organics - amino acids, proteins and DNA Flashcards
what are the functional groups of an amino acid
-amine - NH2
-carboxylic acid - COOH
how are amino acids amphoteric
- amine gives basic character and carboxylic acid gives acidic character
what part of the amino acid molecule varies
the R group
how are most amino acids chiral
- 4 functional groups surrounding C
-COOH, NH2,H and R
what does each amino acid exist as
a zwitterion - as each amine group is protonated by a carboxylic acid group on another molecule
what is a zwitterion
-species that has both a +ve and -ve charge on different parts of the particle
-this means that amino acids are solid at room temp as there is ionic attraction between the zwitterions
what 3 types of molecule can the R group of an amino acid be
-acidic - has COOH
-basic - has OH
-neutral - has neither
what happens to an amino acid if the pH is lowered
-the COO- part of zwitterion will accept a H+ ion to reform COOH
-causes NH2 to become +NH3
what happens if the pH is raised/ base added
-+NH3 part of the zwitterion will donate a H+ to reform the NH2 group
-causes COOH to become COO-
also need to add ion onto R group if it contains COOH
what reactions can the amine part of an amino acid undergo
-protonated by acids
-acylation with acyl chloride/ acid anhydride -nucleophilic sub with halogenoalkanes
what reactions can the carboxylic acid part of an amino acid undergo
-deprotonated by bases
-esterification with alcohols and conc H2SO4
how are peptides formed from amino acids
-in a condensation reaction - join to make dipeptides or polypeptides
-lose molecule of water
-take OH of COOH and H of NH2
how can proteins and peptides be broken down
-by hydrolysis
-uses water to make to constituent amino acids
what is a polypeptide
-long chain molecule formed from many amino acid monomers
-joined together by covalent bonds linking the chains
what is the primary structure of a protein
-sequence of amino acids bonded by covalent peptide bonds
-primary structure is specific to each protein - one alteration can affect the functioning of the protein
what is the secondary structure of a protien
-occurs when the weak -ve N and O interact with the +ve H and form hydrogen bonds - amino and carboxyl group
-two shapes - a helix and beta pleated sheet
-can be broken at high temp and pH changes as distort the structure
how does the a helix shape occur in a protein
-H bonds form bwt every 4th peptide bond
-bwt the oxygen of the COOH and the H of NH2
how does the beta pleated sheet shape occur
-where the protein folds so that two parts of the polypeptide chain are parallel to each other
-enable H bonds to form bwt the parallel bonds
what is the tertiary structure of a polypeptide
-3D arrangement of a single polypeptide chain
- additional bonds form bwt the R groups
-these are
-hydrogen - only bwt R group
-disulphide - only bwt cysteine AA
-ionic - occurs bwt charged R groups
-van der waals - bwt non-polar R groups
what is the quaternary structure of a protein
-arrangement of multiple polypeptide chains or subunits in a protein complex
how are proteins hydrolysed
-polypeptides broken down into amino acids by adding water
-reflus
-conc hydrochloric acid
-boiled as the reaction is slow
-if add enzyme then reaction occurs at room temp
what method is used to identify an amino acids
-after hydrolysis is done use Thin Layer Chromotography
how does thin layer chromatography work
Step 1:
Prepare a beaker with a small quantity of solvent
Step 2:
On a TLC plate, draw a horizontal line at the bottom edge (in pencil)
This is called the baseline
Step 3:
Place a spot of pure reference compound on the left of this line, then a spot of the sample to be analysed to the right of the baseline and allow to air dry
The reference compounds will allow identification of the mixture of compounds in the sample
Step 4:
Place the TLC plate inside the beaker with solvent - making sure that the solvent does not cover the spot - and place a lid to cover the beaker
The solvent will begin to travel up the plate, dissolving the compounds as it does
Step 5:
As solvent reaches the top, remove the plate and draw another pencil line where the solvent has reached, indicating the solvent front
The sample’s components will have separated and travelled up towards this solvent front
step 6:
calculate the Rf value
by
distance moved by component/ distance moved by solvent
what are the two phases of TLC
-stationary
-mobile
what is the stationary phase of TLC
-the phase is commonly a thin plastic/metal sheet coated in silica (or alumia)
-the solute molecules adsorb onto the surface
-depending on the strength of interactions with the stationary phase the separated components will travel particular distances through the plate
-the more they interact with the stationary phase the more they will stick to it
what is the mobile phase
-flows over the stationary phase
-it is a polar or non-polar solvent that carries the components of the compound being investigated
-polar solvents = water or alcohol
