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Biochemistry > Nucleotides - Lec. 34 > Flashcards

Nucleotides - Lec. 34 Flashcards

1
Q

what are the components that make up a nucleotide?

A

nucleotides have three components:

  • a base
  • a ribose (sugar)
  • phosphate group (p-group)
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2
Q

nucleoside

A

nucleoside is only referring to the base and sugar (ribose)

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3
Q

purines of nucleotides (a potential base for a nucleotide) - what are they and how many rings do they have?

A

adenine
guanine
- purines have two rings

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4
Q

pyrimidines of nucleotides (a potential base for a nucleotide) - how many ring(s) does it have?

A

cytosine
uracil
thymine
- pyrimidines have 1 rings

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5
Q

in general, what do these abbreviations stand for regarding nucleotides?
- NMP or NDP or NTP

A
  • N represents the base that is used
  • the varying M, D, T stands for the number of phosphate groups present (M=1, D=2, T=3)
  • P indicates the phosphate group
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6
Q

what is a NDP nucleotide?

A

a nucleotide that has two phosphate groups (D is the indication of this as D stands for di = two)

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7
Q

what is a NTP nucleotide?

A

this a nucleotide with three phosphate groups ( T is the indication of this as T stands for tri = 3)

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8
Q

what is a NMP nucleotide?

A

this is a nucleotide that has one phosphate group (M is the indication of this as M stands for mono = 1)

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9
Q

what are these nucleotides called?

  • ATP
  • AMP
  • ADP
A

adenosine tri-phosphate
adenosine mono-phosphate
adenosine di-phosphate

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10
Q

what are these nucleotides called?

  • CTP
  • UDP
  • TTP
  • GMP
A
  • cytosine tri-phosphate
  • uracil di-phosphate
  • thymine tri-phosphate
  • guanine mono-phosphate
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11
Q

what is orientation of DNA and RNA on their chains? (what are their ends labeled as and how is it read)

A

they have a 5’ (5 prime) and a 3’ (3 prime) end

when reading the chains, you read it top-down, in other words, in the 5’-to-3’ direction

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12
Q

at which end can nucleotides be added to? (5’ or 3’)

A

3’ end of the growing strand

- the nucleotide will be cut at the 5’ position and then attached to the 3’ position

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13
Q

what is the general mechanism of connecting bases to a growing chain? (where is it cut and where is it added)

A

the nucleotide will be cut at the 5’ prime location and then will be added onto the 3’ position of the growing chain (*REMEMBER: RNA and DNA is read from the 5’ to the 3’ position)

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14
Q

if a guanine is at the 5’ position and a uracil is at the 3’ position how would this be read?

A

5’ GU 3’

read in a 5’ to 3’ position

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15
Q

what’s the main difference between a DNA nucleotide and an RNA nucleotide?

A

it is the second carbon on the ribose (the 2’ position)
DNA has a deoxyribonucleoside (so it lacks the oxygen and only has a H)
RNA has a ribonucleoside (does not lack the oxygen and has OH at the 2’ position)

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16
Q

full name of DNA

A

deoxyribonucleotide

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17
Q

full name of RNA nucleotide

A

ribonucleotide

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18
Q

why is DNA more stable than RNA?

A

since DNA has a H only at the 2’ position versus RNA that has an OH group at the 2’ position, DNA becomes more stable than RNA do to this reason and our cells use DNA to store our genetic material

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19
Q

what are the possible bases of RNA?

A

A (adenine)
G (guanine)
C (cytosine)
U (uracil)

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20
Q

what are the possible bases of DNA?

A 
A (adenine)
G (guanine)
C (cytosine)
T (thymine)
** so the only difference is it lack the uracil (U) --> way to remember is thinking how U stands for "ugly" and we don't want "ugly" in our DNA
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21
Q

what two combinations will you never see in RNA and DNA?

