Amino Acids, Proteins And DNA Flashcards
What are amino acids?
Molecules that contains both a carboxylic acid group and an amine group on the same carbon
The carbon is bonded to a hydrogen and a variable R group
Why do amino acids show optical isomerism? What is the exception for this?
All amino acids contain a chiral carbon, so the carbon is bonded to four different groups.
Except glycine, because it’s R group is hydrogen
What does amphoteric mean?
A substance that acts as both an acid and a base
Why are amino acids amphoteric?
The amine group can react with H+ to form NH3+ (acts as a base)
The carboxyl acid can react with OH- to form COO- and water (acts as an acid)
What is the isoelectronic point?
The pH at which a molecule has no net electrical charge
What is it called when the isoelectronic point is reached in an amino acid?
A zwitterion
What is a zwitterion?
An amino acid where the carboxyl group donates a proton, that is accepted by the amine group.
The amino acid has no overall electrical charge so it has reached its isoelectronic point
Why do different amino acids have different isoelectronic points?
Due to their R groups
If the R group is more acidic, the isoelectronic point (pH) will be lower
If the R group is more basic, the isoelectronic point (pH) will be higher
How does pH affect the structure/ nature of amino acids?
If pH is below isoelectronic point, it acts as a base and accepts H+ (to make NH3+)
If pH is above isoelectronic point, it acts as an acid and donates H+ (to make COO- and water)
What are physical properties of amino acids that are a fault of them being zwitterion ions?
Crystalline solid structures that have higher mp and bp- due to zwitterions forming ionic bonds with each other that require lots of energy to be overcome
Dissolve in water, but not do dissolve easily in non-polar solvent- as zwitterions interact strongly with polar solvent molecules, so the amino acid can dissolve
What are peptides?
Peptides are compounds made of amino acids joined by peptide links, in a condensation reaction that removes a molecule of water
What is an amino acid residue?
What remains of an amino acid when in a peptide, after the molecule of water has been removed in the condensation reaction
What are polypeptides?
Condensation polymers of amino acids
How can different dipeptides/ polypeptides be formed by a condensation reaction between the same amino acids?
Depending on the order in which they are joined with peptide links
What is hydrolysis?
The breaking of bonds using water
Describe the two different hydrolysis of peptides
ACID HYDROLYSIS-
6 Moldm-3 HCl
Heat reflux for 24 hours
ALKALINE HYDROLYSIS
Moderately concentrated NaOH
Aqueous, heat
After hydrolysis, how can mixtures of amino acids be separated and visible?
Using thin layer chromatography
Locating agents- ninhydrin and UV light. This will turn them purple
What is two dimensional TLC, why and how is it used?
Used when amino acids have very similar Rf values in a particular solvent, so cannot be differentiated
(Or used to give greater confidence when identifying amino acids)
- a square TLC plate is used, the mixture is spotted in one corner of the plate.
- these spots separate along the endless of the plate
- the plate is then turned 90*
- chromatogram is ran again with a different solvent, the amino acids with similar Rf values will separate
- each spot will now have two Rf values that can be compared with a reference in the data base
This gives greater confidence when identifying the spots
What are proteins?
Naturally occurring condensation polymers of amino acids, joined by many peptide links
Describe the structure of the primary structure in proteins
Primary structure is the sequence of amino acids, each amino acid residue is linked to the next by peptide links
Relatively stable, due to the string covalent bonds (peptide links) between amino acids
Describe the secondary structure of proteins
Regular 3D structure formed by part of the amino acids chain
Such as a-helix or b-pleated sheet
Held together by hydrogen bonds between the NH of one amino acid and the CO of another
Weaker than the covalent bonds in 1 structure, so cannot be disrupted easily by changes of pH or temp
What are the features of a-helix and b-plated sheet secondary structures?
A-helix: spiral structure where the R groups of each amino acid residue point out of the spiral
B-pleated sheet: planar arrangement with a polypeptide backbone, where the R groups of each amino acid residue point above and below the plane
Describe the tertiary structure of a protein
The three dimensional arrangement of a single polypeptide chain
Held by bonds between the SIDE CHAINS:
Hydrogen bonds (between side chains containing H and O or N)
VDW forces (between non-polar side chains)
Sulfur-sulfur bonds (between the -SH of two amino acid residues)
Ionic bonds (between side chains with COOH and NH2 as they can be polarised)
Easily disrupted by changes of temp, pH or polarity of a substance they are dissolved in
What are sulfur-sulfur bonds in the tertiary structure of proteins? Between which amino acids do they occur?
