unit 6 section 4 amino acids, proteins and DNA Flashcards

1
Q

what two functional groups does an amino acid have

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

are amino acids amphoteric and what does that mean

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

how can an amino acid act as an acid

A

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

COOH = COO^- + H +

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

how can an amino acid act as a base

A

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

NH2 + H^+ = NH3^+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

how do you name an amino acid systematically

A
  • 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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is a zwitterions

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

where can zwitterions exist and what is an isoelectric point

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

when does an amino acid become a zwitterion

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

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

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

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

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

in what conditions is a zwitterions formed

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

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

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

how do you make an amino acid visible (coloured)

A

-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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

how do you identify amino acids

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what is the formula for the Rf value

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what is a protein and what is it made of

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

explain how two amino acids join together to form a dipeptide

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what happens if two different amino acids combine together

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

how do you break up a protein into its amino acids

A

you use hydrolysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what is the method of hydrolysing proteins

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

how do you describe the structure of proteins

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what is the primary structure of an protein

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what is the secondary structure of a protein

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

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

A

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

25
Q

what is the tertiary structure of a protein

A

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

26
Q

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

A

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

27
Q

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

A

the two main types are hydrogen bonds and disulfide bonds

28
Q

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

A

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

29
Q

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

A

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.

30
Q

what is a residue

A

it is an amino acid that is part of a protein

31
Q

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

A

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

32
Q

what do enzymes do

A

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

33
Q

what molecules do enzymes act upon

A

substrates

34
Q

what is the active site of an enzyme

A

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

35
Q

what is the lock and key model

A

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

36
Q

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

A

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

37
Q

what is an inhibitor

A

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

38
Q

what factors affect the inhibitation

A

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

39
Q

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

A

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.

40
Q
A
41
Q

explain how an inbitor can be used as a drug

A

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

42
Q

how are the inbitors that are drugs found

A

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.

43
Q

what does DNA stand for and what does it contain

A

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

44
Q

what is DNA made of

A

they are made up of lots of monomers called nucleotides

45
Q

what are the main three components that make up a nucleotide

A

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

46
Q

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

A

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

47
Q

what is the sturcture of a nucleotide

A

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

48
Q

what is a polynucleotide

A

it is a chain of nucleotides

49
Q

how does a polynucleotide occur

A

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

50
Q

how is the sugar backbone of phosphate formed

A

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

51
Q

what is the structure of DNA

A

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

52
Q

what bonds hold bases together

A

strong hydrogen bonds

53
Q

what are the base pairs

A

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

54
Q

why do the bases only pair to a certain other base

A

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

55
Q

what is cisplatin

A

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

56
Q

what is the difference between cisplatin and transplatin

A

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

57
Q

how is cisplatin and anticancer drug

A

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

58
Q

what are the adverse affects of cisplatin

A

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

59
Q

how can the adverse affects of cisplatin be reduced

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