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Chemistry > 3.3.13 Amino acids, proteins and DNA > Flashcards

3.3.13 Amino acids, proteins and DNA Flashcards

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1
Q

Draw structure of amino acid

A
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2
Q

AMINO ACIDS ARE AMPHOTERIC SO THEY HAVE ACIIC AND BASIC PROPERTIES.

AMINO ACIDS ARE CHIRAL MOLECULES EXCEPT GLYCINE (as it has H instead of side chain). SO THEY ROTATE PLANE POLARISED LIGHT

A
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3
Q

How do you name amino acids

A
  1. find longest carbon chain
  2. number carbons starting from carboxyl group
  3. note which carbon the NH2 is attached to (named amino)
  4. name any other groups in standard way

so it is an …amino….oic acid

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4
Q

define zwitterion, explain this with the structure of amino acid as a zwitter ion

A

a molecule with both positive and negative ions

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5
Q

An amino acid only exists as a zwitterion at its isoelectric point, define isoelectric point

A
  • the pH at which the average overall charge is 0.
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6
Q

What is th isoelectric point of an amino acid dependant on

A

its R group

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7
Q

Explain the change that occurs if pH gets altered above or below the isoelectric point of the amino acid

A
  • if pH is lower than isoelectric point then COO- is likely to accept a H+

-if pH is above isoelectric point then NH3 is likely to lose a H+

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8
Q

How can we identify different amino acids and why is this possible

A

via Thin layer chromatography

  • TLC allows us to separate and identify amino acids as they have different solubilities
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9
Q

Explain the process of TLC and the equipment/reagents

A
  • TLC uses stationary phase of silica or alumina mounted on a glass/metal plate
  • pencil base line drawn on plate
    -drops of different amino acid mixture along base line
  • solvent in beaker must be below base line level
  • cover beaker with lid to prevent solvent evaporating
  • leave solvent to move near top of plate
    -remove, mark solvent front and let dry
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10
Q

How do you spot amino acid front on the chromatogram if amino acids are colourless?

A

1: VIA FLUORESCENT DYES AND UV LIGHT
- add fluorescent dye to silica/alumina
-shine UV light to see
-colourless spots block glow from fluorescent dye
-circle round these spots to mark

2: VIA IDOINE/NINHYDRIN
- place chromatogram in sealed jar with few iodine crystals
-iodine vapour sticks to chemicals on plate dying it purple

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10
Q

How do you spot amino acid front on the chromatogram if amino acids are colourless?

A

1: VIA FLUORESCENT DYES AND UV LIGHT
- add fluorescent dye to silica/alumina
-shine UV light to see
-colourless spots block glow from fluorescent dye
-circle round these spots to mark

2: VIA IDOINE/NINHYDRIN
- place chromatogram in sealed jar with few iodine crystals
-iodine vapour sticks to chemicals on plate dying it purple

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11
Q

How to calculate Rf values and find what compound it is

A

Rf = distance travelled by spot / distance travelled by solvent front

compare your experimental Rf value to library of know Rf values to find the amino acid / compounds

(CONDITIONS FOR YOUR EXPERIMENT MUST BE THE SAME AS IN LIBARY OF VALUES IN ORDER TO CORRECTLY COMPARE Rf VALUES)

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12
Q

What links amino acid monomers to form a polypeptide?

A

peptide bond/link

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13
Q

Draw the structure of a dipeptide or repeating unit of polypeptides

A
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14
Q

In order to hydrolyse polypeptides, what conditions does it require

A
  • 6 moldm-3 HCL
  • 110 degrees celcius
  • under REFLUX FOR 24 HRS
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15
Q

describe a primary protein structure

A

the sequence of amino acids in the polypeptide chain

16
Q

describe secondary protein structure

A

hydrogen bonds exist between the peptide links in polymer chain and this results in alpha helix coiling or beta pleased sheet folding

17
Q

describe tertiary protein structure

A

due to the interactions (hydrogen bond, ionic bond, disulphide bond) between the R groups of adjacent amino acids , the polypeptide chain further twists and folds into its unique tertiary structure

18
Q

in proteins what causes the chain to hold a protein shape and what does this shape allow for

A
  • disulphide bonds, CYSTEINE amino acid has -SH group, it lose H and form S-S bond

-hydrogen bonds, between highly electronegative elements e.g O AND N in -NH2 and -OH in amino acids

This specific 3d tertiary shape determines the proteins function

19
Q

How does temp and pH affect tertiary structure

A

it affects hydrogen bonding and the formation of disulphide bonds

19
Q

How does temp and pH affect tertiary structure

A

it affects hydrogen bonding and the formation of disulphide bonds

20
Q

Why can enzymes have chiral centres?