A covalent bond formed between the -thiol (-SH) groups of a pair of cysteine amino acid residues
This bond releases H2
What is an enzyme?
A protein based catalyst that speeds up the reactions of biochemical reactions in the body
Describe the general structure of an enzyme
Consist of one or more polypeptide, with co-factors
Active site, which has a specific complimentary structure to substrate
What is a substrate?
The compound that an enzyme acts upon
What is the active site?
The region responsible for the enzymes catalytic activity
Complimentary shape to the substrate
Describe the structure of an active site, an how it carries out the lock and key hypothesis
The active site is a cleft on the surface of an enzyme, with a specific complimentary structure 3D shape.
Contains the R groups from the amino acids residues in the polypeptide, which interact with the substrate to hold it in place.
Uses hydrogen, ionic, DP-DP and VDW’s forces
What is stereospecificity?
Where an enzymes active site is so selective it will only catalyse the reactions of one enantiomer of an optically active compound/substrate
This is because only one enantiomer will have the correct special arrangement of its atoms to interact (form bonds with) the R groups in the active site
Give an example of a substrate ad enzyme that has stereospecificity
Lactic acid ( CH3CH(OH)COOH ) has a chiral carbon, so has two enantiomers
Oxidation is catalysed by the enzyme lactate dehydrogenase, which will only bind to one of the enantiomers
What are enzyme inhibitors and how do they work?
Compounds that prevent an enzyme catalysed reaction
They have a similar shape to the substrate, so bind to the active site and block it, preventing any substrates from binding and being catalysed
What is structure directed drug design?
A modern day technique used to used to design drugs that inhibit enzymes that catalyse harmful diseases
The tertiary structure of the enzyme/ active site is determined using techniques such as NMR
Chemists use computer modelling to design molecules that will inhibit the enzymes involved in the disease
Give an example of a drug made from structure directed drug design, and what it is used for
Relenza
Prevents influenza infection, by inhibiting the enzymes neuraminidase
What does DNA stand for, and what is its structure?
Deoxyribose nucleic acid
Double stranded, two polynucleotides in the form of a double helix
Phosphodiester bonds between nucleotides
Hydrogen bonds between complimentary bases (3 between G and C, 2 between T and A)
What is a polynucleotide?
Single strand of DNA
Phosphodiester bonds between the phosphate group of one nucleotide and the sugar of another
Forms a sugar-phosphate backbone
What is the structure of one nucleotide? Hope are they formed?
2-deoxyribose sugar
Phosphate group
1 of 4 bases (adenine, thymine, guanine, cytosine)
Condensation reactions between phosphate and sugar, and the bases and sugar. Both reactions produce a molecule of water
Where does a phosphate group bind to a 2-deoxyribose sugar?
Between the OH on the phosphate, and the CH2OH on the sugar
Where does a base and 2-deoxyribose sugar bond?
Between the NH on the base, and the OH on carbon 1 in the sugar
What are genes?
Specific sequences of DNA bases, that code for proteins
What are benefits of hydrogen bonds between bases in DNA?
They are weaker than the covalent (phosphodiester) bonds between nucleotides, so they can break and separate the double helix without breaking the polynucleotide
This allows transcription and DNA replication to occur
What is cisplatin and its structure?
An anticancer drug
A cis isomer of a complex of platinum (II)
[PtCl2(NH3)2]
Square planar structure
How does cisplatin stop cancer?
Cancer is caused by cells in the body dividing uncontrollably
Cisplatin binds to a N atom in a guanine residue in DNA.
This blocks DNA transcription and replication, and triggers programmes cell death (apoptosis)
Explain the mechanisms of the action of cisplatin
1- cisplatin is hydrolysed inside the cell
[PtCl2(NH3)2] + H2O <—> [PtCl(H2O)(NH3)]+ + Cl-
2- ligand substitution reaction between a N in guanine and the H2O in the complex
[PtCl(H2O)(NH3)]+ + —N: —> [PtCl(—N)(NH3)]+ + H2O
3- second ligand substitution reaction between another N from a nearby guanine and Cl-
4- cisplatin complex causes the DNA double helix to bend/ kink
5- DNA cannot unwind and be copied correctly, this triggers cell death
What are the adverse effects of cisplatin?
Cisplatin binds to the guanine of DNA in normal cells as well as cancerous cells
Hair cells, RBC and WBC replicate most frequently, so are most affected
This causes hair loss, immune suppression and anaemia
