unit 6 section 4 amino acids, proteins and DNA

Question 1

what two functional groups does an amino acid have

Answer 1

it has a carboxyl group (COOH) and an amine group (NH2)

Question 2

are amino acids amphoteric and what does that mean

Answer 2

yes amino acids are amphoteric, this means that they have the properties of an acid and a base

Question 3

how can an amino acid act as an acid

Answer 3

they can act as an acid because the carboxyl group is acidic - it can donate an proton

COOH = COO^- + H +

Question 4

how can an amino acid act as a base

Answer 4

they can act as a base because the amino group ( amine group ) is basic - it can except a proton

NH2 + H^+ = NH3^+

Question 5

how do you name an amino acid systematically

Answer 5

• find the longest chain that has the carboxylic acid group and write its name
• number the carbons in the chain starting with the carbon in the carboxylic acid group as number 1
• write down the position of any NH2 groups and use the word amino to show that
  -write down the name of any other functional groups and say what carbon they are on

Question 6

what is a zwitterions

Answer 6

amino acids can exist as zwitterions. a zwitterions is an ion that is dipolar - it has both positive and negative charge in different parts of the molecule

Question 7

where can zwitterions exist and what is an isoelectric point

Answer 7

zwitterions only exist near an amino acids isoelectric point. the isoelectric point is the PH where the overall charge of the amino acid is zero.

Question 8

when does an amino acid become a zwitterion

Answer 8

an amino acid becomes a zwitterion when its amino group is protonated into NH3^+ and its COOH group is deprotonated into COO^-

Question 9

what happens to the amino acid when the conditions is more acidic ( low ph ) than the isoelectric point

Answer 9

in conditions more acidic than the isoelectric point, the NH2 group is likely to be protonated but the COOH group is unchanged - so the amino acid will carry positive charge but not a negative charge.

Question 10

what happens to an amino acid when the conditions is more basic ( high ph ) than the isoelectric point

Answer 10

in conditions more basic than the isoelectric point, the COOH group is likely to loose a proton but the NH2 group will be unchanged - so the amino acid will carry a negative charge but not a positive charge.

Question 11

in what conditions is a zwitterions formed

Answer 11

only at or near when the isoelectric point are both the carboxylic group and the amino group are likely to be ionised - forming a zwitterion

Question 12

how do you separate mixtures of amino acids and why does that happen

Answer 12

through thin layer chromatography (TLC)
- this is because the amino acids have different R groups, they will have different solubilities in the same solvent

Question 13

how do you make an amino acid visible (coloured)

Answer 13

-this can be done by spraying ninhydrin on the plate which will make the amino acid turn purple.
- another way is by using a special plate which has fluorescent dye added to it. the dye glows in UV light. when there are spots of chemicals on the plate, they cover the fluorescent dye - so the spots appear dark.

Question 14

how do you identify amino acids

Answer 14

this is done by using the chromatogram to calculate the Rf value

Question 15

what is the formula for the Rf value

Answer 15

Rf = x/y = distance travelled by spot/ distance travelled by solvent

Question 16

what is a protein and what is it made of

Answer 16

proteins are condensation polymers of amino acids- they are made of up lots of amino acids joined together by peptide links .

Question 17

explain how two amino acids join together to form a dipeptide

Answer 17

this is done by removing a molecule of water between the two amino acids. and OH from on of the COOH groups will be remove and from the other amino acid a H will be removed from the NH2 group

Question 18

what happens if two different amino acids combine together

Answer 18

then two different dipeptides will form because the amino acid can join either way round.

Question 19

how do you break up a protein into its amino acids

Answer 19

you use hydrolysis

Question 20

what is the method of hydrolysing proteins

Answer 20

this can be done by adding 6 mol dm^-3 of hydrochloric acid, and then heat the mixture under reflux for 24 hours

Question 21

how do you describe the structure of proteins

Answer 21

proteins are big. so they are describe in four levels, primary, secondary, tertiary and quaternary.

Question 22

what is the primary structure of an protein

Answer 22

the primary structure is the sequence of amino acids in a long chain that makes up the protein.

Question 23

what is the secondary structure of a protein

Answer 23

the peptide links can form hydrogen bonds with each other, meaning the chain isnt a straight line. the shape of the chain is called the secondary structure.

Question 24

what are the common structures for a secondary structure of a protein

Answer 24

the most common secondary structure is spiral called α-helix. another common secondary structure a β-pleated sheet. this is a thin layer of protein folded like a concertina

Question 25

what is the tertiary structure of a protein

Answer 25

extra bonds can form between different parts of the polypeptide chain, which gives the protein a 3 dimensional shape.