A

as they are made up of amino acids

21
Q

define stereospecific in terms of enzymes

A

enzymes have a specific active site which is only complementary to one enantiomer

22
Q

How can an inhibitor affect rate of reaction and what is an inhibitor

A
  • an inhibitor is a substance that has a similar shape to substrate that fits into active site of enzyme
  • it blocks active site from substrate binding
  • higher the conc of inhibitor, the more active site blocked so ROR decreases
  • also the strength of the inhibitor binding affects the ROR, if poorly bonded then ROR won’t be reduced by much
23
Q

Explain how drugs e.g antibiotics can work as inhibitors

A
  • they block the active site of the enzyme responsible for making cell wall of bacteria cell.
  • if no cell wall then bacteria cell bursts and dies
24
Q

How are scientists advancing on drug making compared to before?

A
  • making new drugs needs trial and error method
  • scientists try different inhibitors to see what works and refine molecule on ones that work
  • NOW computer modelling is used to speed process up
  • computer modelling designs new drugs to act as inhibitors to fit specific active sites
  • computer models allow testing of drug response to enzyme without making the drug
  • CHEAPER AND QUICKER
25
Q

Why might it be hard to find compatible inhibitors to drugs?

A

because active sites are STEREOSPECIFIC, so one one of the enantiomers will work

26
Q

What is a nucleotide made of?

A
  • phosphate group
  • pentose sugar
  • base of either adenine, cytosine, thymine, guanine
27
Q

How do nucleotides bond,

A
  • phosphates on one nucleotide are covalently bonded to a pentose sugar on another
  • sugar-phosphate backbone made
28
Q

What bond is formed when adjacent nucleotides link

A

phosphodiester bond

29
Q

What holds the adjacent polynucleotide strands together

A
  • hydrogen bonds between bases
30
Q

what bases are complementary to each other?

A

cytosine and guanine
adenine and thymine

31
Q

Specifically, how are hydrogen bonds formed between the bases and how many?

A
  • if theres delta +ve hydrogen interacting with electronegative element with lone pair ( O OR N) at the correct distance, hydrogen bond forms

adenine and thymine form 2 hydrogen bonds
cytosine and guanine form 3 hydrogen bonds

32
Q

Why are only A,T and C,G pairs allowed?

A
  • partially charged atoms would be too close and repel
    OR
  • not close enough for hydrogen to form hydrogen bond
33
Q

Describe the structure of Cis-platin

A
  • square planare
  • central platinum atom
  • 2 NH3 and 2 Cl atoms datively bonded to central atom
  • Cl/NH3 atoms are on the same side of the plane hence it is Cis
34
Q

Describe the structure of Cis-platin

A
  • square planare
  • central platinum atom
  • 2 NH3 and 2 Cl atoms datively bonded to central atom
  • Cl/NH3 atoms are on the same side of the plane hence it is Cis
35
Q

How does cis-plating affect cancer?

A
  • it binds to DNA in cancer cells
  • as its attached, it prevents cell reproduction through cell division (mitosis)
  • cell dies as it cant repair itself
  • chloride ions in complex displace easily and detach from complex
  • platinum can bond to nitrogen atoms on guanine base within DNA (another guanine base can do same with 2nd chlorine in cis-platin)
  • as comple bonds it makes distortion in DNA strand so it cant unwind and be copied
36
Q

What are the cons of cis-platin

A
  • aso prevent healthy cells from reproducing
    e.g affect cells in blood, suppressing immune system and increase risk of infection or prevent hair regeneration

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