Introduction to amino acids and protein folding - week 1 Flashcards
What abbreviation options are there for amino acids?
full name, letter code, letter
Ala - A
Alanine
Arg - R
Argeinine
Asn - N
Asparagine
Asp - D
Aspartic acid
Cys - C
Cysteine
Glu - E
Glutamic acid
Gln - Q
Glutamine
Gly - G
Glycine
His - H
Histidine
Ile - I
Isoleucine
Leu - L
leucine
Lys - K
Lysine
Met - M
Methionine
Phe - F
Phenylalanine
Pro - P
Phenylalanine
Ser - S
Serine
Thr - T
Threonine
Trp - W
Tryptophan
Tyr - Y
Tyrosine
Val - V
Valine
what are amino acids?
- building blocks of proteins
How many principle amino acids are found in proteins?
20, but other non-protein amino acids are found in all organisms
What do proteins consist of?
- chiral alpha-carbon
- amine group (NH2/NH3+)
- carboxyl group (COOH/ COO-)
- hydrogen atom
- R-group
What is a zwitterion?
- at neurotral pH amino acids exist as dipolar ions
- amino groups is protonated, carboxyl group is depronated
Is the amino group of a zwitterion protonated?
Yes
Is the carboxyl group of a twitter ion protonated?
No - its deprotonated
What happens to the end groups at a ph of lower than 4? (properly at 2)
Both groups protonated
What happens to the end groups at a ph of higher than 6? (properly at 10)
both groups deprotonated
What pH allows for the highest concentration of zwitterions?
3 to 8
What is the aC in amino acids?
chiral
In what two forms which mirror each other can amino acids exist?
L and D isomers
Where is the NH3+ group on an L isomer in comparison to a D isomer?
left side on L, right side on D
Where is the COO group on an L isomer in comparison to a D isomer?
right side on L, left side on D
What four things makes the properties of L and D amino acids vary in certain conditions?
- different shape alters biological activity
- D-isomer cannot be digested
- cannot interact with tRNA (steric hinderance)
- can be found in some portions in both Pro and Eukaryotes
Which form of isomer is almost exclusively found in proteins?
L-isomer
what defines the properties of the amino acid?
Chemical nature of R group
Name the 6 key features of R groups in amino acids
size
shape
charge
hydrogen bonding capacity
hydrophobicity
chemical reactivity
What amino acids have a negative charged side chain?
Asp, Glu
What amino acids have a positive charged side chain?
arg, Lys, His
What amino acids have an uncharged polar side chain?
Asn, Gln, Ser, Thr, Tyr
What amino acids have a nonpolar side chain?
Ala, Gly, Val, Leu, Ile, Pro, Phe, Met, Trp, Cys
What amino acids are hydrophilic?
proteins with a negative, positive, and uncharged polar side chain
What amino acids are hydrophobic?
proteins with non polar side chains
Describe glycine
- smallest amino acid
- R group is a hydrogen atom
What do Glycine, alanine, valine, leucine, isoleucine and methionine have in common?
all have aliphatic R groups of increasing size
What increases with an increasing allopathic chain?
hydrophobicity
Where are hydrophobic amino acids often found?
on the inside of proteins away forms he aqueous cellular environment
What does methionine contain?
a thioether (-s-) group which contains a sulphur atom
list alanine, glycine isoleucine, leucine, valine and methionine from increasing size and hydrophobicity
glycine, alanine, valine, isoleucine and methionine
What type of R group does proline have?
cyclic aliphatic
What is unique about Proline’s R group?
- bonded to amino group and aC
- more structurally restricted
- often found in bends in proteins
List the three so called Aromatic amino acids
phenylalanine, tyrosine, tryptophan
what do phenylalanine, tyrosine, tryptophan have in common?
- all contain a phenyl ring
- all hydrophobic
Why do tyrosine and tryptophan have some hydrophilic properties?
-OH and -NH groups respectively
What part of tyrosine is quite reactive
-OH group
List Phenylalanine, Tryptophan, Tyrosine from increasing to decreasing size
Phenylalanine, Tyrosine, Tryptophan
Describe cysteine
- similar to serine
- contains reactive thiol group -SH
- Paris of thiol groups come together to form disulphide bond
Describe lysine and arginine
- basic amino acids
- contain side chains that are positively charged at neutral pH
Describe histidine
- basic amino acid
- contains imidazole ring
- has pKA of 6 so can be charged or uncharged at pH near to neutral
Where is histidine often found at?
the active site of enzymes where it can bind and release protons
What enzyme is an important buffer of pH in blood?
histidine
Is the pKa of histidine in haemoglobin different from that of free histidines? and why?
Yes - neighbouring groups affect the pKA
What is the pKA for oxyhemoglobin?
6.8
What is the pKA for deoxyhaemoglobin?
7.8
Name two acidic amino acids
aspartic acid and glutamic acid
What are aspartic acid and glutamic acid also called?
aspartate and glutamate
What charge do aspartic acid and glutamic acid have at physiological pH?
negative
Where are the carboxyl groups located in aspartic acid and glutamic acid?
at the end of a side chain
What are asparagine and glutamine?
uncharged derivatives of aspartate and glutamate
What is different after the conversion of aspirate and glutamate into asparagine and glutamine?
