Amino acids and proteins Flashcards
What groups are on the basic structure of an amino acid?
Amino group, carboxyl group, hydrogen and R which surround an alpha carbon
What configuration is prominent in proteins and peptides, trans or cis?
Trans, so they don’t interfere with eachother
How many different amino acids are there in proteins?
20
What is the main carbon in an amino acid called?
Alpha carbon
What is the most simple amino acid?
Glycine
What is the r group in glycine?
Hydrogen
Symbol for glycine
Gly, G
What is the R in asparagine?
CH2 and CONH2
Symbol for asparagine
Asn, N
What is the R group in glutamic acid?
CH2, CH2 and COOH
Symbol for glutamic acid
Glu, E
What is the R group in Tyrosine?
CH2, phenyl group, OH
Symbol for tyrosine
Tyr, Y
How to tell L from D amino acids?
Read clockwise, if CO->R->N then it is L
What does it mean that amino acids are amphoteric?
They have both acid and basic group
What does pKa tell you?
Strength of an acid
Does a strong acid have a high or low pKa?
Low, less than zero
The lower the stronger
What is the definition of pH
Measure of the concentration of hydrogen ions in an aqueous solution
What is a zwitterion?
Ion with two functional groups, both a positive and negative
Why does the line not increase linearly during titration?
Because of buffer
What is the pI?
The isoelectric point
What is the electric charge of the molecules at the isoelectric point?
Net charge is zero
What is the second most simple amino acid?
Alanine
What is the pI? (Definition)
The pH where the average charge of all the amino acid species in solution is zero
Why can an amino acid act as a buffer?
Because it can react with added acid and bases to keep the pH nearly constant
What is the pKa 1 because of?
The carboxyl group
What is the pKa 2 because of?
The amino group
Why do some amino acids have 3 pKa?
Because the have 2 amino groups
What bond forms between 2 amino acids?
Peptide bonds
What reaction happens when bond forms between 2 amino acids?
Dehydration or condensation reaction (elimination of water molecule)
What is a peptide formed by 2 amino acids called?
Dipeptide
What are the 8 classifications of the R group?
Hydrophobic, hydrophilic, aromatic, aliphatic, polar, neutral, positively charged, negatively charged
2 amino acids with OH group
Serine and Threonine
What can amino acids with OH be?
Phosphorylated
Most common amino acid with a sulfur group?
Cysteine
3 amino acids that can be phosphorylated?
Serine and Threonine and Tyrosine
What decides if the charge of an amino acid is postive or negative?
The pH
What happens to the positive and negative charge in a protein in an aqueous solution?
The hydrophobic aminoacid go in the middle and the hydrophilic go to the outside, called the hydrophobic effect
What is the hydrophobic effect ?
Folding of protein because the hydrophobic goes away from the water
Most important concept in folding of proteins?
The hydrophobic effect
What is the fisher projection useful for seeing?
Stereoisomers
When do strong hydrophobic interaction occur?
When aromatic groups are stacked in the phenylalanine side chains
What are covalent disulphide bonds formed between?
2 molecules of cysteine or cysteine residues in a protein
Where does the electrostatic interaction happen?
Between the positively charged side chain and negatively charged side chain
How many essential amino acids are there?
9
How do we get the essential amino acids?
Through the diet, we don’t produce them ourselves
What makes proline different from other amino acids?
The side chain is a pyrrolidine ring which includes both the alpha amino group and the alpha carbon
What forces are bend in a polypeptide chain?
Proline
What can the bend in a polypeptide chain do?
Change the direction of the chain
What links together 2 chains of insulin?
Disulphide bridges
Antioxidant which helps prevent damage due to reactive oxygen species
Glutathione
What decides the degree of rotation?
The R group
Is the peptide bond always a double bond?
No but it has a tendency to forma a double bond
Can the alpha carbon rotate?
Yes
What part of the protein rotate?
The alpha carbon
What charge does a phosphate group have?
Negative
What is the most common type of regulatory modification?
