13. Amino acids, Proteins and DNA Flashcards
What category do amino acids come under?
Amines and acids
What groups do amino acids have?
Amino and carbonyl groups
Do amino acids always only have one of each functional group?
No - they may also contain other functional groups
Why is the amine group in amino acids basic?
It has a tendency to accept protrons
Why is the carboxyl group in amino acids acidic?
It has a tendency to donate protons
What are the simplest amino acids?
α amino acids
What are α amino acids?
Amino acids with the amino group on the C atom adjacent to the carboxyl group (i.e. 2nd C atom)
Example of an α amino acid?
Alanine
What types of amino acids are there?
Alpha, beta, gamma
IUPAC name of alanine?
2-aminopropanoic acid
IUPAC name of aspartic acid?
2-amino butadioic acid
IUPAC name of lysine?
2,6 - diamino hexanoic acid
IUPAC name of phenylalanine?
2-amino 3-phenyl propanoic acid
IUPAC name of serine?
2-amino 3-hydroxyl propanoic acid
Which amino acid is not chiral?
Glycine
What does it mean that amino acids are chiral?
They have an asymmetric C atom and are optically active
What is zwitterion?
A dipolar ion
Why is zwitterion formed?
As a result of the lone pair of electrons on the nitrogen of amine group being able to accept a proton from the acid group
Do amino acids have both acidic and basic properties?
Yes
What is the isoelectric point of an amino acid?
The pH where the overall charge on the amino acid is zero
What pH are Zwitterions formed at?
Unique pH value for each amino acid
Is Zwitterion an acid-base property?
Yes
What will happen, in terms of Zwitterions, in acidic conditions?
- pH is lower than isoelectric point
- so NH2 group protonated (acting as base)
- COOH group unchanged
What will happen, in terms of Zwitterions, in basic conditions?
- pH is higher than isoelectric point
- so COOH group deprotonated (acting as acid)
- NH2 group unchanged
When naming amino acids, what does the longest chain have to contain?
The carboxyl group
In what reaction will two amino acids react together?
Condensation reaction
How are two amino acids joined when they react together?
Via peptide link - a peptide bond
What compound is formed when two amino acids react?
Dipeptide
How are polypeptides formed?
If either end of a dipeptide reacts with another amino acid
What are proteins made of?
One or more long polypeptide chains
What are condensation polymers of amino acids also called?
Proteins
In our bodies, what catalyse the condensation reaction to form proteins?
Enzymes
How many levels of structure do proteins have?
3 or 4 - primary, secondary, tertiary and quaternary
What forms the primary structure of any protein?
The sequence of amino acids in a polypeptide chain
What does the primary structure of a protein determine?
Its shape and hence its function
How can the primary structure of a protein be represented?
By the sequence of three letter names of the relevant amino acids
(e.g. - gyl - ala - ala - val - leu -)
How is secondary structure of proteins formed?
Within the peptide chains, hydrogen bonds form between amino acids at various points - meaning it is not a straight chain
In amino acids, where are there strong dipoles?
In the C=O in the carboxyl group, and in the O-H in a hydroxyl group
What can the secondary structure of proteins be in the form of?
- α-helix
* β - pleated sheets (folded structures)
Why the secondary structure of proteins easier to disrupt than the primary structure?
- hydrogen bonds responsible for 2°, covalent for 1°
* hydrogen bonds are IMFs which are weak so easier to disrupt than the primary structure e.g. by heating
How are tertiary structures of proteins be formed?
When additional bonds are formed at different positions in the helix or pleated sheet
What bonds can be formed to make tertiary proteins?
- hydrogen bonds
- disulphide bonds
- ionic bonds
Do Van der Waals forces exist between proteins?
Yes - as they do between all molecules
What do Van der Waals forces mean for proteins?
The structure twisting and folding, forming the tertiary structure
What do disulphide bonds form between?
Amino acids that contain a thiol group (-SH)
How are disulphide bonds formed?
The thiol group (-SH) lose their hydrogen atom and a bond is formed between the two sulphur atoms
What type of bond is a disulphide bond?
