Primary structure - L7

The primary structure is the..

linear sequence of amino acids

Formation of peptide bond

• happens through a condensation reaction - H2O removed

• happens between COOH group of one amino acid and Nh2 group of another amino acid

• forms peptide bond

• peptide group is CONH

• process requires energy

amino acids in proteins are called..

amino acid residues

what are teh amino aicds on each terminal called

• the amino group on one terminal is called N terminal

• the carboxyl group on other terminal is called C terminal (can form another peptide bond)

Chains are usually drawn

left (N terminus) → right (C terminus)

what are Eupeptide bonds

peptide bonds formed from a carboxyl group of one amino acid and an amino group of another

Isopeptide bonds

peptide bonds formed from Carboxyl group from a side chain of an amino acids and an amine group from another amino acid side chain

why do Proteins absorb light at 190-220 nm?

due to peptide bond

Peptide bond is… (properties)

planar and rigid

little flexibility/ little rotation around the bond

what is the cis conformation of peptide bond and what is the torsion angle

more likely found in proline residues

what is the trans conformation of peptide bond and what is the torsion angle

more common

Proposed proposed the α-helix and β-sheet structure of proetisn assuming ..

• Peptide bond is planar

• All amino acid residues are equivalent in terms of backbone conformation

• each amide proton is hydrogen bonded to an oxygen atom of another residue with an N–O distance of 2.72 Å

the 3 main torsion angles in peptides..

• Omega → 180, as peptide bond is rigid and planar

• Pie → between alpha carbon and nitrogen, can be naything as C-N bond is a single bond

• Psi → between alpha carbon and carboxyl group, can be anything as C-C bond is a single bond

as we have so many possible pie and psi bonds soes this mean we can have mu;tiple combinsations

no because only a limited number are possible due to steric hindrance (collisions or clashes between atoms)

what does a Richmand plot show?

are accessible values for pie and Psi torsion angles which are displayed

what does the white area show?

shows area where atoms come closer than the sum of there van der walls radii

this is sterically disallowed

what are the dark green regions?

regions where there are no steric clashes

sterically allowed

what do light green areas show ?

are regions where slightly smaller VDW radii are used, atoms are allowed to come a little close together

what are teh 2 amino acids that look different in their richmand plot?

• Glycine → as has no side chain and so can adopt angles in all 4 quadrants

• Proline → has a 5 membered ring in side chain making it more restricted in the amount of angles that can form

2 amino acids that are covalently bonded are called..

dipeptide

when a few amino acids joined together called..

oligoepetide

when have many amino acids joined together called..

polypeptide

name peptides form..

left → right

Examples of Oligonucleodtides

Aspartame → artifitial, non-carbohydrate sweetner, its a methy ester from dipeptide of aspartic acid + phenyalanine, used in soft drinks

Oxitosin → secreted by pituitary gland, induces labor, it is a cyclic nanopetpid protein

Glutathione → tripeptide where glutamic residues Y carbon contribute to peptide chain, good reducing agent and protects cells

Endophins → natural painkiller secreted by pituitary glands, interacts with receptors in brain to inhibit pain signals. e.g. B - endophin contains 31 amino acid residues

what is molecular weight given in

Dalton D

1 D = 1g/mol

how to moleuclar weight of peptid

addition of isotopic masses of all amino aids in peptide +isotopic mass of 1 water molecule

What is averadge moleular weight of a protein and 1 amino acid

protein →110 D

amino acid → 128 D

how do we c compare DNA sequences, across species and within one species?

through multiple sequence alignments (MSAs)

when amino acids are identical in 2 seuqnced

they are absolutely conserved shown by *

when the amino acids are similar

they are conserved/ invariant shown by :

when there is no similarity

not conserved

what does this tell us

so studying MSAs tells us areas that are conserved are very important to the function of that protein

helps us locate motifs (usually only small amino aicds long)

what are examples of motifs:

• active sites

• binding sites

• post - translation modification sites

• repeats (AAs that are repeated could be important for structure)

how many codons are there:

• 61

• 64 including 3 stop signals

Motifs are visualized with..

consensus sequences

what does this show

• the height indicates how conserved that position is

• the height of each symbols shows how common that amino acid is

Proteins that have diverged from a common ancestral gene are known as

Homoglos

what are orthologs

homologous proteins that are the same as our ancestors do the same things, found in many species that share a common ancestor

what are paralogs

Homologous proteins with same genome, arise due to gene duplication, there function has now changed