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biomolecular science > nucleotides and nucleic acids > Flashcards

nucleotides and nucleic acids Flashcards

1
Q

name the 3 components of the nucleotide structure and how theyre bound

A

pentose 5 carbon sugar is bount to a nitrogenous base and a phosphate group. and are joined by glycosidic bonds

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2
Q

DNA is made up of a series of what

A

nucleotides

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3
Q

DNA hold what

A

all the genetic info

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4
Q

name the 2 structures in a nucleoside

A

pentose sugar
and a nitrogenous base

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5
Q

name the 2 possible cyclic furanoses of pentose sugar

A

ribose and deoxyribose

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6
Q

how many nitrogenous bases are there
and name derivatives of nitrogen bases

A

Five nitrogen-containing bases are components of nucleotides.

Three of them are derivatives of pyrimidine and two are derivatives of purine.

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7
Q

what are nucleotides building blocks of

A

RNA and DNA

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8
Q

what nitrogen bases are derived from purines

A

adenine and guanine

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9
Q

what nitrogen bases are derived from pyrimidines

A

uracil, thymine, and cytosine

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10
Q

why does thymine base structure differ from the rest

A

has a methyl group in it

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11
Q

sugar and base are linked via what reaction to produce what
and what bond is formed and where

A

condemnation reaction to produce a nucleosome

N-glycidic bond is formed at 1 prime carbon

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12
Q

what is the phosphate group called and whats its characteristics like

A

nucleic acid
so acid characteristics

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13
Q

describe the properties of the phosphate group at physiological PH

A

has neg charge and polar

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14
Q

Addition of a phosphate group to the sugar via a condensation reaction gives us what

A

either a ribonucleotide or a deoxynucleotide (phosphate esters of the corresponding nucleoside)

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15
Q

to add a phosphate to the sugar what reaction does it go though

A

condemnation reaction

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16
Q

name examples of nucleotides found in nature

A

Cyclic adenosine monophosphate, cAMP
Adenosine di- and tri- phosphate

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17
Q

describe Cyclic adenosine monophosphate, cAMP

A

Has many signalling roles in cells – acts as a secondary messenger for several hormones which are unable to enter the cell e.g. triggers the utilisation of glycogen

it also activates protein kinase A, by binding to regulatory subunits and releasing the inactive catalyst units as active catalyst units

Energy yielding metabolic reactions such as photosynthesis or carbohydrate oxidation produce ATP.

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18
Q

describe adenosine di and tri phosphate

A

ATP is used for energy transfer at molecular level in all living organisms.

ADP has adenine bound to ribose with 2 phosphates
ATP has adenine bound to ribose , bound to triphosphate

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19
Q

give examples of 4 coenzymes (also nucleotides, or their derivatives, found in nature)

A

FAD, NAD, NADP, Coenzyme A

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20
Q

explain the coenzyme Flavin Adenine Dinucleotide (FAD)

A

Coenzyme required in many redox reactions

Can exist in two different redox states:
FAD + 2H+ + 2e- <====> FADH2

FAD - oxidising agent (accepts electrons)
FADH2 - reducing agent (donates electrons)

its structure is a flavin bound to a ribitol(monosaccharide). both of these together form riboflavin which is to do with vit B2, and this is bound to a adenine diphosphate(nucleotide)

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21
Q

explain the oxidation and reduction in FAD/FADH2

A

from oxygen to hydrogen so id redox reaction
as the FADH2 gains 2 hydrogen atoms

22
Q

explain the coenzyme Nicotinamide Adenine Dinucleotide (NAD+)

A

Coenzyme required in many redox reactions

Can exist in two different redox states:
NAD+ + H+ + 2e- NADH

NAD+ - Oxidising agent (accepts electrons)
NADH - Reducing agent (donates electrons)

its structure consist of nicotinamide (Nicotinic acid and its amide are collectively known as Niacin (Vit B3)) bound to ribose , which is then bound to ADP

Vit B3 deficiency is known as “Pellagra” (symptoms - dermatitis, dementia, and diarrhoea)

23
Q

describe coenzyme A

A

Involved in the transfer of acetyl groups in metabolic pathways

Needed to form Coenzyme-A and essential to the metabolism of carbohydrates and fats and some amino acids.

its structure is 2-aminoethanethiol (Has an -SH group) bound to Phosphorylated ADP, which is then bound to Pantothenic acid

Pantothenic acid - Vitamin B5 (deficiency is rare as it is is widely present in food )

24
Q

name polynucleic acids

A

DNA and RNA

25
Q

what do DNA and RNA exist as and allow

A

Exist as macromolecular polymers and allow hereditary characteristics to be passed on from one generation to another.

theyre macro, as theyre big
theyre a polymer as there’s many joined together

26
Q

what the function of DNA

A

Deoxyribonucleic acids (DNA) - serves as the master copy for most information in the cell.

27
Q

whats the function of RNA

A

Ribonucleic acids (RNA) - several types but overall acts to transfer information from DNA to the rest of the cell through protein synthesis.

28
Q

explain the occurrence of DNA and RNA

A

Bacteria have one strand of DNA

Mammals contain scores of DNA strands grouped together in chromosomes.

Retroviruses, contain only RNA rather than DNA.