Covalent
What effect will a disulphide bond have on the tertiary structure of a protein?
Stabalises the structure
In tertiary protein structures, where are ionic bonds formed?
Between any carboxyl and amine groups not involved in forming the peptide forms
Why can changes in pH break ionic bonds in tertiary structures?
The charges on carboxyl and amine groups are dependent on the conditions
How can the sequence of amino acids in a protein be found?
By breaking the peptide bond (primary structure) in a hydrolysis reaction
What can the hydrolysis of peptide bonds in a protein show?
The sequence of amino acids
How is the hydrolysis of peptide bonds in a protein carried out?
Heating protein under reflux with an acidic or alkaline solution for 24 hours
In the hydrolysis of peptide bonds in a protein, what do the conditions (acidic/alkaline) determine?
The form the amino acids take after (anion or cation)
In acidic hydrolysis of proteins, what form are the amino acids produced in?
Cationic form
In alkaline hydrolysis of proteins, what form are the amino acids produced in?
Anionic form
What does the hydrolysis of proteins allow chemists to do?
Deduce which amino acids are present in a sample of a protein
How can different amino acids in a protein by identified?
Thin-layer chromatography (TLC)
How does TLC differ from paper chromatography?
The paper is replaced by a thin-layer chromatography plate (a piece of plastic or glass)
What is the stationary phase in TLC?
The thin-layer chromatography plate
How does TLC work to identify amino acids?
- amino acid mixture placed onto chromatography plate and allowed to separate
- compare Rf values
What is an Rf value in TLC of amino acids?
The distance each amino acid (spot) moves up the plate compared to the solvent
In TLC, what is the indicator for when to remove the plate from the tank?
When the solvent has almost reached the top
How to calculate Rf value?
distance spot travelled / distance solvent travelled
What happens in TLC if two amino acids have similar Rf values?
2-dimensional TLC is used
How is 2-dimensional TLC carried out?
- carry out TLC as normal using a square piece of TLC film and placing the spot in one corner
- once amino acids have separated, rotate the TLC film by 90° and run it again using a different solvent
- this enables 2 Rf values to be calculated (one of each solvent) and if both values match to those for a known amino acid identification can be more confirmed
Are amino acids colourless?
Yes
As amino acids are colourless, how are the positions they reach identified?
- use of developing agent e.g. iodine or ninhydrin, which reacts with amino acids to form a purple compound
- or UV light can be shone onto plate to identify amino acids
What are enzymes?
Usually globular proteins that catalyse chemical reactions in living cells
What are substrates?
The molecules that enzymes act upon
What is an active site?
An area on an enzyme which the substrate fits into so that it can interact with the enzyme
What is the active site part of?
The tertiary structure of the enzyme of the protein
What does it mean that the active sites of enzymes are stereospecific?
It will only work on one or the other of a pair of enantiomers of a substrate - the other enantiomer will not fit into the active site, meaning the enzyme cannot work on it
What are enzyme inhibitors?
Molecules that have a similar shape to the substrate
What do enzyme inhibitors do?
Compete with the substrate to bond with the active site and therefore the appropriate substrate cannot bind - and no reaction follows
What does the amount of enzyme inhibition depend on?
The concentrations of inhibitors and substrate, and how strongly it bonds to the active site
How do antibiotics work?
By blocking the active site of an enzyme
How is enzyme inhibition utilized in some drugs?
If an enzyme that catalyses a harmful reaction can be blocked, then the reaction can be stopped
Why might it be especially difficult to find a drug molecule that will fit into the active site?
If the molecule is chiral
How do chemists use computers in drug development?
They use computers to model the shape of the enzyme active sites and predict how well potential drug molecules will interact with it
What does DNA stand for?
Deoxyribonucleic acid
What is DNA?
A polymer made up of four different monomers, which are called nucleotides
How many components are nucleotides made up of?
3
What are the 3 components that nucleotides are made up of?
- phosphate ion - each with a -ve charge, making nucleic acids highly charged
- 2-deoxyribose
- nitrogen-containing organic base
What makes nucleic acids highly charged?
