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Aqa a level chemistry > Amino acids, DNA etc > Flashcards

Amino acids, DNA etc Flashcards

1
Q

proteins = notes from specification

A

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.

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2
Q

acid vs base

A

Acid = proton donor and electron acceptor

Base = proton acceptor and lone pair donor

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3
Q

general formula of amino acids

A

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

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4
Q

zwittertons

A

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

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5
Q

protonated vs deprotonated

A

Amine group = gains proton (protonated)

Carboxyl group = looses proton (deprotonated)

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6
Q

acid solution

A

Acid solution = NH3+ and COOH

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7
Q

neutral solution

A

Neutral solution = NH3+ and COO-

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8
Q

alkaline solution

A

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+

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9
Q

acid hydrolysis of amino acids

A

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

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10
Q

cysteine (expection)

A

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

-formation of disulfide bridges

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11
Q

glyciene =

A

not optically active

2 of same groups around chiral carbon

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12
Q

what do R groups affect

A

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

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13
Q

optically active

A

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

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14
Q

fiborous proteins

A

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

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15
Q

globular proteins

A

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

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16
Q

naming amino acids

A

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

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17
Q

melting point = zwitterton

A

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.

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18
Q

amino acids as buffers

A

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.

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19
Q

proteins

A

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

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20
Q

in acidic conditions

A

all amine groups turn to NH3+

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21
Q

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

A

change all COOH groups to COO-

22
Q

solubility

A

However, it’s not just lysine.

All amino acids form zwitterions.

So, all amino acids are soluble in water.

23
Q

alpha helixes

A

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)

24
Q

beta pleated sheets

A

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

25
Q

enzymes as biological catalysts

A

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

26
Q

enzyme specifity

A

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

27
Q

drug receptor interactions

A

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

28
Q

DNA nucelotide

A

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

29
Q

hydrogen bonding

A

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

30
Q

ionic interactions

A

NH3+ and COO-

31
Q

hydrogen bond = teritary structure

A

H and oxygen from OH group on 2 amino acids

32
Q

under acidic conditions =

A

affect COO- group

33
Q

amino acid + alcohol

A

ester + water

34
Q

heat proteins with concentrated HCl

A

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

35
Q

3D arrangement

A

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

36
Q

stereospecific active site

A

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.

37
Q

enzymes

A

-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

38
Q

glyciene

A

-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

39
Q

ribose vs deoxyribose

A

Ribose = 3 OH groups

Deoxyribose = 2 OH groups

40
Q

deoxyribose = known as

A

2-deoxyribose

41
Q

numbering pentose sugar

A

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

42
Q

binding to dexoyribose

A

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

43
Q

hydrogen bonds

A

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)

44
Q

anti cancer drugs

A

-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

45
Q

cisplatin

A

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

46
Q

explain how these hydrogen bonds form

A

electron deficient hydrogen attracts lone pair of electrons on oxygen

47
Q

name the compounds H2N(CH2)6NH2

A

hexane-1,6-diamine

48
Q

structure of 2-amino propanoic acid

A

NH2CH(CH3)COOH

49
Q

suggest why urea is effective at separating the complementary DNA strands

A

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

50
Q

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

A

administer in small amounts to target mainly tumour cells

Aqa a level chemistry (26 decks)

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