3.3.13 Amino acids, Proteins and DNA (A2)

Question 1

what is the formula of the amine group?

Answer 1

H2N

Question 2

what is the formula of the carboxyl group?

Answer 2

COOH

Question 3

what does bifunctional mean?

Answer 3

molecule has two functional groups

Question 4

how many different side chains are there? (amino acids)

Answer 4

20

Question 5

what is a chiral carbon?

Answer 5

carbon with 4 different functional groups attached

Question 6

how many of the 20 amino acids are chiral?

Answer 6

19

Question 7

what are zwitterions?

Answer 7

molecules with both a positive and negative charge

Question 8

what are the properties of zwitterions?

Answer 8

ionically bond due to charges
highly soluble in water
high melting points
white solids at room temp.

Question 9

which end of an amino acid do we name it from?

Answer 9

carboxyl group end

Question 10

state why each amino acid has a different Rf value when using TLC

Answer 10

each amino acid has different (relative) affinity/attraction to/solubility in
stationary and mobile phases

Question 11

how can the amino acids be made visible after a TLC experiment?

Answer 11

UV light/lamp

Question 12

which two bases in DNA form 3 hydrogen bonds between them?

Answer 12

cytosine and guanine

Question 13

which bases in DNA form 2 hydrogen bonds between them?

Answer 13

adenine and thymine

Question 14

what is the functional group of an amide?

Answer 14

RCONR’R’’

R - C - N - R’
O R’’

Question 15

what is the functional group of an amine?

Answer 15

nitrogen atom with a lone pair

Question 16

Suggest a suitable reagent for the hydrolysis of a protein (in TLC)

Answer 16

Conc HCl

Question 17

what do amino acids react together to form?

Answer 17

peptides

Question 18

what type of reaction happens between two amino acids?

Answer 18

condensation reaction

Question 19

what is released in a condensation reaction?

Answer 19

molecule of water

Question 20

what is a peptide bond?

Answer 20

secondary amide group

Question 21

what is a peptide bond also called?

Answer 21

amide bond

Question 22

what is a polypeptide?

Answer 22

a polymer of up to 50 amino acid residues

Question 23

what is a protein?

Answer 23

a polymer of more than 45 amino acid residues

Question 24

what is an amino acid residue?

Answer 24

what’s left after H2O is lost

Question 25

how can a peptide bond / amide bond be broken?

Answer 25

heating with moderately concentrated acid or alkali

Question 26

in living organisms how are proteins hydrolysed?

Answer 26

enzymes

Question 27

what amount of bonds gives nitrogen a single positive charge?

Answer 27

4

Question 28

why does nitrogen have a positive charge when it has 4 bonds attached?

Answer 28

forms a dative / coordinate bond

Question 29

how is the alpha helix structure held together?

Answer 29

hydrogen bonds

Question 30

what do hydrogen bonds form between in amino acid secondary structure?

Answer 30

d+ hydrogen in the N-H bond the oxygen lone pair in the C=O bond in another amino acid residue

Question 31

what are not included in hydrogen bonding in amino acids?

Answer 31

the R groups

Question 32

are hydrogen bonds amino acid specific? why?

Answer 32

no R groups not involved in H bonds

Question 33

what level of protein structure is amino acid specific?

Answer 33

tertiary

Question 34

what do ionic bonds form between in tertiary structure?

Answer 34

R groups which can be ionised

Question 35

what do disulphide bridges (covalent bonds) form between in tertiary structure?

Answer 35

cysteine side chains

Question 36

what is the process of disulfide bridges forming between cysteine side chains called?

Answer 36

oxidation ( loss of H2 )

Question 37

are the hydrogen bonds involved in protein tertiary structure amino acid specific? why?

Answer 37

yes occur between R groups containing O/N

Question 38

what happens when an amino acid is put in alkaline solution?

Answer 38

the hydrogen ion is removed from the -NH3+ group no longer a zwitterion only has a negative charge on the COO

Question 39

what happens when an amino acid is put in an acidic solution?

Answer 39

the COO- part of the zwitterion picks up a hydrogen ion. no longer a zwitterion only has a positive charge on the NH3

Question 39

what method can we use to work out which amino acids are present once we have hydrolysed the peptide?