Question 26

what causes the protein to fold or twist in a secondary or tertiary structure

Answer 26

the secondary and tertiary structure of proteins are formed by intermolecular forces causing the amino acid chain to fold or twist

Question 27

what two main types of bond hold the shape of a protein

Answer 27

the two main types are hydrogen bonds and disulfide bonds

Question 28

explain where hydrogen bonds exist within an protein and how they are formed

Answer 28

hydrogen bonding only exists between polar groups such as -OH and NH2. these groups contain electronegative atoms that induce a partial positive charge on the hydrogen atom. the hydrogen is then attracted to lone pairs of electrons on adjacent polar groups and a hydrogen bond is formed

Question 29

explain when disulfide bonding occurs within a protein and how it occurs

Answer 29

disulfide bonding occurs between residues of the amino acid cysteine. cysteine contains a thiol group (SH) and this thiol group can loose its H atom and join together to form a disulfide -s-s- bond with another thiol group. these disulfide bonds link together different parts of the protein chain, and to help stabalise the tertiary structure.

Question 30

what is a residue

Answer 30

it is an amino acid that is part of a protein

Question 31

what factors can affect hydrogen bonding and the formation of disulfide bonds

Answer 31

factors such as temperature and PH affect hydrogen bonding and the formation of disulfide bonds and so can change the shape of the protein.

Question 32

what do enzymes do

Answer 32

the speed up chemical reactions by acting as a biological catalyst. they catalyse every metabolic reaction in the bodies of living organisms

Question 33

what molecules do enzymes act upon

Answer 33

substrates

Question 34

what is the active site of an enzyme

Answer 34

it is an area of the enzyme that the substrate fits into so that is can interact with the enzyme.
the active site is three dimensional- it is part of the tertiary structure of a protein enzyme

Question 35

what is the lock and key model

Answer 35

Enzymes are specific and only work with certain substrates. the lock and key models states that, for an enzyme to work, the substrate must fit into the active site

Question 36

” the active site of enzymes are sterospecific “ what does sterospecific mean

Answer 36

it means that they only work with one enantiomer of a substrate

Question 37

what is an inhibitor

Answer 37

it is a molecule that has a similar shape to the substrate. they compete with the substrate to bond with the active site of the enzyme however it does not cause a reaction and it stays in the active site and blocks it

Question 38

what factors affect the inhibitation

Answer 38

the concentration of inhibitors to substrate and the strength of the bond that the inhibitor has to the active site.

Question 39

give an example of how an inhibitors can be used as a drug

Answer 39

some antibiotics work by blocking the active site of enzymes of bacteria that helps to make the their cell walls. this causes the cell wall to weaken over time, so the bacteria eventurally burst.

Question 41

explain how an inbitor can be used as a drug

Answer 41

some drugs are inhibitors that block the active site of enzymes that stops them from working

Question 42

how are the inbitors that are drugs found

Answer 42

often new inhibitors are found by trial and error. scientist will carry out experiments using lots of compounds to see if they work as an inhibitor for a particular enzyme. they then adapt the one that works to improve them. this takes a long time, however this can be sped up by using a computer to model the active site of the enzyme.

Question 43

what does DNA stand for and what does it contain

Answer 43

deoxyribonucleic acid, it contains all the genetic information of an organism.

Question 44

what is DNA made of

Answer 44

they are made up of lots of monomers called nucleotides

Question 45

what are the main three components that make up a nucleotide

Answer 45

a phospate group, the pentose sugar 2-deoxyribose, and a base

Question 46

what are the 4 types of bases that can be in a nucleotide

Answer 46

one of either adenine (A), cytosine (C) , guanine (G), thymine (T)

Question 47

what is the sturcture of a nucleotide

Answer 47

a phosphate ion bonded to a pentose sugar bonded to a base

Question 48

what is a polynucleotide

Answer 48

it is a chain of nucleotides

Question 49

how does a polynucleotide occur

Answer 49

covalent bonds form between the phosphate groups of one nucleotide and the sugar of another- this makes what is called the sugar-phosphate backbone of the chain

Question 50

how is the sugar backbone of phosphate formed

Answer 50

it is formed by condensation polymerisation- the molecule fo water is lost and the phosphodiester bond is formed

Question 51

what is the structure of DNA

Answer 51

DNA is made up of two polynucleotides stands that spiral together to form a double helix structure.

Question 52

what bonds hold bases together

Answer 52

strong hydrogen bonds

Question 53

what are the base pairs

Answer 53

A-T ( adenine - thymine )
C-G ( cytosine - guanine )

Question 54

why do the bases only pair to a certain other base

Answer 54

this is because the bases are complimentary, the hydrogen’s form hydrogen bonds with anything that is highly electronegative ( N O F )

Question 55

what is cisplatin

Answer 55

it is a complex of platinum(II) with two chloride ion ligands and two ammonia ligands in a square planar structure

Question 56

what is the difference between cisplatin and transplatin

Answer 56

cis - functional groups are next to each other
trans - functional groups are opposite each other

Question 57

how is cisplatin and anticancer drug

Answer 57

the cisplatin stops the tumor cells from reproducing by stopping the DNA strands from unwinding by causing a kink.

Question 58

what are the adverse affects of cisplatin

Answer 58

cisplatin can also bind to DNA in normal cells. this is a problem for any healthy cell that reproduces regularly as it can stop them from reproducing. this can lead to hair loss and suppress the immune system

Question 59

how can the adverse affects of cisplatin be reduced

Answer 59

• give to patient in low dosages
• target the tumor cells directly, use a method to transport it directly to the tumor cells.