A
  • dUTP –> this is representative of a DNA nucleotide that would NOT happen because DNA does not combine with a uracil base
  • TTP –> this is representative of a RNA nucleotide that would NOT happen because RNA does not combine with thymine
22
Q

complimentary bases: 2 examples &

what is the general rule?

A

A=T (2 hydrogen bonds)
C=G (3 hydrogen bonds)
* general rule is that the bases always match with one purine and one pyrimidine

23
Q

what are the two pathways that allow conversion of RNA to DNA?

A

glutaredoxin or thioredoxin which allows the ribonuclease to convert NDP to dNDP (from RNA nucleotide to DNA nucleotide)

24
Q

ribonucleotide reductase (enzyme)

A

this is a key enzyme that converts ribonucleotides to deoxyribonucleotides (the synthesis of DNA from RNA)

25
Q

why is ONLY the NDP used to convert RNA to DNA and not NTP or NMP?

A

only the di-phosphate nucleotide is able to work with the ribonucleotide reductase

26
Q

what are the two regulator sites that regulate enzyme activity?

A

primary regulatory site

substrate-specificity site

27
Q

what regulatory site is mainly for regulation of NDP and dNDP?

A

primary regulatory site
- when we have a lot of ATP (adenosine triphosphate) that means our ratio of RNA is very high so ATP will bind to the ribonucleotide reductase and enhance the activity to convert ultimately RNA to DNA nucleotides

28
Q

how is the conversion of RNA to DNA regulated? (what is acting as an inhibitor?)

A
  • when we have more DNA than we need the dATP will be very high and so dATP will bind to the ribonucleotide reductase enzyme (acting as an inhibitor) and inhibit the activity of the enzyme to block production of more DNA ribonucleotides, essentially decreasing the rate of RNA to DNA production
29
Q

what does the substrate-specificity site regulate?

A

this site deals with more of the ratio of purine and pyrimidine nucleotides

  • when too much ATP and dATP is present (purine nucleotides) they will bind to the substrate specificity site and enhance the conversion of pyrimidine nucleotides only (not purine nucleotide)
  • if there are too many dTTP then it will also bind to the substrates specificity site and inhibit the conversion of pyrimidine nucleotide only, while at the same time, enhance production of dGTP (purine nucleotide)
30
Q

what does the substrate-specificity site regulate?

A

this site deals with more of the ratio of purine and pyrimidine nucleotides

  • when too much ATP and dATP is present (purine nucleotides) they will bind to the substrate specificity site and enhance the conversion of pyrimidine nucleotide only (not purine nucleotide)
  • if there are too many dTTP then it will also bind to the substrates specificifity site and inhibit the conversion of pyrimidine nucleotide only, while at the same time, enhance production of dGTP (purine nucleotide)
31
Q

what is nucleotide degradation?

A

how nucleotides degrade within our cells

32
Q

how does purine degradation work? what is the final product? (what are the two pathways used)

A

there are two pathways (GMP and AMP) that occur, but both are similar and merge once they are in base form:

  • removes phosphate group
  • removes ribose (sugar)
  • from the GMP degradation pathway the base guanine is left
  • from AMP degradation pathway hypoxanthine base is left
  • then those two remaining bases will converge and form the final product of uric acid
33
Q

what are the two bases that are left from purine nucleotide degradation? (what base is formed from GMP and what one is formed from AMP?)

A
  • guanine from GMP (both have a G!)

- hypoxanthine from AMP (HA!)

34
Q

why is too much uric acid bad?

A

uric acid is bad and will eventually lead to gout

- uric acid is insoluble

35
Q

hypoxanthine

A

this is the base form that is left during purine degradation which will eventually converge with the other base form from the AMP degradation side and ultimately produce uric acid

36
Q

how does pyrimidine nucleotide degradation occur? (what are the two pathways? and what is the final product?)

A

two pathways again just like purine degradation

  • the two pathways are UMP and CMP
  • removal of the phosphate group
  • removal of the ribose (sugar)
  • then the base that is left is uracil, which will ultimately produce malonyl-CoA
37
Q

what is the base that forms from pyrimidine nucleotide degradation?

