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BDS1 > Molecular biology 1 - nucleosides and nucleotides > Flashcards

Molecular biology 1 - nucleosides and nucleotides Flashcards

1
Q

Role of nucleotides

A
  1. energy currency
  2. chemical links (second messengers) in cellular response to external stimuli (e.g. hormones)
  3. Form structure of enzyme cofactors (e.g. NAD) and metabolic intermediates
  4. form nucleic acids
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2
Q

2 types of nucleic acids

A

deoxyribonucleic acid (DNA), ribonucleic acid (RNA)

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3
Q

Functions of nucleic acids

A

transmit genetic information, protein synthesis

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4
Q

What are the monomers of nucleic acids (DNA and RNA)

A

(ribo/deoxyribo) nucleotides

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5
Q

What components make up a nucleotide?

A

pentose sugar, phosphate(s), nitrogenous base (nitrogenous, aromatic, heterocyclic ring) - phosphorylated nucleosides

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6
Q

pentose sugar in DNA

A

deoxyribose

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7
Q

pentose sugar in RNA

A

ribose

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8
Q

2 types of nitrogenous base

A
  1. pyrimidine - monocyclic
  2. purine (dicyclic ring - pyrimidine ring fused to imidazole ring)
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9
Q

What feature makes each nitrogenous base unique?

A

The attachment of NH2, CH3, and C=O groups

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10
Q

What are the purine bases?

A

adenine and guanine

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11
Q

What are the pyrimidine bases?

A

cytosine, thymine, uracil

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12
Q

Which group is found in adenine?

A

-NH2

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13
Q

Which group is found in guanine?

A

-C=O and -NH2

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14
Q

Which group is found in cytosine?

A

-NH2 (as well as C=O)

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15
Q

Which group is found in uracil?

A

C=O (2)

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16
Q

Which group is found in thymine?

A

C=O (2) and -CH3

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17
Q

How are the carbon atoms in the pentose sugar of the nucleotide numbered?

A

1’ to 5’ clockwise from O atom (prime ‘ indicates that the C atoms are of the sugar not the nitrogenous base)

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18
Q

Difference between ribose and deoxyribose

A

Attached to C2, ribose has an OH group whereas deoxyribose has a H group.

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19
Q

What components make up a nucleoside (e.g. adenosine)?

A

nitrogenous base and pentose sugar (linked by N-glycosidic bond)

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20
Q

What bond links the pentose sugar and nitrogenous base in nucleosides/nucleotides?

A

N-glycosidic bond (beta)

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21
Q

How does the N-glycosidic bond between the nitrogenous base and pentose sugar form?

A

Between 1’C of pentose sugar and N9 of purine or N1 of pyrimidine ring via a hydrolysis reaction.

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22
Q

Which OH group on the sugar is usually esterified by the addition of a phosphate to form a nucleotide (phosphate ester of nucleoside)?

A

OH group on 5’C (forms a nucleoside 5’-phosphate)

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23
Q

How are nucleosides named?

A

nucleoside + 5’ (usually 5’C) + (mono/di/tri) phosphate

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24
Q

Is AMP a ribonucleotide or deoxyribonucleotide?

A

Ribonucleotide (has OH group on 2’C)

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25
Q

How are the phosphates in a nucleotide named?

A

first / mono phosphate is alpha, second / di is beta, third / tri is gamma

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26
Q

unabbreviated name of AMP

A

adenosine 5’-monophosphate (deoxyadenylate)(ribonucleotide)

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27
Q

Unabbreviated name of dAMP

A

deoxyadenosine 5’-monophosphate (deoxyadenylate) (deoxyribonucleotide)

28
Q

Which base cannot form a deoxyribonucleoside/deoxyribonucleotide?

A

Uracil

29
Q

Which base cannot form a ribonucleoside/ribonucleotide?

A

Thymine

30
Q

Name of deoxyribonucleoside formed with deoxyribose and adenine

A

deoxyadenosine

31
Q

Name of ribonucleoside formed with ribose and adenine

A

adenosine

32
Q

Which is the main NTP (nucleoside triphosphate) hydrolysed to provide chemical energy for cellular reactions?

A

ATP (adenosine 5’-triphosphate - a ribonucleotide)

33
Q

Where is ATP produced?

A

in the mitochondrion

34
Q

What is the bond that joins a ribose and alpha phosphate?

