Amino acids, proteins and DNA Flashcards
What does the primary structure of a protein describe?
The order in which the amino acids are joined together.
What does the secondary structure of a protein describe?
How a chain of atoms in a protein molecule fold, coil and pucker. This usually involves the coiling of the amino acid chain due to hydrogen bonds between the peptide links.
What does the tertiary structure of a protein describe?
The final folding of the protein molecule to form a globular protein. This is effected by the different groups on the main chain.
Why do amino acids have a higher than expected melting point?
The structure of a zwitterion (opposite polarity ends) means ionic bonding can occur between molecules.
Why are amino acids only soluble in polar solvents?
The zwitterions can form ionic bonds with polar solvents.
The lack of solubility in non-polar organic solvents such as hydrocarbons is because of the lack of attraction between the solvent molecules and the zwitterions. Without strong attractions between solvent and amino acid, there won’t be enough energy released to pull the ionic lattice apart.
Why do amino acids have weakly basic and acidic properties?
The acidic carboxyl group and the basic amino group undergo acid base reactions to form a dipolar ion (zwitterion) with a COO- group and a NH3+ group.
How do amino acids react with each other to form proteins?
Condensation polymerisation can occur between the carboxyl end of molecule and the amino end of another.
What is the bond linking two amino acids called?
Peptide link (CONH bond)
How do amino acids behave in alkaline conditions?
The COOH deprotonates to form a COO-
How do amino acids behave in acidic conditions?
The NH3 group is protonated to form NH3+
What is the alpha helix shape and how is it held together?
Right handed helix that is held together by hydrogen bonds between the polar C=O and N-H groups on different peptide bonds
What is the beta pleated sheet shape and how is it held together?
Amino acid chains are lined up side by side . Hydrogen bonding occurs between Peptide bonds which are facing each other on neighbouring molecules.
What interactions contribute to the tertiary structure of a protein?
Hydrogen binding between side chain groups.
Disulphide bridges
Salt bridges
Hydrophobic and hydrophilic interactions
Size of side chains
What are fibrous proteins and what do they make up?
Mainly secondary structure
Tough, thread like molecules that are insoluble in water and resistant to the actions of acids and alkalis.
They form, skin, muscles, and hair
What are globular proteins and what do they make up?
Secondary and tertiary structure
Small, almost spherical (due to folding) proteins that are water soluble.
Form haemoglobin, insulin and antibodies.
What are enzymes?
Enzymes are biological catalysts
Compare an enzyme to its substrate
Enzymes have Mr of >12000 and so most substrates are much smaller molecules.
What is an active site?
A specifically shaped area on the surface of an enzyme that can interact with the substrate and hold it in place while the reaction is underway.
Can enzymes catalyse reactions with both enantiomers of a substance?
No, they are stereospecific.
Why are enzymes effected by temp and pH?
Enzymes are globular proteins, this means that temp and pH can effect the hydrogen bonding that maintains their tertiary structure. This will change the shape of their active sight and denature them.
What is the optimum temp and pH for enzyme activity?
In animals, it is approx 37 degrees and pH 7 but this changes with enzymes.
What does DNA stand for?
deoxyribonucleic acid
What is the structure of DNA
2-deoxyribose (sugar) molecules are held together by phosphate ions. These sugar molecules are also bonded to a base. The differing bases form hydrogen bonds with each other which cause two strands to coil together into a double helix structure.
What is a nucleotide?
A single unit of a base bonded to a sugar with a phosphate ion.
Which carbons on 2 deoxyribose are bonded with phosphate ions and bases?
Carbon one is bonded to a base
Carbon 5 is bonded to a phosphate group and this group bonds with a carbon 3 on the next sugar along.
What are the base pairs?
Adenine (A) and thymine (T) pair together, and cytosine (C) and guanine (G) pair together.
How many H bonds form between each pair?
AG forms two bonds, GC forms three.
Between which species do the H bonds form in A-T hydrogen bonding
A — T
NH2 — O=
NH — N
Between which species do the H bonds form in C-G hydrogen bonding
C — G
=O — HNH
NH — N
HNH — O=
What is cisplatin made of?
Cisplatin consists of a central platinum ion with two chloride ligands and two ammonia ligands attached.
What does cisplatin do?
Cisplatin is able to bond to one of the guanine bases on one of the polynucleotide chains. This prevents DNA replication. And so mutated cells (cancer) won’t replicate.
What is the process of cisplatin preventing cell replication?
- First ligand substitution reaction. One of the chloride ligands on cisplatin is substituted for water molecules.
- Second ligand substitution reaction. The newly-substituted water molecules is, in turn, replaced by one of the guanine nitrogen atoms. Dative covalent bonds are formed between the lone pair on one nitrogen atom on a guanine base and the central platinum ion at the centre of cisplatin.
- The process is repeated for the other chloride ligand
- DNA shape is distorted. This prevents DNA replication from taking place.
What are the side effects of cisplatin and why do these occur?
Cisplatin is unable to differentiate between the DNA of cancerous cells and those of healthy cells.
Therefore the cisplatin drug attacks healthy cells causing side effects such as kidney and nerve damage, and hair loss.
Why are polyesters biodegradable but polymers like polythene aren’t?
The C=O and C-O bonds in polyesters are polar so they are susceptible to nucleophilic attack in hydrolysis. The C-C backbone of polythene is non polar so cannot be easily broken down
What are the two types of enzyme inhibition?
Competitive and noin competitive
How do competitive inhibitors work?
They fit into the enzymes active site so that the substrate cannot fit and therefore can’t be catalysed.
How do non competitive inhibitors work?
They attach to the enzyme and alter the shape of the active site so that the substrate cannot fit.
What is the isoelectric point of an amino acid?
The isoelectric point of an amino acid is the point at which the amino acid has no net electrical charge so it exists as its zwitterion.
What are disulfite bridges?
Bonds between the -SH groups on cysteine residuates.
What is terylene or poly(ethylene terephthalate) made of?
benzene-1,4-dicarboxylic acid with ethane-1,2-diol
What is commonly made using PET and why?
Plastic drinking bottles as they can be collected, com pasted and recycled.
What is nylon made off?
1,6-diamino hexane and adipic acid (hexane-1,6-dioic acid)
What can you replace dioic acid with when forming nylon?
Diacyl chloride molecule. (Hexanedioyl dichloride)
What is kevlar made off?
Benzene-1,4-dicarboxylic acid and benzene-1,6-diamine
Why is cisplatin more effective than transplatin?
The Cl atoms are on the same side of the molecule and so can effectively bond to the same DNA strand. As in trans they are on different sides of the molecule, they cause a much more radical distortion and so these bonds are more likely to be broken.
