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B3 Biochem > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Central Dogma of Molecular Biology

A

DNA replication

Transcription

Translation

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2
Q

DNA stores information to be:

A

Transcribed to make RNA

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3
Q

RNA is modified and use as a template:

A

Translated to make protein`

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4
Q

5-carbon sugar examples

A

Ribose

Deoxyribose

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5
Q

Purines

A

Dicyclic

Adenine and Guanine

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6
Q

Pyrimidines

A

One ring

Cytosine, thymine, and uracil

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7
Q

DNA contains:

A

Adenine, guanine

Cytosine, thymine

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8
Q

RNA contains:

A

Adenine guanine

Cytosine uracil

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9
Q

What are the building blocks of DNA and RNA?

A

Nucleic acids

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10
Q

Where does the energy for nucleic acid synthesis come from?

A

Nucleotide di- and tri-phosphates, their anhydride bonds

Energy is released

ATP, GTP, ADP, or NTPs generally

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11
Q

Carbon 1

A

Glycosidic bond, linked to base

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12
Q

Carbon 2

A

Hydroxyl in RNA

No oxygen in DNA

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13
Q

Carbon 3

A

Hydroxyl group in both DNA and RNA

Required for polymerizaiton of nucleic acids. 3’ to 5’ phosphodiester bond

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14
Q

Carbon 5

A

Linked to one of more phosphates

Joined to carbon 3 via phosphodiester bond of an adjacent nucleotide

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15
Q

DNA is polar or nonpolar?

A

Polar

5’ end and 3’ end

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16
Q

At the 5’ end…

A

Free phosphate group

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17
Q

At the 3’ end…

A

Free hydroxyl group

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18
Q

Nucleotides in DNA are joined by

A

Phosphodiester bonds

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19
Q

Bases are linked to C2 by

A

Glycosidic bonds

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20
Q

DNA is always written in what direction?

A

5’ to 3’

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21
Q

If phosphate groups are indicated in nucleic acids

A

pTpApCpG

Or for DNA:
dTdAdCdG

Or for RNA:
rUrArCrG

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22
Q

DNA strands are always

A

Antiparallel and Complementary

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23
Q

Antiparallel

A

Two strands are opposite in direction

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24
Q

Complementary

A

A pairs with T

G pairs with C

Via H-bonds

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25
Q

A::T base pairing

A

2H bonds

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26
Q

G::C base pairing

A

3H bonds

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27
Q

Chargaffs rule

A

If there is 20% G, then there is 20% C.

Then that means there 60% A/T.

28
Q

DNA Structure

A

Double helix, with major and minor grooves for regulatory proteins

Hydrophilic sugar-phosphate backbone is on the outside of the helix, contains net NEGATIVE charge

Hydrogen bonded base pairs are hydrophobic , “stairs” of helix, perpendicular to axis of symmetry

Amphipathic!

29
Q

Right-handed helix

A

Watson-Crick DNA

B-DNA

30
Q

Left-handed helix

A

Rarer form

High GC content

Z-DNA

Important for gene regulation

31
Q

Denaturation of DNA results in:

A

ssDNA

Via heat, alkali, or chemicals

Aka “melting”

Hydrogen bonds between base pairs are broken on dsDNA

32
Q

High GC content has a _____ Tm, high AT content has a _____ Tm.

A

Higher, lower

33
Q

What is Tm?

A

Temperature required to melt 50% of the DNA in a sample

34
Q

Once denatured, if DNA is allowed to cool…

A

The ssDNA will becomes renatured and H-bonds will reform

DNA will reanneal

35
Q

Genomes of most organisms are ____ compares to the size of the cell

A

‘UGE

36
Q

Length of DNA in a single human cell

A

About 2 meters

37
Q

Omg. If you isolate ALL the DNA in all of your cells..

A

It would stretch to the sun and back. Wtf.

38
Q

In prokaryotes and mDNA, the DNA is

A

Supercoiled

39
Q

What relaxes Supercoiled DNA? What Supercoils DNA?

A

Relax- DNA topoisomerase 1

Coil - DNA Gyrase

40
Q

What do quinolones do?

A

Inhibited DNA Gyrase, keeping DNA in relaxed formation

Toxic in high concentrations

41
Q

What are nucleosomes?

A

DNA wrapped around histones

42
Q

What is chromatin?

A

Tightly packed nucleosomes

43
Q

Histones are rich in:

A

Lysine and arginine

+charged basic AAs

44
Q

Histones bind strongly to:

A

Negatively charged DNA

45
Q

Two units of each histone form:

A

A histone octamer

Via 2 units of H2A, H2B, H3, and H4

46
Q

A group of free nucelosomes (without H1) are called

A

“Beads on a string”

Sensitive to nuclease degradation

Necessary to Gene Expression

47
Q

If nucleosomes contain H1…

A

They are tightly packed, not free

Nucleofilament

48
Q

Further condensation of nucleosomes form:

A

Chromatin and chromosomes

Important for Cell Division**

49
Q

fun fact about tRNA

A

RNA can base pair back on itself.

50
Q

___ stores genetic info.

___ is used to express genetic info.

A

DNA

RNA

51
Q

Types of RNA

A

mRNA, rRNA, tRNA

Via transcription, used for translation to proteins

52
Q

Eukaryotic mRNA vs prokaryotic mRNA

A

Eukaryotic - 5’ terminus contains a m7G-cap structure
- 3’ terminus contains a poly A tail (50-200 adenine residues)

Prokaryotic - mRNAs don’t have special terminal structures

BOTH have 5’ untranslated region and 3’ untranslated region and a coding region

53
Q

rRNA

A

Prokaryote - 3 distinct sizes (larger)

Eukaryotes - 3 distinct sizes (smaller)

Combine with proteins to make ribosomes

Eukaryotic rRNA code for more proteins

54
Q

rRNA 80s

A

S=size of rRNA given in units, stands for Svedberg

Sedimentation value

55
Q

Ribosome size between Eukaryotes/Prokaryotes

A

Pro- 70s ribosome, 60s (large) and 40s (small) subunits.

Euk- 80s ribosome, 60s (large) and 40s (small) subunits

56
Q

tRNA

A

Approximately 80 nucleotides

Covalently linked to a specific AA

At least one specific tRNA for each of the 20 AA

Cloverleaf structure, similar to dsDNA

Unusual bases, many modified bases, primarily methylated bases

57
Q

Where does the AA attach to tRNA?

A

CCA-3’ terminus end

58
Q

How is tRNA similar to dsDNA?

A

Extensive intrachain base pairing

59
Q

Which RNA is the only one that contains a T?

A

tRNA, single thymine has a methyl group on its ring structure

60
Q

What is the anticodon loop?

A

On the tRNA, determines AA specifically by base pairing with mRNA during translation

61
Q

hnRNA

A

Heterogenous nuclear RNA, also called pre-mRNA

Represents mRNA in various stages of processing in the nucleus of eukaryotes

62
Q

snRNA

A

Small nuclear RNA, only in the nucleus of eukaryotes

Combine with certain proteins to form snRNPs, used for splicing hnRNA to form mRNA

63
Q

RNAs that act as enzymes

A

Ribozymes

64
Q

What is used for splicing hnRNA to form mRNA?

A

snRNA

65
Q

What is pre-mRNA, and represents mRNA in various stages of processing in the nucleus of eukaryotes?

A

hnRNA

B3 Biochem (4 decks)

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