29
Q

name the DNA and the RNA bases

A

contain four bases each: two purines and two pyrimidines.

In DNA the bases are: A, G, C, T

In RNA the bases are: A, G, C, U

A and G are the purines
U, T, and, C are the pyridines
Thymine is diff again as has the methyl group

30
Q

what is the charge on the Phosphate group at physiological pH in polynucleic acids

A

negative

31
Q

explain the primary structure of DNA

A

Sugar/phosphate backbone - formed of phosphate and sugar

Base groups protruding from the chain at regular intervals.

Primary structure is the sequence of bases.

The primary structure is formed by 3’-5’ phosphodiester bonds between nucleotides - 3’ end ends in OH, 5’ ends with phosphate

32
Q

what is the Convention for listing sequence of nucleotides in primary structure

A

Give the sequence from the 5’ end, which (phosphate ester), to the 3’ end (free hydroxyl group).

DNA: -dT-A-G-C-C- “d” denotes deoxy ribose
RNA: -U-C-G-A-U-

33
Q

for the secondary structure what is chargaffs rule

A

Biochemist Erwin Chargaff obtained data from many different organisms. This showed the following pattern of base occurrence in DNA:

				%A = %T
				%G = %C

The amounts of total purines and total pyrimidines were also the same

In human DNA, for example, A=30.9% and T=29.4%; G=19.9% and C=19.8%.

34
Q

what is the base % composition in human DNA

A

Contains approximately:

30% adenine,
30% thymine,
20% guanine,
20% cytosine

All together it should all = 100%

35
Q

explain the double helix model

A

DNA is a double stranded double helix.

The bases on one strand hydrogen bond to complementary bases on the other strand of DNA.

The two strands run antiparallel (in opposite directions to each other).

The location of the sugar-phosphate backbones on the outside of the molecule, coupled with the twist, produces two grooves on the surface of the double helix.

These grooves may provide binding sites for molecules which interact with DNA.

36
Q

explain base pairing in terms of size

A

The size of the interior of the DNA double helix limits the base pairs that can hydrogen bond to one another.

Only pairs involving one small base (a pyrimidine) and one large base (a purine) correctly “fit” within the helix interior.

37
Q

what base pairing does hydrogen bonding favour

A

favours A-T and G-C pairings, and these combinations are the only two that normally occur in DNA. They are said to be complementary.

38
Q

how are complimentary strands written

A

5’ -dT-A-G-C-C- 3’
3’ -dA-T-C-G-G- 5’

39
Q

how many hydrogen bonds are between C and G

A

3

40
Q

how many hydrogen bonds are between A and T

A

2

41
Q

name the forces that stabilise the double helix

A

hydrogen bonding
electrostatic interactions
hydrophobic affects
stacking interactions

42
Q

how do hydrogen bonding forces stabilise the double helix

A

large number of relatively weak H bonds contribute greatly to preventing the strands from separating under normal physiological conditions

43
Q

hoe do electrostatic interactions stabilise the double helix

A

involves the phospho-diester group of the DNA backbone and a cation especially Mg2+

44
Q

how do hydrophobic affects stabilise the double helix

A

produced by hydrophobic purines/ pyrimidine rings moving away from the aqueous solvent into the interior of the double helix.

45
Q

how do stacking interaction stabilise the double helix

A

stacked base pairs form weak Van der Waals attractions. These forces are additive. Therefore the greater the number of base pairs the more stable will be the helix.

46
Q

name and describe the 3 types of RNA

A

Ribosomal RNA (rRNA) combines with a series of proteins to form complex structures, called ribosomes, that serve as the physical sites for protein synthesis (translation).

Messenger RNA (mRNA) carries genetic instructions for protein synthesis from DNA to the ribosomes.

Transfer RNA delivers specific individual amino acids to the ribosomes for protein synthesis.

47
Q

how do DNA and RNA differ

A

RNA is single stranded and much smaller than DNA.

The sugar unit in the backbone is ribose.

Uracil in RNA replaces thymine. Uracil pairs with adenine.

48
Q

explain polymerisation in terms of replicating DNA

A

Involves addition of free nucleoside triphosphates (high energy compounds). This energy is needed to form bonds between the nucleotides.
The phosphate is the energy source

The strands unwind and separate

Each then acts as a template for a complementary strand to be built.

Base pairing always involves C pairing with G and A pairing with T

49
Q

what are the 2 main stages to replication

A

polymerisation
and control

50
Q

explain the ‘control’ step in terms of DNA replication

A

DNA polymerase builds new double helices and repairs slightly damaged ones, by lining up nucleotides in the right order.

  • A section of double stranded DNA.
  • Polymerase binds to the double helix by wrapping around it.
  • The enzyme pulls the helix apart.
  • The nucleotides are brought in to build a new strand of DNA.
51
Q

what is the Polymerase Chain Reaction (PCR)

A

Mimics nature for the rapid production of multiple copies of a DNA nucleotide sequence in the laboratory.

Developed after the discovery of DNA polymerase.

52
Q

why was PCR developed

A

Discovery of heat stable DNA polymerase from the thermophilic eubacterium Thermus aquaticus (TAQ) solved the problem of enzyme denaturation after each cycle

biomolecular science (6 decks)

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