Amino acids, DNA etc Flashcards
proteins = notes from specification
Proteins are sequences of amino acids joined by peptide
links.
The importance of hydrogen bonding and sulfur–sulfur
bonds in proteins.
The primary, secondary (α-helix and β–pleated sheets)
and tertiary structure of proteins.
Hydrolysis of the peptide link produces the constituent
amino acids.
Amino acids can be separated and identified by thin-layer
chromatography.
Amino acids can be located on a chromatogram using
developing agents such as ninhydrin or ultraviolet light
and identified by their Rf
values.
acid vs base
Acid = proton donor and electron acceptor
Base = proton acceptor and lone pair donor
general formula of amino acids
General formula of amino acids = RCH(NH)2COOH
zwittertons
Amino acids exist as zwittertons which have both a permanent positive and permanent negative charge
protonated vs deprotonated
Amine group = gains proton (protonated)
Carboxyl group = looses proton (deprotonated)
acid solution
Acid solution = NH3+ and COOH
neutral solution
Neutral solution = NH3+ and COO-
alkaline solution
Alkaline solution NH2 and COO-
If there are 2 COOH groups in a strongly alkaline solution both will change to COO- as both molecules loose H+
acid hydrolysis of amino acids
Acid hydrolysis of amino acids. Boil 6moldm-3 HCl for 24 hours
cysteine (expection)
-two cysteine side chains end up next to eachother due to the folding in the peptide chain (CH2S)
-formation of disulfide bridges
glyciene =
not optically active
2 of same groups around chiral carbon
what do R groups affect
R groups = affect the size, polarity and name of amino acids
optically active
All amino acids except glyciene are optically active since its bonded to 4 different groups around central carbon atom
fiborous proteins
Fiborous proteins = formed from parallel polypeptide chains held together by cross links. These form long rope-like fibres with high tensile strength and are generally insoluble in water
globular proteins
Globular proteins = spherical shape caused by tightly folded polypeptide chains. Usually folded hydrophobic groups on the sinide with hydrophilic groups on the outside. This makes golbular proteins soluble in water
naming amino acids
-amino = prefix, root = longest carbon chain, suffix = oic acid
melting point = zwitterton
Amino acids are often solids
The ionic interaction between zwitterions explains the relatively high melting points of amino acids as
opposed to the weaker hydrogen bonding that would occur in the no charge form.
amino acids as buffers
Amino acids act as weak buffers and will
only gradually change pH if small
amounts of acid or alkali are added to the
amino acids.
proteins
Proteins are polymers made from
combinations of amino acids.
The amino acids are linked by peptide links,
which are the amide functional group.
in acidic conditions
all amine groups turn to NH3+
draw an amino acid that reacts with NaOH at a high pH
change all COOH groups to COO-
solubility
However, it’s not just lysine.
All amino acids form zwitterions.
So, all amino acids are soluble in water.
alpha helixes
The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)
beta pleated sheets
The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
enzymes as biological catalysts
Enzymes are biological catalysts
‘Biological’ because they function in living systems
‘Catalysts’ because they speed up the rate of chemical reactions without being used up or changed
enzymes are globular proteins
enzyme specifity
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
drug receptor interactions
Receptors are proteins found on enzymes, cell membranes or DNA
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
Drug-receptor interaction has become very important in drug design
Computers are widely used to model drug-receptor interactions
DNA nucelotide
A nucleotide is a building block consisting of a phosphate group, 2-deoxyribose and a nitrogenous base such as adenine, guanine, cytosine and thymine
hydrogen bonding
The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases
These hydrogen bonds always occur between the same pairs of bases:
The purine adenine (A) always pairs with the pyrimidine thymine (T) – two hydrogen bonds are formed between these bases
The purine guanine (G) always pairs with the pyrimidine cytosine (C) – three hydrogen bonds are formed between these bases
This is known as complementary base pairing
These pairs are known as DNA base pairs
ionic interactions
NH3+ and COO-
hydrogen bond = teritary structure
H and oxygen from OH group on 2 amino acids
under acidic conditions =
affect COO- group
amino acid + alcohol
ester + water
heat proteins with concentrated HCl
If proteins are heated with concentrated hydrochloric acid
or concentrated strong alkalis they can be hydrolysed and split
back into their constituent amino acids.
3D arrangement
The 3D arrangement of amino acids with the
polypeptide chain in a corkscrew shape is held in
place by Hydrogen bonds between the H of –Nδ- —Hδ+ group and the –O of Cδ+=Oδ- of the fourth
amino acid along the chain
stereospecific active site
Stereospecific active site
If the substrate is chiral then its likely that only one enantiomer will have the correct stereochemistry to fit
in the active site of the enzyme and so only one isomer will be catalysed.
enzymes
-enzymes are proteins. Drugs = enzyme inhibitor by blocking the active site
-enzymes are biological catalysts + globular proteins
Active site = stereospecific = only catalyse one type of enantiomer
-enzyme inhibition = cyanide, sarin gas
glyciene
-most amine acids are optically active as they have chiral molecule (4 groups) bonded to the central carbon atom
-glyciene is the only amino acid not optically acid NH2CH2COOH
ribose vs deoxyribose
Ribose = 3 OH groups
Deoxyribose = 2 OH groups
deoxyribose = known as
2-deoxyribose
numbering pentose sugar
Number deoxyribose from carbon to the right of the central oxygen atom in the pentose sugae
binding to dexoyribose
Phosphate binds to 5th carbon on deoxyribose and it looses a H to form O- (proton donor)
Bases attach in place of OH group on first carbon of deoxyribose
hydrogen bonds
Guanine and cytosine = 3 hydrogen bonds (O-H-HN / N-H-N / NH-H-O)
Adenine and thymine = 2 hydrogen bonds = (N-H-N / HN-H-O)
anti cancer drugs
-cancer = forms as the result of uncontrollable cell division. As cells multiply it can grow into a tumour and can sometimes spread to other parts of the body
-cisplatin = anti cancer drug
cisplatin
Cisplatin binds to guanine on DNA, distorting the shape of DNA and preventing replication. Two chloride ions leave as well
Cisplatin also bonds to DNA of healthy cells. As cancer cells replicate more quickly than normal cells the effect of the drug is greater on cancer cells.
Coordinate bond to nitrogen
Hydrogen bond to oxygen
Risk of anti-cancer drugs = kill healthy cells as they attach to DNA in healthy cells
explain how these hydrogen bonds form
electron deficient hydrogen attracts lone pair of electrons on oxygen
name the compounds H2N(CH2)6NH2
hexane-1,6-diamine
structure of 2-amino propanoic acid
NH2CH(CH3)COOH
suggest why urea is effective at separating the complementary DNA strands
amino acids in urea are able to subsitute hydrogen bonds in DNA
explain one way the administration of cisplatin can be done to reduce side effect
administer in small amounts to target mainly tumour cells