-non-polar = alkanes
how are the components identified in TLC
-if the components are coloured the spots are easily identified on the chromatogram
-if the components are not coloured then we can locate the spots and draw around them in pencil
-this is done by
-UV light
-ninhydrin - carcinogenic
-potassium manganate
-iodine vapour
why should the baseline/ start line be drawn on in pencil
-any other medium would interact with the ample components and solvent
-so would contaminate it
why do the amino acids separate in TLC
-depends on each AA affinity for the stationary phase compared to the affinity for the mobile phase
-depends on the IMF acting bwt the AA and solvent
-stronger they are the closer they are to the solvent front
why is a lid placed over the tank of the amino acid TLC
-so that the inside of the tank is saturated with solvent vapour and the solvent can then travel up the plate
what are enzymes
biological catalysts
-speed up the rate of reactions without being used up or changed
what is the site of binding known as in an enzymes and why is it specific
Enzymes have an active site where specific substrates bind forming an enzyme-substrate complex
The active site of an enzyme has a specific shape to fit a specific substrate- due to the bonds that hold the tertiary structure
Extremes of heat or pH can change the shape of the active site, preventing substrate binding – this is called denaturation
Substrates collide with the enzymes active site and this must happen at the correct orientation and speed in order for a reaction to occur
what enables an enzyme to be specific
The specificity of an enzyme is a result of the complementary nature between the shape of the active site on the enzyme and its substrate(s)
The shape of the active site (and therefore the specificity of the enzyme) is determined by the complex tertiary structure of the protein that makes up the enzyme:
Proteins are formed from chains of amino acids held together by peptide bonds
The order of amino acids determines the shape of an enzyme
If the order is altered, the resulting three-dimensional shape changes
how do drugs inhibit enzymes
Most drugs work by their ability to bind to receptors stopping their normal biological activity and interrupting the development of disease
Drugs bind to receptors generally using intermolecular forces or ionic bonds
The stronger the interaction the more effective the drug activity
how does optical isomerism in drugs affect enzymes
Many naturally occurring organic molecules consist of enantiomers, in which only one enantiomer is biologically active
Similarly, many drugs have enantiomeric forms in which only one form of the drug is active
The site where the drug binds to the biomolecule can only accept one orientation; it is said to be stereoselective
what is DNA
deoxyribonucleic acid
-two stranded double helix molecule - 3D
-polynucleotide - many nucleotides bonded together in a long chain
what is DNA made up of
-phosphate group - it is an ion
-2-deoxyribose
- 4 base pairs
-adenine
-thymine
-guanine
-cytosine
what is a nucleotide made up off
-phosphate
-sugar
-base
what holds the sugar-phosphate backbone together
-covalent bonds known as phosphodiester bonds
what are the bonds bwt base pairs and how do u find them on the individual molecule
-hydrogen bonds
-look for single NH
what way does the sugar phosphate backbones on the two strands run
-antiparallel
-one way 3’-5’
-the other -5’ to 3’
what are the comp base pairs
-adenine and thymine
-guanine and cytosine
what enables DNA to break apart in transcription
-weak hydrogen bonds are more easily broken than the covalent bonds in the sugar-phosphate backbone
-enable exposed bases to occur
what is the structure and shape of cisplatin
square planar
Cl
I
NH3- Pt - Cl
I
NH3
what is cisplatin
anti-cancer drug
how does cisplatin work
-The cis-platin passes through the cell membrane and undergoes ligand exchange where the chlorines are replaced by water molecules
-The nitrogen on a guanine base is a better ligand than water and forms dative covalent bonds with the cis-platin
-the lone pair of electrons on the nitrogen form a dative covalent bond with the platinum
-the other chlorine then does the same
-The cis-platin distorts the shape of the DNA and prevents the DNA from replicating - kinks the strand
what are the benefits of cisplatin as an anti cancer durg
-greater effect on cancer cells as it bonds to the DNA as cancer cells replicate faster than healthy cells
-so treats cancer
what are the adverse affects of cisplatin
- other healthy cells which replicate quickly, such as hair follicles, are also affected by cis-platin
-This is why hair loss is a side-effect of people undergoing cancer treatment
-New therapeutic pathways are constantly under development that aim to deliver drugs that target cancer cells while leaving healthy cells untouched
-supression of immune system
-kidney damage
which nitrogen bonds to the platinum
the 7th one
-which is adjacent/across the valley from the C=O
