Lecture 13 - Amino Acids & Polypeptides Flashcards
we can draw protein structures using a:
PDB file
two aspects of amino acid structure:
- shared properties
- properties unique to each amino acid
what is the central carbon of an amino acid referred to be?
the “alpha carbon”
charge distribution of a zwitterion:
amine (NH3+) end = positive
carboxyl (COO-) end = negative
what happens to amino acids at basic/acidic pH conditions:
in basic and acidic conditions the amino acid can act as it own buffer:
acidic (low pH) = amine group gains a proton = amino acid becomes (+)
basic (high pH) = carboxyl group gives off proton = amino acid becomes ( - )
amino acids are CHRIAL so we structure them accordingly:
“CORN crib” mnemonic for the hand of L^2-amino acids (L - left handed to which the VAST majority of amino acids exist as in biological systems)
[CORN refers to reading the tetrahedral structure from left to right ]
during protein synthesis each amino acid is joined to the next via:
a peptide bond - forming a polypeptide
a peptide bond results from:
the linkage of the carboxyl group of one amino acid to the amine group of it neighbour, with the elimination of a molecule of water
formation of a peptide bond is:
CONDENSATION - i.e loss of water
destruction of a peptide bond is:
HYDROLYSIS - i.e usage of one water
how to remember peptide bond structure:
CONH
what sort of bond is a peptide bond?
peptide bonds are PLANAR therefore they do not have any spin
what are peptide bonds planar because of?
peptide bonds are planar due to the sharing of electrons between carbon and nitrogen which creates a resonance that restricts any movement around your bond
the trans-peptide group:
the majority of peptide bonds, whereby -NH point sin one direction and -CO in the other: this allows SOME rotation between the alpha carbons, a little bit of flexibility but not very much
the cis-peptide group:
- very rare where for the peptide bond to be a cis-peptide, only for when it is useful in structure
- the enzyme that makes the peptide bond ‘cis’ is called an isomerase
fully extended conformation of a polypeptide chain shows the:
planarity of each of its peptide groups
the 20 amino acids posses unique properties:
- this is due to the different side chain groups (R-groups)
- in 19 amino acids the alpha carbon is CHIRAL (asymmetrical) because it has four different groups
- can exist as stereoisomers
- the exception is glycine, this is because it’s R group is a hydrogen
enenatiomers - amino acids can be:
- L (laevus = left) or D (dexter = right) isomers
- only L amino acids are found in proteins in living organisms
example which shows the vast combinations of amino acids even from a 100 residue protein (where residue = amino acids):
for a 100 residue protein = 20^100 combinations
the common amino acids are grouped according to whether the side chains are:
acidic
basic
uncharged polar
non-polar
what abbreviations are each amino acids given?
all amino acids are given either a three letter or a one letter abbreviation
what do all non-polar amino acids essentially have as their R-groups?
all non-polar amino acids have hydro-carbon (just C & H) based R-groups
what do all polar amino acids contain within their R groups?
all polar amino acids either have an alcohol (-OH) or (O=C–NH2) within their R-group side chains
what do acidic amino acids have in their R-group side chains?
acidic amino acids have carboxyl groups on the ends of their R-groups
what do all basic amino acids all have on the ends of their R-groups?
all basic amino acids all have amino groups on the ends of their R-groups
unique properties of glycine and proline and their purpose:
glycine - the R-group side chain is only —H, this allows glycine to pack together very closely in a small region
proline - is an actual cyclic amino acid which allows for the introduction of a “kink” in the chain to form a cis-backbone
aliphatic R groups:
more CH = increasingly hydrophobic
aromatic R-groups:
Phe, Tyr & Trp are the aromatic amino acids and they are called aromatic amino acids as they can absorb ultraviolet light (UV)
at a neutral pH Trp & Tyr absorb light at 280nm whereas Phe absorbs light at 260nm
absorbance is routinely used to estimate the protein concentration
disulphide bonds & purpose:
- side chain of cysteine contains highly reactive thiol group
- two thiol groups forms a disulphide bond
- they are there to link together distant amino acids
sequence of the pol,peptide chain is:
the primary strucutre
what does comparison of the primary structure of proteins reveal?
primary structure amino acids reveals evolutionary relationships through comparison of structures
for example cytochrome-c is found in all aerobic organisms
the more identities between two molecules…
… the more recently they have evolved from a common ancestral molecule and thus the closer the kinship of their owners
what gene codes haemoglobin?
the globin gene
in adults haemoglobin =
iron containing heme molecule surrounded by 4 globin proteins: 2 alpha globin and 2 beta globin
how does haemoglobin change during human development?
during developemtrn, different globin genes are expressed which alter the oxygen affinity of embryonic and fetal haemoglobin
sickle cell anaemia:
genetic disease - heterozygous=carriers, homozygous=diseased
sickle-cell anaemia results from defective haemoglobin which causes the haemoglobins to stick together and consequently damaged red blood cells
this causes complications from low oxygen supply to tissues [pain, organ damage, strokes, increased infections]
incidents are highest in african and indian populations
sickle cell haemoglobin:
significant change in structure caused by the single mutation
how are amino acids classified?
amino acids are classified via their properties
