Amino Acids, Proteins And DNA

Question 1

What are amino acids?

Answer 1

Molecules that contains both a carboxylic acid group and an amine group on the same carbon
The carbon is bonded to a hydrogen and a variable R group

Question 2

Why do amino acids show optical isomerism? What is the exception for this?

Answer 2

All amino acids contain a chiral carbon, so the carbon is bonded to four different groups.

Except glycine, because it’s R group is hydrogen

Question 3

What does amphoteric mean?

Answer 3

A substance that acts as both an acid and a base

Question 4

Why are amino acids amphoteric?

Answer 4

The amine group can react with H+ to form NH3+ (acts as a base)
The carboxyl acid can react with OH- to form COO- and water (acts as an acid)

Question 5

What is the isoelectronic point?

Answer 5

The pH at which a molecule has no net electrical charge

Question 6

What is it called when the isoelectronic point is reached in an amino acid?

Answer 6

A zwitterion

Question 7

What is a zwitterion?

Answer 7

An amino acid where the carboxyl group donates a proton, that is accepted by the amine group.
The amino acid has no overall electrical charge so it has reached its isoelectronic point

Question 8

Why do different amino acids have different isoelectronic points?

Answer 8

Due to their R groups
If the R group is more acidic, the isoelectronic point (pH) will be lower
If the R group is more basic, the isoelectronic point (pH) will be higher

Question 9

How does pH affect the structure/ nature of amino acids?

Answer 9

If pH is below isoelectronic point, it acts as a base and accepts H+ (to make NH3+)
If pH is above isoelectronic point, it acts as an acid and donates H+ (to make COO- and water)

Question 10

What are physical properties of amino acids that are a fault of them being zwitterion ions?

Answer 10

Crystalline solid structures that have higher mp and bp- due to zwitterions forming ionic bonds with each other that require lots of energy to be overcome

Dissolve in water, but not do dissolve easily in non-polar solvent- as zwitterions interact strongly with polar solvent molecules, so the amino acid can dissolve

Question 11

What are peptides?

Answer 11

Peptides are compounds made of amino acids joined by peptide links, in a condensation reaction that removes a molecule of water

Question 12

What is an amino acid residue?

Answer 12

What remains of an amino acid when in a peptide, after the molecule of water has been removed in the condensation reaction

Question 13

What are polypeptides?

Answer 13

Condensation polymers of amino acids

Question 14

How can different dipeptides/ polypeptides be formed by a condensation reaction between the same amino acids?

Answer 14

Depending on the order in which they are joined with peptide links

Question 15

What is hydrolysis?

Answer 15

The breaking of bonds using water

Question 16

Describe the two different hydrolysis of peptides

Answer 16

ACID HYDROLYSIS-
6 Moldm-3 HCl
Heat reflux for 24 hours

ALKALINE HYDROLYSIS
Moderately concentrated NaOH
Aqueous, heat

Question 17

After hydrolysis, how can mixtures of amino acids be separated and visible?

Answer 17

Using thin layer chromatography
Locating agents- ninhydrin and UV light. This will turn them purple

Question 18

What is two dimensional TLC, why and how is it used?

Answer 18

Used when amino acids have very similar Rf values in a particular solvent, so cannot be differentiated
(Or used to give greater confidence when identifying amino acids)

• a square TLC plate is used, the mixture is spotted in one corner of the plate.
• these spots separate along the endless of the plate
• the plate is then turned 90*
• chromatogram is ran again with a different solvent, the amino acids with similar Rf values will separate
• each spot will now have two Rf values that can be compared with a reference in the data base
  This gives greater confidence when identifying the spots

Question 19

What are proteins?

Answer 19

Naturally occurring condensation polymers of amino acids, joined by many peptide links

Question 20

Describe the structure of the primary structure in proteins

Answer 20

Primary structure is the sequence of amino acids, each amino acid residue is linked to the next by peptide links
Relatively stable, due to the string covalent bonds (peptide links) between amino acids

Question 21

Describe the secondary structure of proteins

Answer 21

Regular 3D structure formed by part of the amino acids chain
Such as a-helix or b-pleated sheet
Held together by hydrogen bonds between the NH of one amino acid and the CO of another
Weaker than the covalent bonds in 1 structure, so can be disrupted easily by changes of pH or temp

Question 22

What are the features of a-helix and b-plated sheet secondary structures?

Answer 22

A-helix: spiral structure where the R groups of each amino acid residue point out of the spiral

B-pleated sheet: planar arrangement with a polypeptide backbone, where the R groups of each amino acid residue point above and below the plane

Question 23

Describe the tertiary structure of a protein

Answer 23

The three dimensional arrangement of a single polypeptide chain
Held by bonds between the SIDE CHAINS:
Hydrogen bonds (between side chains containing H and O or N)
VDW forces (between non-polar side chains)
Sulfur-sulfur bonds (between the -SH of two amino acid residues)
Ionic bonds (between side chains with COOH and NH2 as they can be polarised)

Easily disrupted by changes of temp, pH or polarity of a substance they are dissolved in

Question 24

What are sulfur-sulfur bonds in the tertiary structure of proteins? Between which amino acids do they occur?

Answer 24

A covalent bond formed between the -thiol (-SH) groups of a pair of cysteine amino acid residues
This bond releases H2

Question 25

What is an enzyme?

