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NBDE PART 1 BIOCHEM/PHYSIOLOGY > DNA/RNA > Flashcards

Flashcards in DNA/RNA Deck (94):
1

HIV/AIDS virus has the ability to produce __ from an __ molecule

DNA from mRNA

2

the enzyme HIV uses to make DNA from mRNA is called

reverse transcriptase

3

reverse transcriptase is a DNA/RNA polymerase?

it is a DNA polymerase = it makes DNA
it uses RNA as its template to make a DNA strand complementary to the viral RNA = cDNA that is incorporated into the host DNA

4

reverse transcriptase are found in viruses called

retroviruses

5

HIV causes __

AIDS
HIV ==> AIDS

6

the drug AZT used in HIV is a __ of reverse transcriptase

competitive inhibitor

7

reverse transcriptase is used in __ to obtain a copy of a gene form the mRNA

genetic engineering

8

ribosomes in prokaryotes are either free floating in the cytoplasm or __

attached to plasma membrane

9

ribosomes in eukaryotes are either free floating in the cytoplasm or __

attached to endoplasmic reticulum membrane =RER

10

ribosomes have _ activity

enzymatic. b/c they catalyze the formation of peptide bonds

11

T/F all protein synthesis begins on a FREE RIBOSOME

true!

12

if the protein is destined for secretion from cell, incorporation into plasma membrane or into a lysosome, it is transferred from the free ribosome to

a ribosome on the RER

13

The _s ribosome is site of translation = protein synthesis in bacterial cells and chloroplasts

70s - 2 subunits are the 50s and 30s

14

the _s ribosome is in eukaryotes

80s - 2 subunits are the 60s and 40s

15

genetic recombination experiments depend heavily upon which enzymes

dna ligases and restriction endonucleases

16

___ is a technique used to detect mutations in DNA and to identify DNA restriction fragments. it uses restriction enzymes and DNA probes

Southern blotting

17

DNA cloning is used in medicine to make recombinant DNA technology products like

human insulin = DM
anticoagulants = tissue plasminogen factor
erythropoietin for anemia
human growth hormone = dwarfism

18

the first organism used for DNA cloning was ____ and is still the most common host cell

E. Coli

19

plasmids, bacteriophages and cosmids are all

bacterial cloning vectors

20

DNA polymerase I function

fills in the gaps in duplexes by step wise addition of nucleotides to 3'end

21

exonucleases function

remove nucleases from 3' of 5' end depending on the specific one

22

a nuclease cleaves ___ bonds in a nucleic acid

phosphodiester bonds

23

nucleases that cleave internal phosphodiester bonds are called

endonucleases

24

nucleases that cleave external phosphodiester bonds at the 3' or 5' are called

exonucleases

25

in dna replication rna intermediates are used for

primer for DNA polymerase ==> replaced by DNA later

26

DNA polymerase can only add nucleotides to an existing piece of _

nucleic acid = this is why the primer is needed

27

___ synthesizes RNA primer for DNA polymerase and does not need a primer chain

RNA polymerase

28

__ unwinds supercoiled DNA

topioisomerase

29

___ re forms the supercoiled structure once the replication fork has passed

DNA gyrase

30

1.___ unwinds the HELIX
2. __ unwinds supercoiled DNA

1. helicase = separating two annealed nucleic acid strands (i.e., DNA, RNA)
2. topoisomerase = DNA becomes overwound ahead of a replication fork. If left unabated, this tension would eventually halt DNA replication.

31

___relieve superhelical tension by creating a temporary break in one or both DNA strands. they do this and then ligate the strands back together. by doing this, they allow for the strands to quickly rotate to relieve (also known as 'relax') any tension that has been built up.

topoisomerases

32

___ separate the two strands of the DNA. in fact, if a helicase is unwinding the DNA, it will be creating superhelical tension in front of it. thus, helicases work best when there is a topoisomerase present at the same time to relive that tension.

helicases

33

only difference bw products of rna and dna hydrolysis are

ribose and uracil

34

DNA is double/single stranded

double ALWAYS

35

RNA is double or single stranded

single stranded ALWAYS

36

nitrogenous bases of DNA

ADENine
GUANine
THYMine
Cytosine ==== not cysteine!!!!!

37

nucleoside vs nucleotide

Nucleotide = sugar (ribose/deoxyribose), phosphate, and nitrogenous base
Nucleoside = sugar and base (NO PHOSPHATE) = to remember look at the word nucleoside = s for sugar and nucleo for base

38

a single base, sugar, phosphate is called a

nucelotide

39

individual nucleotides linked together to form

polynucleotide chain

40

phosphodiester bonds are bw

sugar and phosphates

41

the purines and pyrimidines are

nitrogenous bases

42

the sugars in DNA and RNA are hexose/pentoses

pentoses

43

the backbone of nucleic acids are made of

phosphate and pentose units with a purine/pyrimidine base attached

44

does the catabolism of a nucleotide produce ATP energy

no.
only lipids, proteins and carb catabolism do

45

do we get our purines and pyrimidines (nitrogenous bases) exogenously or endogenously

endogenously

46

ribonucleotides are synthesized first and then the 2-deoxyyribonucleotides. T/F

True

47

is uric acid soluble

poorly soluble in water. therefore it can cause kidney stones, and gout when it forms sodium urate in the joints

48

phosphodiester bonds link the _ of one sugar to the other

3'OH to a 5'OH

49

the variable part of the DNA is the

base sequences

50

when we write a base sequence, unless otherwise noted, it is written in which direction

5' ==>3'
5'-ATCCG-3'

51

purine bases consumed in diet in form of DNA/RNA are mostly _

excreted in form of uric acid.

