Amino acids, DNA etc

Question 1

proteins = notes from specification

Answer 1

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.

Question 2

acid vs base

Answer 2

Acid = proton donor and electron acceptor

Base = proton acceptor and lone pair donor

Question 3

general formula of amino acids

Answer 3

General formula of amino acids = RCH(NH)2COOH

Question 4

zwittertons

Answer 4

Amino acids exist as zwittertons which have both a permanent positive and permanent negative charge

Question 5

protonated vs deprotonated

Answer 5

Amine group = gains proton (protonated)

Carboxyl group = looses proton (deprotonated)

Question 6

acid solution

Answer 6

Acid solution = NH3+ and COOH

Question 7

neutral solution

Answer 7

Neutral solution = NH3+ and COO-

Question 8

alkaline solution

Answer 8

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+

Question 9

acid hydrolysis of amino acids

Answer 9

Acid hydrolysis of amino acids. Boil 6moldm-3 HCl for 24 hours

Question 10

cysteine (expection)

Answer 10

-two cysteine side chains end up next to eachother due to the folding in the peptide chain (CH2S)

-formation of disulfide bridges

Question 11

glyciene =

Answer 11

not optically active

2 of same groups around chiral carbon

Question 12

what do R groups affect

Answer 12

R groups = affect the size, polarity and name of amino acids

Question 13

optically active

Answer 13

All amino acids except glyciene are optically active since its bonded to 4 different groups around central carbon atom

Question 14

fiborous proteins

Answer 14

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

Question 15

globular proteins

Answer 15

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

Question 16

naming amino acids

Answer 16

-amino = prefix, root = longest carbon chain, suffix = oic acid

Question 17

melting point = zwitterton

Answer 17

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.

Question 18

amino acids as buffers

Answer 18

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.

Question 19

proteins

Answer 19

Proteins are polymers made from
combinations of amino acids.
The amino acids are linked by peptide links,
which are the amide functional group.

Question 20

in acidic conditions

Answer 20

all amine groups turn to NH3+

Question 21

draw an amino acid that reacts with NaOH at a high pH

Answer 21

change all COOH groups to COO-

Question 22

solubility

Answer 22

However, it’s not just lysine.

All amino acids form zwitterions.

So, all amino acids are soluble in water.

Question 23

alpha helixes

Answer 23

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)

Question 24

beta pleated sheets

Answer 24

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

Question 25

enzymes as biological catalysts

Answer 25

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

Question 26

enzyme specifity

Answer 26

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

Question 27

drug receptor interactions

Answer 27

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

Question 28

DNA nucelotide

Answer 28

A nucleotide is a building block consisting of a phosphate group, 2-deoxyribose and a nitrogenous base such as adenine, guanine, cytosine and thymine

Question 29

hydrogen bonding

Answer 29

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

Question 30

ionic interactions

Answer 30

NH3+ and COO-

Question 31

hydrogen bond = teritary structure

Answer 31

H and oxygen from OH group on 2 amino acids

Question 32

under acidic conditions =

Answer 32

affect COO- group

Question 33

amino acid + alcohol

Answer 33

ester + water

Question 34

heat proteins with concentrated HCl

Answer 34

If proteins are heated with concentrated hydrochloric acid or concentrated strong alkalis they can be hydrolysed and split back into their constituent amino acids.

Question 35

3D arrangement

Answer 35

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

Question 36

stereospecific active site

Answer 36

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.

Question 37

enzymes

Answer 37

-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

Question 38

glyciene

Answer 38

-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

Question 39

ribose vs deoxyribose

Answer 39

Ribose = 3 OH groups Deoxyribose = 2 OH groups

Question 40

deoxyribose = known as

Answer 40

2-deoxyribose

Question 41

numbering pentose sugar

Answer 41

Number deoxyribose from carbon to the right of the central oxygen atom in the pentose sugae

Question 42

binding to dexoyribose

Answer 42

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

Question 43

hydrogen bonds

Answer 43

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)

Question 44

anti cancer drugs

Answer 44

-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

Question 45

cisplatin

Answer 45

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

Question 46

explain how these hydrogen bonds form

Answer 46

electron deficient hydrogen attracts lone pair of electrons on oxygen

Question 47

name the compounds H2N(CH2)6NH2

Answer 47

hexane-1,6-diamine

Question 48

structure of 2-amino propanoic acid

Answer 48

NH2CH(CH3)COOH

Question 49

suggest why urea is effective at separating the complementary DNA strands

Answer 49

amino acids in urea are able to subsitute hydrogen bonds in DNA

Question 50

explain one way the administration of cisplatin can be done to reduce side effect

Answer 50

administer in small amounts to target mainly tumour cells

Question 51

reaction condition for elimination of haloalkane

Answer 51

ethanolic KOH high temperatures

Question 52

2 toxic gases formed when NaBr reacts with H2SO4

Answer 52

Br2 and SO2 H2SO4 = acts as an oxidising agent

Question 53

nucelophilic subsitution to alcohol =

Answer 53

NaOH = aqueous heat under reflux

Question 54

reagent for nucelophilic addition to form hydroxynitrile

Answer 54

KCN + H2SO4

Question 55

increase yield of X through nucelophilic subsitution

Answer 55

lower temperature less concentrated KOH

Question 56

optical isomerism formed through electrophilic addition

Answer 56

chiral compound = enatiomers 2 non-superimposible mirror images of eachother -secondary planar carbon attacked from both sides with equal probability 2-bromo isomer has chiral carbon

Question 57

equation for nitrile - amine

Answer 57

CNCH2CH2CN + 4H2 --> NH2 (CH2)4 NH2