Answer 25

A protein based catalyst that speeds up the reactions of biochemical reactions in the body

Question 26

Describe the general structure of an enzyme

Answer 26

Consist of one or more polypeptide, with co-factors Active site, which has a specific complimentary structure to substrate

Question 27

What is a substrate?

Answer 27

The compound that an enzyme acts upon

Question 28

What is the active site?

Answer 28

The region responsible for the enzymes catalytic activity Complimentary shape to the substrate

Question 29

Describe the structure of an active site, an how it carries out the lock and key hypothesis

Answer 29

The active site is a cleft on the surface of an enzyme, with a specific complimentary structure 3D shape. Contains the R groups from the amino acids residues in the polypeptide, which interact with the substrate to hold it in place. Uses hydrogen, ionic, DP-DP and VDW’s forces

Question 30

What is stereospecificity?

Answer 30

Where an enzymes active site is so selective it will only catalyse the reactions of one enantiomer of an optically active compound/substrate This is because only one enantiomer will have the correct special arrangement of its atoms to interact (form bonds with) the R groups in the active site

Question 31

Give an example of a substrate ad enzyme that has stereospecificity

Answer 31

Lactic acid ( CH3CH(OH)COOH ) has a chiral carbon, so has two enantiomers Oxidation is catalysed by the enzyme lactate dehydrogenase, which will only bind to one of the enantiomers

Question 32

What are enzyme inhibitors and how do they work?

Answer 32

Compounds that prevent an enzyme catalysed reaction They have a similar shape to the substrate, so bind to the active site and block it, preventing any substrates from binding and being catalysed

Question 33

What is structure directed drug design?

Answer 33

A modern day technique used to used to design drugs that inhibit enzymes that catalyse harmful diseases The tertiary structure of the enzyme/ active site is determined using techniques such as NMR Chemists use computer modelling to design molecules that will inhibit the enzymes involved in the disease

Question 34

Give an example of a drug made from structure directed drug design, and what it is used for

Answer 34

Relenza Prevents influenza infection, by inhibiting the enzymes neuraminidase

Question 35

What does DNA stand for, and what is its structure?

Answer 35

Deoxyribose nucleic acid Double stranded, two polynucleotides in the form of a double helix Phosphodiester bonds between nucleotides Hydrogen bonds between complimentary bases (3 between G and C, 2 between T and A)

Question 36

What is a polynucleotide?

Answer 36

Single strand of DNA Phosphodiester bonds between the phosphate group of one nucleotide and the sugar of another Forms a sugar-phosphate backbone

Question 37

What is the structure of one nucleotide? Hope are they formed?

Answer 37

2-deoxyribose sugar Phosphate group 1 of 4 bases (adenine, thymine, guanine, cytosine) Condensation reactions between phosphate and sugar, and the bases and sugar. Both reactions produce a molecule of water

Question 38

Where does a phosphate group bind to a 2-deoxyribose sugar?

Answer 38

Between the OH on the phosphate, and the CH2OH on the sugar

Question 39

Where does a base and 2-deoxyribose sugar bond?

Answer 39

Between the bottom right NH on the base, and the OH on carbon 1 in the sugar

Question 40

What are genes?

Answer 40

Specific sequences of DNA bases, that code for proteins

Question 41

What are benefits of hydrogen bonds between bases in DNA?

Answer 41

They are weaker than the covalent (phosphodiester) bonds between nucleotides, so they can break and separate the double helix without breaking the polynucleotide This allows transcription and DNA replication to occur

Question 42

What is cisplatin and its structure?

Answer 42

An anticancer drug A cis isomer of a complex of platinum (II) [PtCl2(NH3)2] Square planar structure

Question 43

How does cisplatin stop cancer?

Answer 43

Cancer is caused by cells in the body dividing uncontrollably Cisplatin binds to a N atom in a guanine residue in DNA. This blocks DNA transcription and replication, and triggers programmes cell death (apoptosis)

Question 44

Explain the mechanisms of the action of cisplatin

Answer 44

1- cisplatin is hydrolysed inside the cell [PtCl2(NH3)2] + H2O <—> [PtCl(H2O)(NH3)]+ + Cl- 2- ligand substitution reaction between a N in guanine and the H2O in the complex [PtCl(H2O)(NH3)]+ + —N: —> [PtCl(—N)(NH3)]+ + H2O 3- second ligand substitution reaction between another N from a nearby guanine and Cl- 4- cisplatin complex causes the DNA double helix to bend/ kink 5- DNA cannot unwind and be copied correctly, this triggers cell death

Question 45

What are the adverse effects of cisplatin?

Answer 45

Cisplatin binds to the guanine of DNA in normal cells as well as cancerous cells Hair cells, RBC and WBC replicate most frequently, so are most affected This causes hair loss, immune suppression and anaemia

Question 46

Where does the sugar phosphate group form between two nucleotides?

Answer 46

Between the top OH of the phosphate, and the bottom OH of the 2-deoxiribose (As shown on the data sheet)

Question 47

Where does the bond between the base and deoxiribose form in a DNA nucleotide?

Answer 47

Between the bottom right NH of the base, and the toon right OH of the sugar (As shown on the data sheet)

Question 48

Where does the bond between the phosphate and sugar from in a single DNA nucleotide?

Answer 48

Between the OH of the CH2OH in the sugar, and the bottom OH of the phosphate (As shown in the data book)