Phosphate ions, each with a negative charge
What is 2-deoxyribose?
A 5 carbon sugar (pentose)
What are the nitrogen containing bases that can be in DNA?
- cytosine
- thymine
- adenine
- guanine
How are the phosphate group, base and sugar held together in DNA?
Covalent bonds
What is formed when nucleotides are joined together?
Polynucleotide chains
What bonds nucleotides together to form polynucleotide chains?
Covalent bonds
In what reaction are polynucleotide chains formed?
Condensation polymerisation
How are sugar-phosphate polymer chains formed?
Condensation polymerisation - the OH group of a phosphate group in one nucleotide reacts with the OH group in the 2-deoxyribose of another nucleotide
What are the bases attached to in a sugar-phosphate polymer chain?
Sugars
What do two polynucleotide strands form?
DNA
How many polynucleotide chains form DNA?
2
What do two polynucleotide strands spiral together to form?
A double helix
What is a double helix formed from?
Two polynucleotide chains, held together by hydrogen bonds between bases
How is a double helix held together?
Hydrogen bonds between bases
What does adenine always pair with?
Thymine
What does guanine always pair with?
Cytosine
What are complimentary base pairings due to?
The arrangement of atoms in the base - to bond the atoms have to be the right distance apart
How many hydrogen bonds can cytosine and guanine form?
3
How many hydrogen bonds can adenine and thymine form?
2
Why would other pairings (i.e. not C-G and A-T) not work?
Would put the partially charged atoms too close (they would repel), too far apart or the bonding atoms would not line up correctly
Why does the DNA double helix have to twist?
So the bases are in the right alignment and the right distance apart for the complementary bases to bond
What is cisplatin?
A complex with Pt(II) as the central metal ion and two chloride ion ligands and two ammonia ligands
What is the shape of cisplatin?
Square planar
What is cisplatin formed from?
Pt(II) as the central metal ion and two chloride ion ligands and two ammonia ligands bonded to it
What is the molecular formula for cisplatin?
Pt(NH₃)₂Cl₂
What would cisplatin be called if the chloride ions were opposite instead of next to each other?
Transplatin
How does cisplatin work as an anti-cancer drug?
By bonding to strands of DNA, distorting their shape and preventing replication of the cancer cells
What is cancer?
When cells mutate and start dividing uncontrollably to form tumours
What must happen in order for a cell to divide?
It has to replicate its DNA, which requires the two DNA strands in the double helix to unwind so they can be copied
Specifically, how does cisplatin stop DNA from replicating?
Both chloride ion ligands in cisplatin are replaced when a nitrogen atom on a guanine base in DNA forms a coordinate bond with the central Pt(II) ion (a ligand substitution reaction)
Describe the ligand substitution reaction in which cisplatin stops DNA from replicating
Both chloride ion ligands in cisplatin are replaced when a nitrogen atom on a guanine base in DNA forms a coordinate bond with the central Pt(II) ion
(NOTE: the guanine molecules can be from the same strand or opposte strands in the DNA)
Why do nitrogen atoms on a guanine base replace chloride ion ligands?
They replace chloride ions because they are better ligands
What effect does the presence of the cisplatin complex bound to the DNA strands have?
Causes the strands to kink, preventing it from unwinding and being copied - in turn preventing cells from replicating
What is the effect of cisplatin bonding to DNA in healthy cells?
It stops healthy cells from replicating, as it does cancerous cells - problem for cells that frequently replicate
What are the adverse effects of cisplatin?
- hair loss
- suppress immune system
- kidney damage
Why is the effect of cisplatin greater on cancer cells that on normal cells?
Cancer cells replicat much faster than normal cells
Why is cisplatin still used as an anticancer drug, although it has some adverse effects?
The long-term positive side effects outweight the short term negative effects
How can side effects of cisplatin be minimised?
- using low dosages
- targeting the tumour directly - method that delivers drug directly to the cancer cells preventing the chances of it attacking healthy cells
