Week 1 Flashcards
The peptides
Amino acids can be linked covalently by a peptide bond
Polymers of aa for peptides and protiens
AA combine in a reaction that release a H2O molecule, forming a peptide bond is a condensation reaction, breaking a peptide bond is hydrolysis.
Chains of amino acids form in order of size/complexity
-dipeptides,Tripeptides
-oligopeptides
-polypeptides
-protiens
Oligopeptides and polypeptides
This a pentapeptide with 5 residues
Sequence is written from the amino (N) terminus to the carboxyl (C) terminus
The amino acid sequence is the primary structure of a protein.
When a protein has 2 or more interacting polypeptide chains it is said to have quaternary structure
If at least 2 polypeptide chains in the protein are identical it is said to be oligomeric and the identical units are called protomers.
Conjugated proteins
Simple proteins contain only aa, conjugated proteins contain additional permanently associated chemical components.
The non-amino acid part of a protein is called a prosthetic group
We classify conjugated proteins on the basis of their prosthetic group
Some proteins have more than one prosthetic group.
Prosthetic groups usually have important roles in the function of a protein.
Levels of protein structure - primary
Sequence of a chain of amino acids
Linear sequence of aa
Composed of peptide bonds formed between aa
Formed during translation
Involved in post translational modifications
Levels of a protein structure- secondary structure
Local folding of the polypeptide chain into helicases or sheets
Either a- helix or b-sheets
Encompasses hydrogen bonds
Forms collage, elastin, actin, myosin and keratin- like fibres
Involved in forming structures such as cartilages, ligaments and skin etc
Levels of protein structure- tertiary structure
3D folding pattern of a protein due to side chain interactions
Globular
Encompasses disulphide bridges, salt bridges and hydrogen bonds
Includes enzymes, hormones, albumin, globulin and haemoglobin.
Involved in metabolic functions of the body
Levels of a protein structure - quaternary structure
Protein consisting of more than one amino acid chains
Ionisation in peptides
In solution peptides usually contain 1 fee a-amino and one free a-carboxyl group (the N and C termini)
The ionisation pattern in the peptide depends on the r- group of the amino acid
This gives peptides particular properties , and determines their isoelectric point (pl)
Secondary structure- the a-helix
Stabilised by hydrogen bonds between C=O AND N-H groups in the main chain of amino acid.
Right handed helicases are by far the most common
AMINO ACID SEQUENCE AFFECTS STABILITY OF THE A-HELIX
Alanine has the greatest tendency to form a-helix, gylicine and proline have the lowest tendency’s
Interactions among r-groups play and important role in determining secondary structure
In a- helicases interactions between r- groups 3-4 residues apart are important
Secondary structure - b-strands and b-sheets
Zigzag or pleated structure (not a helix)
Serval strands can pack together to form a b- sheet
Hydrogen bonding between strands is stronger in antiparallel b-sheets that parreel b-sheets because the C=O and N-H groups are better aligned
Secondary structures involves interactions among residues close together in sequence, while tertiary structure involves interactions between residues far away from each other
Flexible loops and turns link regions of secondary structure: pro,thr,ser and gly are common residues here.
Circular dichroism is a technique to identify secondary structures
Circular dichroism (CD) spectroscopy.
Circularly polarised uv light is absorbed differently by a- helicases, b sheets and unstructured regions of proteins
Useful tool to see whether proteins are properly folded , estimate what fraction of protein is in each conformation, and monitor transitions between folded and unfolded states.
Hydrophobic interactions
These amino acids orient themselves towards the centre of the polypeptide to avoid the water
Disulphide bridge
The amino acid cystine forms a bond with another cystine group through its r group
Hydrogen bonds
Polar “ r “ groups on the amino acids form bonds with other polar r groups
Hydrophilic bonds
These amino acids orient themselves outward to be close to the water
Ionic bonds
Positively charged R groups bond together
Fibrous protein’s
Long sheets, extensive regions of a single type of secondary structure
Insoluble- rich in hydrophobic residues
Most proteins that provide support, shape and external protection to vertebrates
Globular proteins
Roughly spherical shape, serval types of secondary structure folded together
Often soluble- hydrophobic residues burrow inside, hydrophilic residue sticks outside
Most enzymes are regulatory proteins.
Protiens folding, unfolding and misfolding
Proteins are synthesised at the ribosomes but may not fold spontaneously
Chaperone may be needed to aid folding
Misfolded proteins are targeted for degradation
Accumulation of misfolded protiens can lead to some diseases including Alzheimer’s and Parkinson’s.
Proteins are dynamic but can be denatured
Proteins are rarely completely static, but they do undergo conformational changes
However denatured proteins usually lose their function
Common ways to denature protiens
Heat= breaks weak interactions, including hydrogen bonds
Change in pH =distrusts electrostatic interactions
Detergents= disrupt hydrophobic effect
Chaotropic agents =eg eres = disrupts hydrogen bonds and hydrophobic effect.
Ligands
Most proteins need to transiently interact with other molecules
A molecule that reversible binds to a protein is called a ligand : This can be any molecule, including another protei.
A ligands binds a protein at it binding site, this complements the ligands size,shape and charge
Proteins are specific for their ligands and can discriminate between similar molecules
Binding a lizard might cause conformational changes in a protein, such as induced fit.
Proteins that bind ligands , usually must also be able to release ligands
Proteins that bind and chemically alter molecules are called enzymes.
Association and disassociation
Association is when a protein binds a ligand, disassociation is when the ligand is released
The reversible binding of a protein (p) to a ligand(L) can be thought of using this equation
P+L <=> PL
The disassociation constant Kd is the [L] when half the binding sites are occupied
A protein that binds with a ligand very tightly have a low Kd - a lower concentration of a ligand is needed to occupy half the binding sites