52

Xanthine oxidase catalyzes

formation of uric acid from purines

53

tetrahydrofolic acid (TFA) is used in

purine and pyrimidine synthesis.

54

tetrahydrofolic acid (TFA) used as a target for

antimetabolites = for cancer chemotrherapy

55

UV light effect in DNA

makes pyrimidine dimers = interfere with replication and transcription.

56

UV induced pyrimidine dimers are removed by

endonucleases = excise 12 bp fragments around the dimer

57

__ fills in the gaps after an endonuclease takes out bp and _ seals the seams

DNA polymerase I
DNA ligase seals or ligates

58

wobble effect means substitution of the __ nucleotide of a codon will have least effect on protein

3rd
ex. Leucine codons are CUU
CUA, CUC, CUG (only the 3rd one is different)

59

there are _# different triplet codons and only _amino acids = degeneracy of the genetic code

64
20
therefore some amino acids coded for by more than one codon

60

what 3 amino acids are the only ones that are coded by only ONE codon

methionine
tryptophan
selenocysteine
Think I "met and tripped on selena"

61

all 17 other amino acids are coded by _ or more codons

2 or more

62

codons that specify the same amino acid are called

synonym

63

initiation codon is

AUG

64

AUG codes for

methionine

65

all proteins begin with

methionine (AUG)

66

termination codons are

UAA = you are an ass
UGA = you go away
UAG = you are gone

67

termination codons are aka

stop codons/nonsense codons

68

anticodons are located in

transfer tRNA = complementary to the codon for an amino acid in mRNA

69

tRNA and mRNA are

antiparallel

70

how many hydrogen bonds bw A and T?
C and G?

A and T = 2
C and G = 3 (to remember, C is the 3rd letter of the alphabet)

71

Watson and crick deduced the _ of base pairing

specificity due to Hydrogen bonding and stearic factors

72

___law of thermodynamics - If two thermodynamic systems are each in thermal equilibrium with a third, then they are in thermal equilibrium with each other.

•Zeroth

73

__ law of thermodynamics - As temperature approaches absolute zero, the entropy of a system approaches a constant minimum.

. •Third

74

__law of thermodynamics - Energy can neither be created nor destroyed. It can only change forms. In any process, the total energy of the universe remains the same. For a thermodynamic cycle the net heat supplied to the system equals the net work done by the system

•First

to remember: 1st law is energy (think E = mc2)
second law is entropy (S) for second
third law is temperature = T

75

__ law of thermodynamics - The entropy of an isolated system not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium.

•Second

76

DNA double helix is held together by what 2 forces?

hydrogen bonding bw nitrogenous base pairs and base stacking interactions facilitated by phosphodiester bonds

77

the helix of DNA forms a major and minor groove. the _ groove is the binding region for many proteins that control the transcriptional activity of the DNA molecule

major

78

the weaker bonding bw A and T or U in RNA is used in transcription to aid in?

release of the newly formed RNA from the dna template

79

The AT base pair promotes helix stabilization in __ but not in __

in DNA but not in RNA

80

are purines or pyrimidines larger

purines (remember the shorter word is bigger)

81

the sum of the purine residues equals

the sum of the pyrimidine residues

82

the melting temperature is a function of the base composition with a higher __ content having a higher melting point

GC content

83

bases are hydrophobic/hydrophilic

phobic

84

the bases lay __ on top of each other

flat like pancake stack

85

the successive bases stacked on each other have __ interaction

van der Waals interactions

86

the strongest NON COVALENT forces in the double helix are the

van der Waals interactions! not the hydrogen bonds

87

dna is right/left handed helix

right handed

88

how many base pairs per turn in dna helix

10.4 bases per turn

89

the ribose phosphate portion of purine and pyrimidine nucleotides comes from

5-phophoribosyl-1-pyrophosphae (PRPP) which is synthesized from ATP and ribose 5 phosphate in the pentose phosphate pathway

90

which type of RNA is the least abundant in the cell:
mRNA, tRNA, or rRNA

mRNA

91

which type of RNA is the MOST abundant in the cell:
mRNA, tRNA, or rRNA

rRNA (ribosomal RNA) > tRNA > mRNA

92

is there any error checking in translation at the ribosome

no. individual enzymes are highly specific for ONE AMINO ACID = amino acyl-rRNA synthetase is the group of ligases (enzymes) that ensure that the correct amino acid is attached to the tRNA with the correct anticodon to be used.

93

__are the major component of ribosomes, which are the physical and chemical structures on which the protein molecules are assembled

rRNA

94

transcription will make what kind of RNA?

mRNA, tRNA and rRNA