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Biochem Block 3 > Nucleic acids > Flashcards

Nucleic acids Flashcards

1
Q

Central dogma

A
  • DNA is replicated and stores information
  • DNA is transcribed to make RNA
  • RNA is modified and translated to make proteins
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2
Q

What carbon position determines if it is ribose or deoxyribose?

A

Carbon position 2

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3
Q

What Bases are different between RNA and DNA

A

DNA has thymine

RNA has Uracil

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4
Q

What carbon position has the anhydride bonds that provide energy?

A

-carbon position 5

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5
Q

What are the building blocks of DNA and RNA?

A
  • 5 carbon sugar

- nitrogenous base

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6
Q

Carbon 1 on sugar

A
  • covalently linked to a base

- glycosidic bond

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7
Q

Carbon 2 on sugar

A
  • hydroxyl group in RNA

- no oxygen in DNA

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8
Q

Carbon 3 on sugar

A
  • hydroxyl group in both DNA and RNA
  • required for polymerization of nucleic acid
  • joined to the 5 carbon by phosphodiester bond
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9
Q

Carbon 5 on sugar

A
  • liked to one or more phosphates

- joined to carbon 3 of an adjacent nucleotide through phosphodiester bond

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10
Q

Is DNA polar or non polar?

A
  • POLAR
  • free phosphate group at the 5’ end
  • free hydroxyl group at the 3’ end
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11
Q

What kind of bonds join the nucleotides in DNA?

A

-phosphodiester bonds

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12
Q

What kind of bonds link bases in DNA?

A

-glycosidic bonds

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13
Q

if no end designation is made, you should assume DNA is going…

A

5’ to 3’

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14
Q

When writing a sequence backwards, how should DNA be written?

A

you have to specify 3’ to 5’

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15
Q

antiparallel

A

-the two strands of DNA are opposite in direction

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16
Q

complementary

A
  • A matches with T
  • C matches with G
  • via hydrogen bonds
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17
Q

How many hydrogen bonds like the complementary bonds?

A

A:T has 2
C:G has 3

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18
Q

Chargaff’s rule

A
  • A=T, C=G

- A+T+C+G=100%

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19
Q

If DNA has 10% G, what is the % of the others?

A

G=10%
C=10%
A=40%
T=40%

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20
Q

What kind of grooves are associated with the double helix?

A
  • major and minor grooves
  • important for regulatory proteins
  • important for gene expression regulation
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21
Q

Which part of DNA is hydrophilic?

A
  • sugar-phosphate backbone
  • has a negative charge
  • is on the outside of the helix
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22
Q

Which part of DNA is hydrophobic?

A
  • hydrogen bonded base pairs
  • perpendicular to the axis of symmetry
  • form the stairs of the helix (on the inside)
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23
Q

DNA is…

A

Directional and amphipathic

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24
Q

What is a right handed helix called?

A
  • watson-crick DNA
  • B-DNA
  • most common
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25
Q

Left handed helix

A
  • less common
  • high CG content
  • Z-DNA
  • function unknown
26
Q

Denaturation and renaturation of DNA

A
  • mechanical and chemical

- important for replication and transcription

27
Q

Melting DNA

A
  • heat denatures double stranded DNA

- Hydrogen bonds between base pairs are broken, but phosphodiester bonds linking nucleotides are not broken

28
Q

Tm

A

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

29
Q

CG content and Tm

A

-high CG content means higher Tm

30
Q

AT content and Tm

A

-high AT content means lower Tm

31
Q

What happens if DNA cools?

A

-hydrogen bonds will reform and the DNA will renature

32
Q

another word for renature

A

reanneal

33
Q

What happens if DNA denatures and then reanneals in a way that is not the most stable?

A

-it will denature again and reanneal until it reaches the most stable form

34
Q

Organization of DNA

A
  • genomes are HUGE
  • length of DNA in one cell is 2 meters
  • DNA is thin and long
35
Q

Supercoiling

A

-DNA gyrase does supercoiling in prokaryotes and mitochondrial DNA

36
Q

Quinolones

A
  • inhibit DNA gyrase

- toxic in high concentrations

37
Q

DNA in the nucleus of eukaryotes

A
  • associates with histone and non histone proteins to form nucleosomes
  • nucleosomes are packaged tightly to form chromatin
38
Q

Why package DNA ?

A
  • protects DNA from denaturation

- but you have to have some DNA loose for gene expression

39
Q

Histones

A
  • rich in lysine and arginine(+charged basic amino acids)

- bind tight to negatively charged DNA

40
Q

Histone octamer

A
  • two units of EACH histone:H2A, H2B, H3, and H4 aggregate and form it
  • DNA wounds around it to make a nucleosome
41
Q

Beads on a string

A
  • a group of free nucleosomes(without H1)
  • sensitive to nuclease degradation
  • necessary for gene expression
42
Q

nucleofilament

A

-histone H1 associates with the DNA between the nucleosomes to further condense the DNA into a thick 30nm fiber

43
Q

Condensation

A
  • important for cell division

- condensation of nucleosomes forms chromatin and chromosomes

44
Q

KEY RNA and DNA differences

A
  • Sugar
  • thymine/uracil
  • DNA is DS and RNA is SS
  • RNA can base-pair back on itself
  • RNA is smaller
  • DNA stores information and RNA expresses information
45
Q

RBC

A
  • no nucleus, so cant store DNA

- they have some mRNA that helps them

46
Q

What are the three major types of RNA that act in conjunction with proteins to allow infor from DNA to be translated into proteins?

A

-mRNA, rRNA, tRNA

47
Q

mRNA

A
  • messenger RNA
  • prepared in a way in which it can get into the cytosol and be recognized
  • vary in size depending on the size of proteins encoded
48
Q

Eukaryotic mRNA

A

5’ terminus contains a m7G-cap structure (contributes to getting recognized and not getting degraded)
-3’ terminus contains poly-A tail(helps ribosomes recognize the end and let it be released)

49
Q

Prokaryotic mRNA

A

-DO NOT CONTAIN SPECIAL TERMINAL STRUCTURES

50
Q

all mRNAs

A
  • 5’ untranslated region
  • 3’ untranslated region
  • coding region
51
Q

rRNA

A
  • associates with proteins

- mostly structural to combine with proteins to form ribosomes

52
Q

What are the different sizes associated with eukaryotes rRNA

A

80s
60s
40s

53
Q

What are the different sizes associated with prokaryotes rRNA

A

70s
50s
30s

54
Q

What are the sizes given in?

A

”s”

  • Svedberg
  • unit of sedimentation value
55
Q

tRNA

A
  • small(80 nucleotides)
  • covalently linked to specific amino acid
  • CCA-3’ terminus acts as amino acid attachment site
56
Q

Anticodon loop

A
  • on tRNA

- determines amino acid specifically by base pairing with mRNA during translation

57
Q

CCA-3’ terminus

A
  • amino acid attachment site on tRNA

- covalently attached

58
Q

Anticodon form

A

-complimentary strand then put it back in 5’-3’ form

59
Q

hnRNA

A
  • heterogeneous nuclear RNA
  • pre-mRNA
  • represents mRNA in various stages of processing in the nucleus of eukaryotes
  • in nucleus, just recently transcribed
60
Q

snRNA

A
  • small nuclear RNA
  • only in nucleus of eukaryotes
  • combine with certain proteins to form snRNPs
61
Q

snRNPs

A
  • used for splicing hnRNA to form mRNA
  • splice out introns
  • in eukaryotes
62
Q

Ribozymes

A

-RNAs that act as enzymes

Biochem Block 3 (10 decks)

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