proteins Flashcards
amino acids:
polymers containing amino and carboxylic acid groups.
protein building blocks.
central carbon bound to amino and carboxylic acid groups plus hydrogen and R group.
R group side chain differs for each aa.
aa linked together by peptide bonds to form proteins.
the 20 most common amino acids are classified into 3 classes based on he structure of their chains.
nucleotides:
nucleotides contain a sugar, a phosphate group and a base.
building blocks for DNA and RNA. RNA= ribose. DNA= deoxyribose.
phosphate groups attach to 5’ carbon.
base attaches to 1’ carbon.
nucleotides are comprised of a sugar, a base and 1-3 phosphate groups.
protein or polypeptide:
the difference between proteins and polypeptides is their size (length).
polypeptides are small proteins, molecular weight <less 5kDa.
also polypeptide or peptide used to describe just a chain of amino aids linked together- protein usually used to describe a fully functional macromolecule.
the composition of proteins:
proteins are made up of repeat units- amino acids joined via a covalent peptide bond.
there are 20 common (standard) amino acids.
protein structure:
primary structure- amino acid sequence.
secondary structure- alpha helix, beta sheet.
tertiary structure- 3D conformation (globular, fibrous).
quaternary structure- multi protein assemblies.
amino acids:
each R group is a different side chain- determines the properties of the amino acid.
substances that can either donate or accept a proton are called ampholytes.
essential amino acids- humans ordinarily cant synthesise Leu, Ile, Val, Phe, Trp, Thr, Lys, His.
stereochemistry:
4 different groups around a carbon atom – chiral carbon.
2 different ways to arrange in space - enantiomers.
All naturally occurring amino acids found in proteins of living individuals
have the “L” configuration (glycine R=H not chiral).
D = Dextro, L = Levo
R for alanine = CH3.
R for aspartic acid.
peptide bond:
in a protein backbone there are restrictions as to which bonds can be rotated these are-
between the Cα and N, this is known as the φ (phi) angle rotation.
between the Cα and C, this is known as the ψ (psi) angle rotation.
The conformation of the main chain atoms is therefore determined by the values of these two angles for each amino acid.
α-helix (2° structure):
Linus Pauling (1951 at CalTech) first predicted that an α-helical structure would be stable &
energetically favourable.
Experimental support from Max Perutz in Cambridge from
haemoglobin diffraction patterns.
John Kendrew – verified with
high-res structure of myoglobin.
Pro and OH-Pro break the αhelix
Ser, Ile, Thr, Glu, Asp, Lys, Arg,
and Gly destabilize the α-helix
Folding (3° structure):
John Kendrew deduced the
structure of myoglobin from Xray crystallographic data
Globular proteins have stable 3-
dimensional conformations at
physiological pH, temperature.
Secondary Structure - α-helix:
has φ and ψ
angle pair
approx -60o
and -50o with
3.6 residues
per turn and
hydrogen
bonds
between C=0
of residue i
and NH of
residue i+4.
secondary structure– β strand :
A β sheet is built up from a combination of several regions of the
polypeptide chain. Β strands are usually from 5 – 10 residues long and are in almost fully extended conformation. The β strands are aligned adjacent to each other such that hydrogen bonds can form between C=O and NH
groups.
β strands can either form parallel or antiparallel and each has a distinct
hydrogen bonding pattern.
why proteins fold:
Protein 3° structure is
influenced by α and β
regions.
Proteins fold in order to expose hydrophilic regions, and bury hydrophobic regions.
Typically enzymes can have an inner core with large hydrophobic regions and/or protected regions to perform
enzymatic reactions needed in the cells.
Phenylalanine vs Tyrosine:
Dietary protein is the principal source of essential amino
acids.
The frequency that each amino acid occurs in a protein
can be different and certain proteins may have a larger number of a certain type of amino acid.
Phenylalanine is an essential amino acid and tyrosine is a semi-essential amino acid.
In humans, tyrosine is synthesized from phenylalanine through phenylalanine hydroxylase, which adds a hydroxyl group to the aromatic ring.
Hydrophobic effect influences protein folding:
Hydrophobic amino acids tend to cluster in the interior of the
protein molecule, avoiding contact with water.
Hydrophilic amino acids tend to be arranged on the outsides of proteins in contact with the aqueous medium.
4° structure of proteins:
Haemoglobin has four subunits-
- Two α chains
- Two β chains
- a heme group associated with each subunit.
Many enzymes have quaternary structures.
Ancient DNA and forensic scientists
are particularly interested in Hb
reactions in the dry state because
both regularly encounter aged, dried
bloodstains.
Blue spectral detection and shift
from dried bloodstains (age
estimates sometimes possible) -
Forensics – finding
evidence with protein(s):
Luminol- The test is based on the ability of the luminol molecule to be oxidized by the
reaction of sodium perborate with an
oxidizing agent such as haemoglobin.
False positives with some household
chemicals.
Bluestar- More recent than Luminol, seems to be more sensitive, as does not need
complete darkness.
- Easier to mix in the field.
- More stable than Luminol, for several
days after mixing.
- Not destructive to DNA.
- Paint and varnishes can give false positives.
- Based on Luminol, with additives.
