PL - Bonding and structure *01 *02

Question 1

general structure of amino acids

Answer 1

have an amino group (NH2) and an carboxyl group (COOH)

H2NCH(R)COOH

Question 2

Formation of proteins

Answer 2

condensation polymers formed from amino acid monomers

amine group and carboxyl group react

molecule has a peptide link (O=C-N-H) and a molecule of water produced

Question 3

acids hydrolysis of proteins and conditions

Answer 3

at the peptide link

requires molecule of water

hot aq conc. (6moldm^-3) HCl and heated under reflux for 24hrs

this produces ammonium salt of the amino acid (has NH3+)

Question 4

techniques and procedures for paper chromatography

Answer 4

1) draw a pencil line near the bottom of a piece of chromatography paper and put a conc. spot of what you want to investigate
2) place paper into beaker with solvent (watch glass on top)
3) when solvent nearly reached top take it out and mark solvent spot

4) to identify spots - ninhydrin solution (purple) / iodine crystals
- circle spots and work out Rf value and use table of known Rf values to identify components of mixture

Question 5

Rf value =

Answer 5

distance travelled by spot / distance travelled by solvent

Question 6

how does Rf values help to identify substances

Answer 6

can compare with table of known Rf values to identify components

Question 7

PAG 6

Question 8

primary structure of proteins

Answer 8

the sequence of amino acids in the long chain that makes up the polypeptide chain (protein)

Question 9

secondary structure of proteins

Answer 9

the peptide links can from hydrogen bonds with eachother, this causes the secondary structure

alpha helix and beta pleated sheet

Question 10

tertiary structure of a protien

Answer 10

the chain of amino acids is often coiled and folded in a characteristic way that identifies that protein

extra bonds can form between different parts of the polypeptide chain, this gives the protein its 3-D shape.

Question 11

what bonds are involved in protein structure - primary

Answer 11

peptide bonds between amino acids

Question 12

what bonds are involved in protein structure - secondary

Answer 12

peptide links form HYDROGEN bonds with each other

Question 13

what bonds are involved in protein structure - tertiary

Answer 13

Forces between R-groups

1. ID-ID - weak attractions between non-polar side groups (eg. CH3)
2. Ionic interaction - formed between charged side groups (eg. NH3+, CO2-)
3. Hydrogen bonds - formed if R groups can (eg. -OH, -COOH, -NH2, -CONH2)
4. disulfide bridges - if R-group contain thiol group (-SH). Two sulfide groups can join together forming disulfide bond

Question 14

What is DNA made of?

Answer 14

phosphate group

deoxyribose

a base

• adenine
• cytosine
• guanine
• thymine

Question 15

what is RNA made of?

Answer 15

phosphate group

ribose

bases

• adenine
• cytosine
• guanine
• uracil

Question 16

How do nucleotides link up? (phosphate and sugar)

Answer 16

Condensation polymerisation

1. when a phosphate and sugar react a molecule of water is lost and a phospahte-ester link is formed
2. still -OH groups in phosphate-ester so further ester links can be formed
   - a polymer forms made up of an alternating phosphate-sugar chain
3. the phosphate group always attaches to the -CH2OH group and the -OH group on the adjacent carbon

Question 17

How do bases join to the sugar? (in DNA and RNA)

Answer 17

condensation reaction

the -OH group on the sugar reacts with the -NH group on the base

a molecule of water is lost

Question 18

What does DNA look like?

Answer 18

exists as a double helix

• made of 2 polynucleotide strands
• the 2 strands spiral together to form a double helix structure which is held together by H bonds between bases

(DNA has to twist so bases are in the right alignment and distance apart for complementary base pairs to form)

Question 19

What are the complementary base pair in DNA? Why?

Answer 19

A and T
- each can form 2 H bonds which allows them to pair up

C and G
- each can form 3 H bonds

other base pairings would put partially charged ions too close together so they would just repel each other, the bonding atoms just wouldn’t line up properly.

Question 20

what are pharmacophores?

Answer 20

in every cell there are receptors

• chemicals can fit into these receptors and temporarily bond with them
• this either inhibits or triggers a series of biochemical reactions

in order to be medicinally active, a drug molecule must have the correct molecular recognition with a receptor

the part of the drug that fits into the receptor and makes it medicinally active is the pharmacophores
- chemists try to design drugs with pharmacophores that fit exactly into target receptors in the body

Question 21

what does the fit of a pharmacophore into a receptor site depend on?

Answer 21

1. size and shape - has to have a particular structure that will fit into the receptor site
2. bond formation - functional groups in the pharmacophore form temporary bonds with functional groups in the receptor
   - mostly ionic interactions or intermolecular forces
3. orientation - if the pharmacophores has E/Z/optical isomers, then only one of the isomers will fit

Question 22

What does the fit of a pharmacophore into a receptor site depend on: Bond formation (in detail)

Answer 22

dipole-dipole interations - can form between receptor and any polar functional groups in the pharmacophore

hydrogen bonding - pharmacophores containing functions groups such as amines, alcohols, carboxylic acids may be able to form hydrogen with receptor site

ionic interaction - acidic and basic functional groups can donate or accept protons to become charged and so form electrostatic attractions with the receptor site

Question 23

What does modifying pharmacophores do?

Answer 23

changes the pharmacological activity

Question 24

How can you modify pharmacophores?

Answer 24

can tweak bits of the molecule to make a drug more effective or to reduce side effects