NH2 groups replaces O in carboxyl group
What is the role of proteins?
- carry out the mechanical, structural and transport functions of the body
- play a crucial role as enzymes
- have a wide variety of shapes and sizes
Name structural proteins
collagen, keratin, amelogenin
name movement proteins
actin, myosin
name enzymes and catalyst proteins
trypsin, DNA pol
name transport proteins
haemoglobin, transferrin
name membrane transport proteins
Na+/Ka+ pump
name hormone proteins
insulin
name receptor proteins
acetylcholine receptor
name defence proteins
antibodies, clotting factors
name gene regulation proteins
histones, transcription factors
name chromosome sorting proteins
tubulin
What is the unit of mass for molecular measurements?
Dalton (Da)
What is the equivalent to one Da?
the molecular weight of 1 Hydrogen atom
What is the unit of distance?
Angstrom
1A= 1(-10)m= 0.1 nm
From how many 3D structures is the portion structure made up of?
4 levels
What is the primary sequence made up of?
sequence of aa in peptide chain including any disulphide linkages
What os the secondary sequence made up of?
folding/ coiling of peptide chain (alpha helix or beta pleated sheet)
What is the tertiary sequence made up of?
peptide chain folds upon itself
What is the quaternary sequence made up of?
folded peptide chains join together
Do polypeptides have direction (polarity) ?
Yes
In what way Is the order of residues read?
from the amino (N) terminal to the carboy (C) terminal
What is the order of amino acid residues in a protein called?
sequence
What bond links two amino acids together?
peptide bond
Describe protein assembly
- hydrogen removed from amino group
- oxygen (or hydroxide) group from carboxyl group
- water released = condensation reaction
- resulting covalent bond = peptide bond
Describe the peptide bond
- double bond characteristics
- ring bond, prevents rotation
- distance between CH and NH groups shortened (1.32 A)
- planar (ie. 2 peptides 6 atoms lie in the same plane )
In what forms can the peptide bond exist?
trans and cis form
In protein bond its almost always cis-form
No- always trans-form (H of amino group trans to O of carboy group)
When are cis peptide bonds long seen?
where the bond is between proline and any other amino acid
In X-pro are trans or cis configurations possible? and why?
- due to steric problems BOTH possible
What forms polypeptides?
many amino acids joined together
What are residues?
the amino acids in a polypeptide
Is the amino terminal residue (NH3+) left or right?
left
Is the carboxyl terminal residue left or right (COO-)?
right
What is the main chain?
the regular repeating part of a polypeptide
What is the main chain often referred to?
the backbone
What are variable regions of an amino acid formed from?
side chains (R groups)
Are side chains involved in peptide bonds?
No
What is a naturally occurring example of a dipeptide?
aspartame (Asp-Phe): artificial sweetener
What is an example of a tripeptide?
glutathione (Glu-Cys-Gly): natural antioxidant
What is an example of a short polypeptide (10-40 aa)?
- peptide hormones eg. glucagon (29 aa)
- neurotransmitter eg. substances P (10 aa)
How many amino acids are in a large polypeptide?
> 40 aa
What is an example of a large protein?
dystrophin (3684 aa, 427 kDa)
Are other covalent linkages contributing to protein structure?
Yes
Name an example for other covalent linkages that contribute to protein structure?
disulphide (S-S) bridges between two Cys residues (joining subunits tithe eg. insulin)
What is the protein conformation?
3D arrangement of protein atoms in its structure
What does the protein conformation depend on?
confirmation is independent of the number of chains in a protein
What is the native structure of a protein?
3D structure of a protein under physiological conditions
When do proteins fail to work?
if they are not in their correct 3D conformation
In what form are proteins translated?
in linear arrays
Describe Anfinsens experiment
- 1950
- used solutions containing 8M urea or 6M guanidine hydrochloride (makes proteins denature into random coils)
- used beta-mercaptoethanol (reducing agent and breaks disulphide bonds)
- dissolved RNAse in solution of beta-mere and 8M urea
- RNAse loses all activity (denatures)
- then removed urea and mere using dialysis
- RNAse spontaneously regains all enzyme activity (RNAse renautre)
What was Anfinsen’s conclusion of his first experiment?
- aa sequences of RNase provides all info required to specify its native structure (final conformation)
What was anfinsen’s further experiments?
- denatured RNAse in urea and merc
- removed mercury but left urea
- observed RNase regained 1% of original activity
- bc only 1 combination of correct disulphide bonds but 105 possible combinations
- urea disulphide bonds form randomly in 1 out of 105 possible combinations to correct bonds pattern is obtained 1/105 = ~ 1%
- then added back traces amounts of mercury to scrambled RNAse (104 incorrect forms of RNAse)
- after ~10 h of RNAse has completely regained its activity
What was Anfinsen’s conclusion for his further experiments?
- correct disulphide bonds were in a lower free energy state and are more energetically favourable
- thermodynamically most stable structure of RNAse is its native conformation - true for all proteins
