Proteins and Amino acids Flashcards
Proteins are made up of which monomers
Amino acids
How is it suggested that eukayotes and Archaea are linked
Why wasnt always believed
It is believed that eukaryotes came from archaea
This wasn’t always believed due to the similarities in appears from bacteria and archaea, where archaea was believed to be a form of bacteria
Now in research we can use the molecular biology of archaea to make informed decisions about human cells
Why is it belived that viruses could be living
The mimivirus, which was discovered was thought to be a bacterium but was actually a virus which is alive
Protein take up what % of of macromolecules in a cell
15%
This is the vast marority compared to other macromolecules
You can describe cells as
Highly organised
Even prokaryotes without a nucleus
All naturally occuring proteins are based upon which type of amino acids
L-amino acids
What type of reaction is it which forms a peptide bond between the two amino acids
What is the name of the reverse of this reaction
Condensation
Hydrolysis
How many common, naturally occuring amino acids
20
Which amino acid is Ala
What is its one letter abbrebiation
Alanine
A
Which amino acid is Arg
What is its one letter abbrebiation
Arginine
R
Which amino acid is Asn
What is its one letter abbrebiation
Asparagine
N
Which amino acid is Asp
What is its one letter abbrebiation
Aspartic acid
D
Which amino acid is Cys
What is its one letter abbrebiation
Cysteine
C
Which amino acid is Glu
What is its one letter abbrebiation
Glycine
G
Which amino acid is His
What is its one letter abbrebiation
Histidine
H
Which amino acid is ile
What is its one letter abbrebiation
Isoleucine
i
Which amino acid is Leu
What is its one letter abbrebiation
Leucine
L
Which amino acid is Lys
What is its one letter abbrebiation
Lysine
K
Which amino acid is Met
What is its one letter abbrebiation
Methionine
M
Which amino acid is Phe
What is its one letter abbrebiation
Phenylalanine
F
Which amino acid is Pro
What is its one letter abbrebiation
Proline
P
Which amino acid is Ser
What is its one letter abbrebiation
Serine
S
Which amino acid is Thr
What is its one letter abbrebiation
Threonine
T
Which amino acid is Trp
What is its one letter abbrebiation
Tryptophan
W
Which amino acid is Tyr
What is its one letter abbrebiation
Tyrosine
Y
Which amino acid is Val
What is its one letter abbrebiation
Valine
V
What group on the amino acids affects its chemical properties
The R group
Which amino acid R group is this?
Alanine
Which amino acid R group is this?
Arginine
Which amino acid R group is this?
Asparagine
Which amino acid R group is this?
Aspartic acid
Which amino acid R group is this?
Cysteine
Which amino acid R group is this?
Glutamic acid
Which amino acid R group is this?
Glutamine
Which amino acid R group is this?
Glycine
Which amino acid R group is this?
histidine
Which amino acid R group is this?
Isoleucine
Which amino acid R group is this?
Leucine
Which amino acid R group is this?
Lysine
Which amino acid R group is this?
Methionine
Which amino acid R group is this?
Phenylalanine
Which amino acid R group is this?
Proline
Which amino acid R group is this?
Serine
Which amino acid R group is this?
Threonine
Which amino acid R group is this?
Tryptophan
Which amino acid R group is this?
Tryonsine
Which amino acid R group is this?
Valine
How many amino acids can be made in cells, and how many much come from the diet of the 20 nautrally occuring amino acids
11 of the core 20 are made in cells
9 amino acids cannot be synthesied in humans
What is the general structure of an amino acids (except proline)
Alpha carbon: chrial in all amino acids (except glycine)
Carboxyl group
Amine group
R-group
Amino acids (bar glycine) are chiral
What does this mean
They have 4 different groups bonded to the central carbon
This means they can form enantiomers in space
What are the two enantiomers of Alanine
L-Alanine and D-Alanine
Amino acids in proteins are always which isomer
L-isomers
They are homochiral
What does Aliphatic mean
Means the R-group chain is not branched
What does Aromatic mean
the R-group is based on a benzene ring (hydrophobic)
What does polar mean
the R group carries a small charge, both positive and negative
What does charged mean
the R-group is ionisable creating +ve or -ve charge depending on pH and type of R group (electrostatic/ionic interactions)
Which amino acids are polar
Serine
Threonine
Cysteine
Asparagine
Glutamine
(These are likely to have C-O or C-N bonds)
Which amino acids are positively charged
Lysine
Hisidine
Arginine
(arginine and hisdine have a delocalised charge)
Which R groups are negatively charged
Aspartate
Gluatamate
In solution, amino acids can ionise
Which two groups allow this
Carboxyl and amine
COOH will loose protons forming COO-
NH2 will gain protons forming NH3+
Amino acids are amphoteric meaning
they can both donate and loose protons
How is the pKa of an amino acid measured if it is amphoteric
is the pH at which a group has equal amount of protonated and unprotoned forms
So at pH below the pKa the group carries a positive charge
Why are we more concerned about the ionisation of the R groups of the amino acids rather than the carboxyl and amine groups
Because the carboxyl and amine groups are used to form peptide bonds
What is pKa in terms of amino acids
proton binding ability
a low pKa meaning it has a low affinity for protons
Which amino acids are acidic at pH 7.4
Aspartic acid
Glutamic acid
Give an example of two amino acids which are basic at 7.4
This means they will have a high affinity for protons
Arginine
Lysine
What is a hydropathy value
It is the ability of an amino acid to dissolve within water
High value = hydrophobic
Low value = hyrdophillic
Which amino acids have a high hydropathy value = hydrophobic
Valine
Leucine
Isoleucine
Methionine
These amino acids are more likely to exist within the protein
Bar tryosine, the aromatic R groups are also hydrophobic
Which amino acids are good for structure and why
Glycine and Alanine because they have really small R groups
Why is proline unique
It causes the back bone of the protein to kink
Why is cysteine unique
cysteine forms covalent disulphide bonds
What are the 4 fundamental forces of molecular biology
Electrostatic interactions (ionic)
Polar interactions (hydrogen bond)
Van der Waals interactions (dipole moment)
Hydrophobic interactions
(they are all non-covalent forces)
The 4 forces that operate in proteins are generate by the sequence of amino acids. They are crucial for ….
- The chemical reactivity of protein as enzyme
- The ability of a protein to fold into the correct shape (conforamtion) required to fulfill its function in the cell
How strong are non-covalent forces compared to covalent bonds
Are individually weak but collectively strong and flexible
Numerous non-covalent and dynamic foces in and between macromolecules
What are electrostatic (ionic) interactions
These occur between atoms that are oppositely charged
They are the strongest as ionic bonds form between fully charged ions
However hydration by water can weaken their strength
Amino acids with charged amino acids can form electrostatic interaction
Which onces are these
Aspartate
Glutamate
Lysine
Arginine
Histidine
What is the most important example of ionic bonds in proteins in human
ATPases
Lysine amino acid R-group bonds ionically to adenosine triphosphate
What are polar bonds
Specialised type of polar interaction that involves a slightly electropositive hydrogen atom that interacts with a electronegative acceptor atoms
Most hydrogen bonds in proteins occur between hydrogen and oxygen/nitrogen
What are polar bonds
Specialised type of polar interaction that involves a slightly electropositive hydrogen atom that interacts with a electronegative acceptor atoms
Most hydrogen bonds in proteins occur between hydrogen and oxygen/nitrogen
Water forms two hydrogen bond per molecule
Why is water very important to protein function:
Provide a solvation shell around the protein
Control the ionic interactions between opposite charges by reducing them