Phosphorylation
Which amino acid has an uncharged side chain under physiological conditions?
Threonine
Which amino acid has a side chain whose pKa is closest to neutral pH?
Histidine
Which is the favoured conformation of peptide bonds?
The sequential alpha carbon is in trans
What is the alpha helix?
Is a right handed helix where the peptide bonds are located on the inside of the chain
How many aa/turn (amino acids/turn) does the alpha helix have?
3.6 aa/turn
Which amino acid is found most frequently at beta turns in the secondary structure of proteins?
Proline
Which secondary structure is most likely to be found in the membrane embedded portion of a protein?
An alpha helix comprised entirely of hydrophobic residue
What interactions contributes most to the thermodynamic stabilisation of a protein’s native structure?
Hydrophobic interactions
What determines a protein’s native structure?
The protein’s linear amino acid sequence
What is the molecular interaction called “the hydrophobic effect”?
The tendency of non-polar molecules to avoid interactions with water and thus aggregate
What is disulphide bonds characterised by?
A covalent linkage
What does the process of protein folding involve?
Progressive stabilisation of correct secondary structural intermediates and unfolding of incorrect structures until the final structure is attained
What functional group is the peptide bond?
Amide
What decides if an amino acid donates a proton or accept a proton (if they are acidic or basic)?
The pH of the medium
What does the ionisable proton become in low pH?
Protenated
What does the ionisable proton become in high pH?
Deprotenated
Two definitions of pKa
pKa= pH at which the non-ionised fraction= the ionised fraction
pKa= pH at which the protonated fraction= deprotonated fraction
Is the pKa a constant?
Yes
In an acidic medium which fraction is the largest, the more or less acidic? (pKa>pH)
The more acidic, the protonated
In a basic medium which fraction is the largest, the more or less acidic? (pKa<pH)
The less acidic, the deprotonated
What are L and D amino acids?
L= amino acid group on left
D= amino acid group on right
What does the Ramachandran plot show?
At which angles the protein structures are stable and which are psi og phi angles
How can you tell if an alpha helix is right handed or left handed?
If you have a helix in front of you, imagine a staircase inside it, the actual helix being the handrail: if you go up the stairs, which hand would you put on the handrail? If the handrail is on your right, that’s a right-hand helix, otherwise it’s a left-handed helix.
Difference between peptides and proteins
Peptides are smaller and contain less amino acids (2-50) where proteins are larger and contain more amino acids (>50)
How many amino acid in a peptide?
2-50
How many amino acids make up a protein?
50 or more
What determines the charge, polarity and hydrophobicity of proteins?
Side chains
Are L and D enantiomers superimposable or non superimposable?
Nonsuperimposable
Why is glycine not a chiral molecule?
Because the R group is a H so the carbon doesn’t have 4 different groups
Which amino acids are chiral molecules?
All but glycine
Which forms can all the chiral amino acids exist in?
D and L
What is Ka?
Acid dissociation constant
What does Ka measure?
How completely an acid dissociates in an aqueous solution
Relationship between Ka and strength of acid
The higher the Ka the stronger the acid (the more it dissociates)
Relationship between pKa and Ka
pKa=-log(Ka)
What does pKa predict?
What a molecule will do at a specific pH
What kind of reaction does the amino acids join together in?
Condensation reaction or dehydration reaction
Do amino acids accept or donate H+ ions?
They can do both as they both an acid and a base group
What happens to an amino acid when it becomes a zwitterion?
Internal acid base reaction: the carboxylic acid group loses H+ ion and the amino group gains the H+ ion
What determines wether an amino acid is acidic, basic or a zwitterion?
The pH of the solution they are in
Do zwitterions form at the same pH for all amino acids?
No it forms at different pH
What is the isoelectric point?
pH of the solution where zwitterions form and exists
What is CO2 produced from cellular metabolism converted to in the red blood cells?
Bicarbonate and H+
What buffers H+ in the red blood cells?
Hemoglobin (Hb)
Phosphate (HPO42-)
Which amino acid has 3 pKa values?
