polymers, amino acids, DNA, proteins

amino acid structure, general name for amino acids

2-amino carboxylic acids (name starts from the cooh group, nh2 is on second carbon)

Zwitterions at intermediate pH and room temperature, what are they, overall charge, state etc

-positive (-NH3+) and negative charge (COO-) at physiological pH (overall neutral charge)

- solid at room temp because, even though overall charge zero, due to ionic bonding (form giant crystal lattices)

which amino acid doesnt contain a chiral carbon, and how can you tell

glycine

use plane polarised light, optical isomers rotate in opposite directions

zwitterion at

zwitterion gets further protonated, just NH3+

in 'excess acid' any other NH2 in the R group also becomes NH3+

zwitterion at >pH 9, and what happens in 'excess alkali'

zwitterion gets further deprotonated, just COO-

in 'excess alkali', any other COOH groups in the R group also becomes COO-

how can amino acids react with other molecules (NOT includign polymerisation)

amino acids are both carboxylic acids and amines, so

as a carboxylic acid:

-react with alcohol to ester (conc H2SO4)

(any amino acids eg serine which have alcohol groups can react with THEMSELVES!! to form esters so cool)

-nucleophillic addition elimination (used as the thing being added onto)

as an amine:

-react in nucleophillic substitution with halogenoalkanes, if haloalkane is in excess will produce a quarternary ammonium salt (cationic surfactant)

-nucleophillic addition elimination to form amide bonds (amine as nucleophile)

condensation polymerisation to form polypeptides

OH from COOH and H from NH2 form water, and these two groups form a peptide/amide bond

hydrogen bonds between amino acids

O in C=O has lone pair, attracted to the delta + H in the NH2

h bonds can also happen between R groups

what is a disulfide bridge

S-S (usually between two cysteines)

how do ionic bonds form in tertiary structure

They form between carboxyl and amino acid groups that are a R group. These ionise into NH3+ and COO-

alpha helix and beta sheets

secondary structure of proteins, held by h bonds

forces in tertiary and what alters them

VAN DER WAALS, ionic, h, disulfide

weird pH/ temperature denatures protein by unfolding them

active site and how they act with eantiomers

Enzymes are proteins. The action of enzymes as catalysts, including the concept of a STEREOSPECIFIC active site that binds to a substrate molecule

only stereospecific to ONE eantiomer in a pair

how do drugs work to prevent E-S complexes forming and what helps deisgn these

-act as competiive inhibitor, bind to active site by having a similar shape so that the actual substrate cant

-computers help to design drug+ ensur

hydrolysis of peptide bond, conditions, catalyst, products

concentrated HCl, high temperature+ under reflux, forms constituent amino acids

TLC method to identify amino acids

1. draw a line in pencil near the bottom of the TLC plate

2. using a capillary tube place a drop of each mixture on the line, allow the spots to dry and do more spots to increase concentration, then allow to dry

3. place the plate into a beaker with a small volume of solvent (mobile phase), with a lid to prevent evaporation

4. solvent level must be below the baseline so it does not dissolve the samples

5.leave the beaker until the solvent has moved almost to the top, carrying pigments

6. remove from the beaker before solvent reaches the top

7. draw a pencil line to mark solvent front (before it evaporates)

8. place paper in fume cupboard to dry, preventing toxic/flammable fumes escaping into the room

9. place under ninhydrin/ UV to make amino acids visible, and calculate Rf values of the amino acids, and compare to KNOWN VALUES

safety measures of TLC method (2)

- wear plastic gloves to prevent contamination

- work in a fume cupboard as solvent may be toxic

why do amino acids have different Rf values?

amino acids have different R groups, so different polarities

this means that those that are more polar will have more attraction/ affinity for polar solvent and vica versa

phosphodiester bond

the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide in condensation

hydrogen bonds between A and T

NH2 bonds to O on C=O

NH bonds to N

hydrogen bonds between C and G

2x NH2 bonds to O on C=O

NH bonds to N

how does cisplatin act as an anti cancer drug, and what are its negatives

1) one of its Cl- ligand is replaced by water

2) the remaining h2O and Cl- ligands each form a coordinate bond with the nitrogen on the double bond in guanine in the SMALLER ring

3) this stops the DNA from replicating uncontrollably

-toxic and has horrible side effects, so can only be used in small amounts to make sure the benefits outweigh the risks

condensation polymer

ong polymer chains through the joining of monomers, accompanied by the elimination of small molecules like water (H2O) or hydrogen chloride (HCl) (if an acyl chloride is used)

Common types of condensation polymers are:

Polyesters

Polyamides

Polypeptides

Polyesters

condensation polymer formed from the reaction between dicarboxylic acids (or derivatives such as acyl chlorides) and diols. The carboxyl (-COOH) and hydroxyl (-OH) groups react

forms water as byproduct

Polyamides

formed from dicarboxylic acids (or derivatives such as acyl chlorides) and diamines.

The carboxyl and amine groups react, forming amide links

can form H2O if with COOH or HCL if with COCL

naming polyamides

nylon-x,y

x = number of carbons in the diamine

y = number of carbons in the dicarboxylic acid

Nylon 6,6

1,6-diaminohexane and hexane-1,6-dicarboxylic acid

used for fibres in clothing, ropes and parachutes

kevlar

benzene-1,4-dicarboxylic acid and 1,4-diaminobenzene

(basically a diamine with the middle being just a benzene, and a dicarboxylic acid with a benzene in the middle)

Kevlar is used for bulletproof vests and sports equipment.

Polypeptides

ondensation polymers formed from amino acids. The carboxyl group of one amino acid reacts with the amine group of another, forming a peptide (amide) link.

bonding in condensation polymers and how this determines properties

intermolecular forces:

Permanent dipole-dipole forces between polarised groups.

Hydrogen bonding between C=O, N-H, and O-H groups.

The presence of stronger intermolecular forces makes condensation polymers:

More rigid and less flexible.

Stronger, with higher melting and boiling points compared to addition polymers.

disposability of each of the 3 condensation polymers and why

polyalkenes non biodegradable as they are non-polar, saturated hydrocarbons

Polyesters and polyamides undergo hydrolysis- makes them potentially biodegradable ( very slow )

The amide bonds can be hydrolysed, breaking the polymer chain into the original dicarboxylic acid and diamine monomers.

landfill pros and cons

nvolves burying plastic waste alongside other types of rubbish

+cheap and quick

-emit methane, a potent greenhouse gas as waste decomposes

why are disulfide bridges stronger than hydogen bonds

disulfide bridges are covalent bonds

educe the type of interaction that occurs between a lysine R group and an aspartic acid R group (NH2 AND COOH)

ionic bonds

PVC and TERYLENE

PVC is poly(chloroethene)

terylene is an ester