L1- Protein structure and function Flashcards
Proteins are macromolecules made of
amino acids
amino acids join…. to form a…..
amino acids join to form a polypeptide molecule
monomers join to form
polymers
amino acid sequence encoded by
gene
polypeptide chain folds into complex and highly specific three dimensional structure determined by
amino acids
folding depends on
chemical and physical properties of the amino acid
central dogma
DNA (transcription) –> RNA (translated) –> proteins
AA sequence pf protein encoded by
gene
Structure of amino acid
amino acids are classified accoring to
R group- changes chemical properties of AA ansd thereofr eth eprotein
when amino acids join together what is lost
water is lost- left with amino acid residues
(only amino acid residues in protien and not amino acid)
- peptide bond
Ionisations state of amino acid
when you add solution to amino acid.. the amino group will
gain a hydrogen
when you add solution to amino acid.. the carboxylic acid will
lost a hydrogen
bases are
proton receivers- become positve
acids are
proton donors- become negative
amino acid residues are when the
amino and carboxyl group are lost- when AAs combine
pKa value
acid dissociation constant for weak acids e.g. amino acids
e.g. how likely the amino acid will ionise or dissociate (how acidic or basic the R group is
high pKa value
less likely to ionise
low pKa valie
more liekly to ionise
if the pH of the soljution is less (more acidic) than the Pk value then the group
will be protonated.
the R group can change the chemical properties e.g.
hydrophobic
hydrophilic
polar
non-polar
acidic
basic
neutral
if the pH of the solution is more (more alkali) than the pKa then the group
will be deprontonated
example of negatively charged R groups
e.g. lysine have a high PkR value
positively charged R groups
e.g. glutamare have a lower PkR (aciddisociation of R group)
at pH 7 (physiological) what will be the predominant form of asparate (pK=2.8)?
at pH 7 the equilibrium will move to the right due to the amino acid being deprontonated
levels of protein structure
primary
secondary
tertiary
quaternary
primary
linear amino acid sequence of the polypeptide chain
secondary
local spatial arrnagment of the polypetide backbone
- localised structre e.g. helices
tertiary
final folded form
quaternary
association between different polypeptides and proteins to form a multi subunit protein
bond between two amino acids
peptide bond- loss of one water
conformation of peptide bond can be
trans( alpha casrbons on oppsoite side of peptide bond) and cis (alpha carbon on same side of the peptide bond- steric clashes)
bonds on either side of the eptide bond are free to
rotate- this define secondary structures
amino acid R groups determine how…
the polpeptide folds and ultimately determine the physical natur eof proteins
isoelectirc point of proteisn
pH at which there is no overall net charge- proteins ahve different isoelectric points
basic proteins
pI (isoelectric point) >7 contain many positively charge amino
acidic proteins have an isolectirc point
pI<7
contain many negatively (acidic) charged amino acids
peptide bonds
planar bonds
- alpha carbon, carbon, oxugen and hydrogen align in the same plan
- rigid no roation
- partial double bond
if pH< pI is
protontated
if pH >pI
is deprotonated
size of peptides
a few amino acids in length
size of polypeptides
many amino acids
biologically active proteins come in a range of
sizes… average weight is 110
protein conformation: sequences detmeines structure, structure determines….
function
which bonds hold the primary structure togetrher
peptide bonds
types of secondary structure
- alpha helix
- Beta sheet
alpha helix structure
3.6 aa. turn, 0.54 nm pitch and right handed
what bonds stabilise the structure of the alpha helix
H bonds run up and down the chain- no othe rbonds holding together
–> backdon of C=O group of one residue is H bonded to the NH group of the residue 4 amino acids away
B-strand also known as
the extended conformation
B-strand/sheet condormation
- Sheets of of polypeptides held together by H bonds above and below
- R groups alternate between opposite sides of chain
types of B-sheet
- antiparallel- adjacent B-strand srun in opp directions with muiltiple H bonds stabiolising the strcuture
- parallel- run in same direction
- mixed- run in mixed direction
tertiary structure
when primary and secondary strucutres come together e.g. globular and fibrous protein
fibrous protein
a lot of very simple repeating secondary structure- supportive structure e.g. collagen
Role: support , shape, protect
Long strands or sheets
Single type of repeating secondary structure
Globular protein
lots of mixed conformation- have many structures e.g. enzymes and transporter molecules e.g. carbonic anhydrase
Role: catalysis, regulation
Compact shape
Several types of secondary structure
domains
part of polypeptide chain that fold into a distinct shape- often a speciifc functional role
folding of membrane protein
Polypeptide chains fold to so that hydrophobic side chains are buried and polar, charged chains are on the surface e.g. myoglobin
• Membrane proteins often show “inside out” distribution of amino acids
Quarternary structure
multi-subinit proteins e.g. haemoglobin e.g. ribosomes
