
- r-group face outwards
- stabilized by hydrogen bonds
how are a helices stabilized by H-bonds
- stabilized by intrachain hydrogen bonds between C double bond O group of each residue with N-H group of amino acids 4 residues away on the polypeptide chain backbone
what affects the stability of a helices
- electrostatic or steric interactions between adjacent side chains can affect the stability of an a-helix
- electrostatic or steric interactions between amino acids 3-4 residues away can affect the stability of an a-helix
- proline and glycine are usually not found in helices
- the nitrogen of proline is in a rigid ring which interferes statically with the backbone
- proline in a peptide bond is missing an amide hydrogen to form hydrogen bonds
- glycine is very flexible and allows for conformations that aren’t suitable for a helices
- glycine is so small so it can’t protect the backbone hydrogen bonds from the aqueous environment
side chains affect protein _________
localization
amphipathic helices
- one side is hydrophobic residues and the other side is hydrophilic residues. Allowing for membrane separation
- helices with a region of hydrophobic residues flanked by hydrophilic residues can allow for membrane spanning
what is a protein with a helices
- a keratin
- forms coiled coils which gives it strength
what are B sheets
- composed of B strands
- stabilized by intrachain hydrogen bonds
- B sheets can be parallel or anti parallel depending on orientation of strands
Parallel B-sheets
- strands run zig zag in the same direction
- hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand
anti-parallel B sheets
- strands run zig zagged in opposite direction
- hydrogen bonds connect each amino acid on one strand to one different amino acid on the adjacent strand
what are some B sheet properties
- B sheets can be twisted
- R groups are perpendicular from the plane of the sheet
Give an example of a B sheet
- silk fibroin
When can B sheet be found in transmembrane
- only if they are a part of the B barrel structure
- hydrophobic side chains line the outer surface of the b barrel