A

ester linkage

35
Q

What is the bond that joins alpha-beta and beta-gamma phosphates?

A

phosphoanhydrides

36
Q

Do ester bond or phosphoanhydride bond hydrolysis yield more energy?

A

Hydrolysis of each anhydride bond (30 kJ/mol) yields more energy than the ester bond (14 kJ/mol)

37
Q

Which ribonucleoside forms part of the structure of many enzyme cofactors?

A

Adenosine (adenine+ribose)

38
Q

Examples of enzyme cofactors which adenosine is a part of

A

NADP (nicotinamide adenine dinucleotide phosphate), NAD, FAD (flavin adenine dinucleotide), coenzyme A

39
Q

Example of nucleotide that is a common second messenger

A

cAMP

40
Q

Unabbreviated name of cAMP

A

adenosine 3’, 5’-cyclic monophosphate

41
Q

How is cAMP synthesised?

A

From ATP in a reaction catalysed by adenyl cyclase

42
Q

How is cAMP broken down?

A

cAMP is broken down into 5’ AMP by phosphodiesterase enzyme.

43
Q

How does cAMP act as a second messenger?

A
  1. Hormone binds to receptors on plasma membrane
  2. stimulates adenyl cyclase
  3. increased cAMP produced
  4. cAMP acts inside cell to alter rate of processes
44
Q

Example of cAMP action

A

cAMP binds to regulatory subunits of protein kinase A causing them to detach from the catalytic subunits. Protein kinase A is now activated

45
Q

Examples of nucleotides as regulatory molecules

A

cAMP (adenosine 3’, 5’-cyclic monophosphate), cGMP, ppGpp (guanosine 5’-diphosphate 3’-diphosphate)

46
Q

Function of cGMP

A

Regulatory functions in many cells (like cAMP)

47
Q

Function of ppGpp

A

serve as starvation signals in bacteria causing large changes in metabolism by increasing or decreasing transcription of hundreds of genes

48
Q

What is a gene?

A

A segment of DNA containing the information required for the synthesis of a functional biological product (RNA or protein).

49
Q

How are successive nucleotides linked in nucleic acids?

A

phosphodiester bonds

50
Q

Description of 3’ to 5’ phosphodiester bond

A

the 3’C of the sugar in a nucleotide is bonded to a phosphate group which is attached to the 5’C of the sugar in the adjacent nucleotide

51
Q

What makes up the backbone of DNA?

A

Deoxyribose and phosphate linked by phosphodiester bridges

52
Q

Structure of DNA double helix

A

2 antiparallel chains wound around each other in a right-handed double-helical arrangement

53
Q

How is the DNA double helix held together?

A

Complementary base pairing ( 2 H bonds between A and T, 3 H bonds between C and G)

54
Q

How far apart are the base pairs stacked?

A

3.4 A (10.5 base pairs per turn therefore each turn is about 34A long)

55
Q

What grooves does the offset pairing of the 2 strands create in DNA?

A

Major and minor groove

56
Q

Which bases are equivalent in number in the DNA molecule?

A

A=T, C=G (due to complementary strands)

57
Q

Chargaff’s rule (4)

A
  1. base composition of DNA varies between species
  2. DNA specimens from the same species have the same base composition
  3. base composition of DNA doesn’t change with an organism’s age, nutrition or environment
  4. A=T and C=G therefore the number of purines=pyrimidines (A+G=C+T)
58
Q

Where is RNA mainly found?

A

in the cytoplasm

59
Q

What direction is the backbone of DNA?

A

5’ - 3’ backbone

60
Q

How is RNA different to DNA?

A
  1. Uracil replaces thymine
  2. ribose replaces deoxyribose
  3. single-stranded
  4. more than one form of RNA (m/t/rRNA)
61
Q

What are the only exceptions to RNA being single stranded?

A

Hairpin

62
Q

How does a hairpin loop form in tRNA?

A

Close-proximity self-complementarity within each strand

63
Q

Structure that can form when there is an inverted repeat sequence in DNA

A

Cruciform (4 way junction of 2 hairpin structures)

64
Q

Order of RNA types abundance in cells

A

80% rRNA, 15% tRNA, 5% mRNA

65
Q

What is the s unit used to measure a molecule’s size?

A

sedimentation coefficient (s)

BDS1 (50 decks)

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