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Flashcards in Nucleic acids Deck (62):
1

Central dogma

-DNA is replicated and stores information
-DNA is transcribed to make RNA
-RNA is modified and translated to make proteins

2

What carbon position determines if it is ribose or deoxyribose?

Carbon position 2

3

What Bases are different between RNA and DNA

DNA has thymine
RNA has Uracil

4

What carbon position has the anhydride bonds that provide energy?

-carbon position 5

5

What are the building blocks of DNA and RNA?

-5 carbon sugar
-nitrogenous base

6

Carbon 1 on sugar

-covalently linked to a base
-glycosidic bond

7

Carbon 2 on sugar

-hydroxyl group in RNA
-no oxygen in DNA

8

Carbon 3 on sugar

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

9

Carbon 5 on sugar

-liked to one or more phosphates
-joined to carbon 3 of an adjacent nucleotide through phosphodiester bond

10

Is DNA polar or non polar?

-POLAR
-free phosphate group at the 5' end
-free hydroxyl group at the 3' end

11

What kind of bonds join the nucleotides in DNA?

-phosphodiester bonds

12

What kind of bonds link bases in DNA?

-glycosidic bonds

13

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

5' to 3'

14

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

you have to specify 3' to 5'

15

antiparallel

-the two strands of DNA are opposite in direction

16

complementary

-A matches with T
-C matches with G
-via hydrogen bonds

17

How many hydrogen bonds like the complementary bonds?

A:T has 2
C:G has 3

18

Chargaff's rule

-A=T, C=G
-A+T+C+G=100%

19

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

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

20

What kind of grooves are associated with the double helix?

-major and minor grooves
-important for regulatory proteins
-important for gene expression regulation

21

Which part of DNA is hydrophilic?

-sugar-phosphate backbone
-has a negative charge
-is on the outside of the helix

22

Which part of DNA is hydrophobic?

-hydrogen bonded base pairs
-perpendicular to the axis of symmetry
-form the stairs of the helix (on the inside)

23

DNA is...

Directional and amphipathic

24

What is a right handed helix called?

-watson-crick DNA
-B-DNA
-most common

25

Left handed helix

-less common
-high CG content
-Z-DNA
-function unknown

26

Denaturation and renaturation of DNA

-mechanical and chemical
-important for replication and transcription

27

Melting DNA

-heat denatures double stranded DNA
-Hydrogen bonds between base pairs are broken, but phosphodiester bonds linking nucleotides are not broken

28

Tm

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

29

CG content and Tm

-high CG content means higher Tm

30

AT content and Tm

-high AT content means lower Tm

31

What happens if DNA cools?

-hydrogen bonds will reform and the DNA will renature

32

another word for renature

reanneal

33

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

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

34

Organization of DNA

-genomes are HUGE
-length of DNA in one cell is 2 meters
-DNA is thin and long

35

Supercoiling

-DNA gyrase does supercoiling in prokaryotes and mitochondrial DNA

36

Quinolones

-inhibit DNA gyrase
-toxic in high concentrations

37

DNA in the nucleus of eukaryotes

-associates with histone and non histone proteins to form nucleosomes
-nucleosomes are packaged tightly to form chromatin

38

Why package DNA ?

-protects DNA from denaturation
-but you have to have some DNA loose for gene expression

39

Histones

-rich in lysine and arginine(+charged basic amino acids)
-bind tight to negatively charged DNA

40

Histone octamer

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

41

Beads on a string

-a group of free nucleosomes(without H1)
-sensitive to nuclease degradation
-necessary for gene expression

42

nucleofilament

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

43

Condensation

-important for cell division
-condensation of nucleosomes forms chromatin and chromosomes

44

KEY RNA and DNA differences

-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

RBC

-no nucleus, so cant store DNA
-they have some mRNA that helps them

46

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

-mRNA, rRNA, tRNA

47

mRNA

-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

Eukaryotic mRNA

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

Prokaryotic mRNA

-DO NOT CONTAIN SPECIAL TERMINAL STRUCTURES

50

all mRNAs

-5' untranslated region
-3' untranslated region
-coding region

51

rRNA

-associates with proteins
-mostly structural to combine with proteins to form ribosomes

52

What are the different sizes associated with eukaryotes rRNA

80s
60s
40s

53

What are the different sizes associated with prokaryotes rRNA

70s
50s
30s

54

What are the sizes given in?

"s"
-Svedberg
-unit of sedimentation value

55

tRNA

-small(80 nucleotides)
-covalently linked to specific amino acid
-CCA-3' terminus acts as amino acid attachment site

56

Anticodon loop

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

57

CCA-3' terminus

-amino acid attachment site on tRNA
-covalently attached

58

Anticodon form

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

59

hnRNA

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

60

snRNA

-small nuclear RNA
-only in nucleus of eukaryotes
-combine with certain proteins to form snRNPs

61

snRNPs

-used for splicing hnRNA to form mRNA
-splice out introns
-in eukaryotes

62

Ribozymes

-RNAs that act as enzymes