Histidine
How many pKa values do most amino acids have?
2
What denotes the pH at which half the molecule of an amino acid in solution have side chains that are charged?
pKa
What is a peptide bond formed between?
N of the amino group and C of the carboxyl group
Possible chemical characteristics of amino acid R groups
Hydrophobic
Polar
Positively charged
Negatively charged
5 aliphatic amino acids
Glycerine
Alanine
Valine
Leucine
Isoleucine
4 aromatic amino acids
Phenylalanine
Tyrosine
Tryptophan
Proline
4 neutral amino acids
Serine
Throenine
Asparagine
Glutamine
2 sulfur containing amino acids
Cysteine
Methionine
2 acidic amino acids
Aspartic acid
Glutamic acid
3 basic amino acids
Histidine
Lysine
Arginine
What is the disulfide compound called?
Cystine
Is insulin highly variable between specie?
No it is highly conserved, only very few amino acid substitutions and none in the regions that affect activity
What is the precursor molecule of insulin?
Proinsulin
How is proinsulin converted into insulin?
Proteolytic cleavage of certain peptide bonds
Are the chains in the active insulin molecule identical or nonidentical?
Nonidentical
Which amino acid can exist in cis-configuration in peptides?
Proline
What are peptide units?
Effectively rigid groups that are linked to a chain by covalent bonds at the alpha carbon
How many degrees of freedom does each peptide unit have?
2
What is the rotation around the alpha C-N bond in a peptide unit called?
Phi
What is the rotation around the alpha C-N bond in a peptide unit called?
Psi
What is the confirmation of the main chain atoms determined by?
The values of the Phi and Psi angles in the peptide units
What is the peptide torsion angle?
The values of the Phi and Psi angles in the peptide units
Where can post-translational modification occur?
On the amino acid side chains
How do post-translational modifications extend the chemical repertoire of the 20 standard amino acids?
By modifying an existing functional group or introducing a new one
What is glycosylation?
The addition of carbohydrates to a molecule
What are oligosaccharides bound to serine or threonine residues by in O-glycosylation?
O-linkages
What are carbohydrates bound to the amide nitrogen of asparagine by in N-glycosylation?
N-linkage
What is fatty acylation?
Addition of lipids to a molecule
What does prenylation involve the addition of?
The farnesyl group (C15) or geranylgeranyl groups (C20)
What are the farnesyl group (C15) and geranylgeranyl groups (C20) synthesised from?
The five-carbon isoprene unit (isopentenyl pyrophosphate)
What is the primary structure of amino acids?
Polypeptide chain
What is the secondary structure of amino acids?
Alpha helix and beta pleated sheets
What is the tertiary structure of amino acids?
Folded sheets and helixes
What is the quaternary structure of amino acids?
Subunits attached
Which enantiomer of amino acids are found in proteins, L or D?
L-amino acids
Why are there 2 different pKa when titrating amino acids?
Because there is the amino group and the carboxylic acid group
At what pH does the zwitterion occur?
Around neutral pH
Name of the starting point of amino acids
N-terminus
Name of the ending point of amino acids
C-terminus
Which side is N-terminus on?
Left
Which side is C-terminus on?
Right
What makes amino acids more hydrophobic?
Long side chains
Why is cysteine very reactive?
Because of the presence of S in its side chain
What kind of bonds are peptide bonds?
Covalent bonds
Is cystine strong or weak?
Very strong
How is a sequence of amino acid written?
Left to right
From amino terminal to carboxyl terminal
How many amino acids are the 2 chains of insulin made up of?
A chain: 21
B chain: 30
What is glutathione made up of?
Glutamyl
Cysteinyl
Glycine
Why is trans confirmation the most common in amino acids?
Because the confirguration is mor linear and the R chains are far away from eachother so they don’t interact
Which 2 metals are the typical intrinsic metal ions?
Iron and zinc
3 types of post-translational modifications of amino acids in proteins
Glycosylation
Lipid addition
Prenylation