Answer 39

chromatography separating compounds in a soluble mixture (all soluble)

Question 39

what is a technique used to determine the secondary and tertiary structure of a protein?

Answer 39

x ray diffraction

Question 40

what are the steps in using TLC?

Answer 40

1. Get the TLC plate but only handle on the sides 2. Using a pencil draw the base line around 1.5cm from the bottom of the plate 3. Put a dot of your mixture in the middle of the baseline 4. fill beaker with 1cm cubed of solvent 5. put the TLC plate into the beaker and use watch glass as a lid 6.Run the chromatogram until solvent reaches near the top 7. Remove from beaker and mark solvent front 8. leave to dry in a fumehood

Question 41

why do we only handle TLC plates from the side?

Answer 41

to not contaminate with the proteins from our hand

Question 42

why do we leave TLC chromatograms in a fumehood to dry?

Answer 42

solvents can be toxic

Question 43

why do we use a lid for TLC?

Answer 43

prevent evaporation of the solvent

Question 44

what is a TLC plate?

Answer 44

glass plate covered in a thin layer of silicon dioxide

Question 45

how can we visualise the amino acids after TLC?

Answer 45

UV light ninhydrin - purple stain

Question 46

name an example of a protein.

Answer 46

enzymes such as DNA helicase DNA polymerase amylase

Question 47

how many reactions does one enzyme catalyse?

Answer 47

one

Question 48

what are globular proteins?

Answer 48

proteins that have a compact spherical shape

Question 49

what is the main property of globular proteins?

Answer 49

soluble in water

Question 50

where does the reaction take place in an enzyme?

Answer 50

active site

Question 51

how does the substrate bind to the active site?

Answer 51

intermolecular forces

Question 52

what do the intermolecular forces form between in enzymes and substrates?

Answer 52

R groups in the enzyme's active site and R groups of the amino acids in the substrate

Question 53

what do the intermolecular forces do when an enzyme binds to the substrate?

Answer 53

promote the movement of electrons within the substrate lover the Ea of the reaction

Question 54

can enzymes tell the difference between E/Z isomers?

Answer 54

yes

Question 55

how can enzymes be stopped in their reaction?

Answer 55

denaturing blocking their active site

Question 56

what do nucleotides contain?

Answer 56

deoxyribose sugar (5C) phosphate group nitrogen base

Question 57

why is the sugar called deoxyribose?

Answer 57

no oxygen bound to carbon number 2

Question 58

why are the nitrogenous bases basic?

Answer 58

they have nitrogen atom which can accept a proton

Question 59

what reaction is used to create nucleotides?

Answer 59

condensation reaction

Question 60

how many molecules of water are released in the condensation of nucleotides?

Answer 60

2 per nucleotide

Question 61

how many condensation reactions happen in the creation of one nucleotide?

Answer 61

2

Question 62

what direction do DNA strands run to each other?

Answer 62

anti parallel

Question 63

what does the 2 ring base hydrogen bond to?

Answer 63

a 1 ring base

Question 64

what does the 2 ring base binding to a 1 ring base ensure?

Answer 64

the DNA structure is straight and uniform

Question 65

why is urea effective at separating the complimentary strands in DNA?

Answer 65

the amino groups are able to substitute for the H bonds in the double helix

Question 66

where is the nitrogenous base located on a nucleotide?

Answer 66

on the first carbon

Question 67

where is the phosphate group located on a nucleotide?

Answer 67

on the third carbon

Question 68

why is cisplatin called so?

Answer 68

two different substituent groups next to each other around the transition metal

Question 69

what is cisplatin?

Answer 69

anti cancer drug

Question 70

what does cisplatin do?

Answer 70

binds to DNA distorts the shape prevents replication prevents cell division

Question 71

where does cisplatin bind to DNA?

Answer 71

nitrogen in two adjacent guanine bases

Question 72

which is the better ligand? water or nitrogen?

Answer 72

nitrogen

Question 73

what are the side effects of cisplatin?

Answer 73

cannot discriminate between healthy and cancerous cells hair follicles also effected because they replicate quickly - much like cancer cells