A

uracil

38
Q

what are the two ways to synthesize nucleotides within our cells? (in general, what do they mean)

A
  • salvaged pathway: used from RNA, DNA, and cofactor degradation (recycling the degraded materials)
  • de novo pathway: make from the beginning with new materials –> important for cell proliferation (need to make sure there is enough material for each daughter cell when cells are reproduced)
39
Q

PRPP (5-phophoribosyl-1-pyrophoshate) is the precursor for what?

A

PRPP is the precursor for the pentose sugar used to form the ribose (sugar) part of the nucleotide

40
Q

purine nucleotide synthesis - how does this work in general?

- it can use both salvage pathway and de novo pathway

A
  • each pathway (de novo and salvage) will use the PRPP precursor for the ribose part of the nucleotide
  • either AMP or GMP will both derive from IMP precursor
  • once either AMP or GMP is formed (adenine- or guanine- mono-phosphate) then it will need to convert to a di-phosphate (add another p-group) which can then synthesize DNA and RNA either the guanine or adenine base
41
Q

regarding purine nucleotide synthesis what is the precursor of GMP and AMP?

A

IMP is the precursor

- both salvage and de novo pathway will use the IMP precursor

42
Q

what happens during the pyrimidine nucleotide synthesis?

A
  • similar to purine nucleotide synthesis –> it will start with either a de novo or salvage pathway and use the precursor UMP (unlike purine synthesis that uses IMP)
  • then the precursor forms UDP and thus can directly synthesize DNA and RNA
43
Q

what is the precursor that is used in pyrimidine nucleotide synthesis?

A

UMP

44
Q

what is the name of the enzyme that is capable of making the U (uracil) to T (thymine) conversion during pyrimidine nucleotide synthesis?

A

thymidylate synthase
- this enzyme can ONLY be used on the dUMP nucleotide specifically (mono- –> not di- or tri-) that will convert it to the dTMP nucleotide

45
Q

in purine nucleotide synthesis what is the base that is used during the salvage pathway?

A

hypoxanthine is the base used in salvage pathway

  • in turn it will produce the precursor used for AMP and GMP, which is the IMP precursor
  • so ultimately the hypoxanthine precursor will form the IMP precursor by combining with the PRPP (ribose precursor)
46
Q

what is the base that is used for salvage pathway to produce to the UMP precursor for the pyrimidine nucleotide synthesis?

A

uracil, which will combine with the PRPP (ribose precursor) and form the UMP precursor

47
Q

how many rings does purine have? where do the components of the ring(s) of purine IMP precursor come from - the nitrogens and carbons? (purine de novo synthesis)

A
  • purine has two rings are built on PRPP (precursor for ribose sugar of the nucleotide)
    The rings are composed of:
  • glutamine provides two nitrogens
  • glycine provides a nitrogen and the carbon skeleton
  • aspartate provides a nitrogen
  • formate provides 2 carbons
  • CO2 molecule provides a carbon
48
Q

where do the four nitrogens come from that form the two rings involved in a pyrimidine nucleotide (forms the IMP precursor)? (HINT: GAG)

A
  • glutamine (provides 2)
  • aspartate
  • glycine
49
Q

for the two precursors involved in purine nucleotide synthesis - where do the nitrogens come from to form the AMP precursor and the GMP precursor?

A

the nitrogen for AMP precursor will come from aspartate

the nitrogen for GMP will come from glutamine

50
Q

pyrimidine nucleotide de novo synthesis: what is the starting material?

A

the starting material is aspartate and carbamoyl phosphate –> the aspartate will build on and combine with carbamoyl phosphate to produce carbamoyl aspartate

51
Q

what is the ring precursor involved in pyrimidine nucleotide de novo synthesis?

A

orotate is the precursor that will attach to PRPP and make UMP

Biochemistry (6 decks)

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