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BMSC 200 > Chapter 10 > Flashcards

Chapter 10 Flashcards

1
Q

what are the physiological roles of nucleotides

A

-energy currency (ATP)
-signalling molecules (cAMP)
-enzyme co-factors (NAD, FAD)
-building blocks of nucleic acid

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2
Q

what are the physiological roles of nucleic acids

A

-genetic information (DNA, RNA)
-all stages of protein synthesis (DNA, mRNA, tRNA, rRNA

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3
Q

what are the building blocks of nucleic acids

A

nucleotides

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4
Q

what are the components that nucleotides share

A

-ribose sugar (ribose or deoxyribose)
-nitrogenous base (purine or pyrimidine)
-phosphate(s)

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5
Q

what back bone do all nucleotides contain

A

a ribose backbone

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6
Q

what form is ribose in within nucleotides

A

it is in cyclized form (B-D-ribofuranose)

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7
Q

in ribose what carbon is where you can see if its oxy or deoxy form

A

on C 2’

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8
Q

RNA contains ____; DNA contains ____

A

ribose, deoxyribose

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9
Q

what are the two families of nitrogenous bases

A

purines and pryimidines

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10
Q

how can you differentiate purines and pyrimidines

A

pyrimidines have a singular ring purines have a two ring system

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11
Q

what are two characteristics of nitrogenous bases

A

they are plainer and relatively non-polar

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12
Q

what are the five standard nitrogenous bases

A

adenine, guanine and cytosine in both DNA and RNA. the fourth base differs; DNA has thymine and RNA has uracil

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13
Q

how are nitrogenous bases linked to ribose

A

through N-glycosidic bonds

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14
Q

what carbon are nitrogenous bases linked to

A

all are linked to C1’ of the sugar

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15
Q

what N is the N-glycosidic bond to of the nitrogenous base in purines

A

N9 of nitrogenous base

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16
Q

what N is the N-glycosidic bond to of the nitrogenous base in pyrimidines

A

N1 of nitrogenous base

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17
Q

how do nucleotides and nucleosides differ

A

-they differ in whether they are phosphorylates at the C5’ position

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18
Q

where do nucleotides ave phosphates

A

nucleotides have 1-3 phosphates of the 5’ position: (one (NMP) two (NDP) three (NTP)

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19
Q

nucleotides are phosphorylated…

A

nucleosides

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20
Q

for nomenclature of nucleotides and nucleosides what are the three things to look at

A

1) which nitrogenous base is present (base name)
2) whether the sugar is ribose of deoxyribose (deoxy prefix)
3) whether there are phosphoryl groups (suffix of osine from nuclosides; ylate for nucleotides)

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21
Q

what is an alternative method for naming nucleotides

A

to specify the number and position of the phosphoryl groups
i.g adenosine 5’-triphosphate rather then adenylate

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22
Q

what is the energy transfer for nucleotides

A

-anhydride linkages in ATP are high energy bonds
-the energy released form the hydrolysis of these bonds drives many biochemical reactions

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23
Q

how what is signal transduction for nucleotides

A

-cyclic AMP, formed form ATP in reaction catalyzed by adenylyl cyclase
-common intracellular messenger produced in response to hormones

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24
Q

how do nucleotides from linear nucleic strands

A

through 3’-5’ phoshodiester linkages

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25
Q

are 3’-5’ phoshodiester bonds the same in RNA and DNA

A

yes they are identical

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26
Q

are 3’-5’ phoshodiester bonds different depending on the nucleotides being joined

A

yes they are identical independent of nucleotides being joined

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27
Q

what is the back bone of nucleic acid

A

strands of sugars linked by phosphodiester bridges

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28
Q

what is it that uniquely characterizes a nucleic acid

A

the sequence of bases

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29
Q

what is the direction nucleic acid strand sequences are presented in

A

5’—>3’

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30
Q

sequences of bases is a form of…

A

linear information (blueprint)

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31
Q

how does RNA differ from DNA

A

-RNA contains ribose rather than deoxyribose
-RNA contains uracil rather then thymine
-RNA is single stranded but can adopt complex 3D structures

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32
Q

what is ribosomal RNA

A

an integral part of ribosomes~ 80% of RNA in cells

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33
Q

what is transfer RNA

A

carry activated amino acids to ribosomes for protein sysnthesis (small molecules 73-95 nucleotides long)

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34
Q

what is messenger RNA

A

code for proteins; contains triplet codons that specify the amino acid sequence of a protein

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35
Q

what is micro RNA (miRNA)

A

short oligonucleotides (22-24 nts in length) that function in transcriptional and post-transcriptional regulation of gene expression

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36
Q

what is more stable DNA or RNA

A

DNA

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37
Q

what makes RNA more reactive

A

the 2’ hydroxyl group of RNA increases its susceptibility to base hydrolysis at the phosphodiester linkage

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38
Q

why does it make sense DNA would me more stable the RNA

A

the greater stability of DNA is consistant with its role as a long term information storage molecules

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39
Q

what is RNAase

A

and enzyme the body produces to destroy RNA

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40
Q

how was double helix descovered

A

-watson and crick postulated the structure of DNA in 1953
-rosalind and wilkins btained the X-ray difraction data that showed DNA is a helix
-they set the stage for watson and crick
-watson, crick, and willson shared the 1962 nobel prize in medicine

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41
Q

what is the specificity of watson-crick base pairing largely determines by

A

they hydrogen bonding groups of the nitrogenous bases

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42
Q

what is chargaffs rule

A

A+G=T+C

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43
Q

what is the number of pyridines equal to in duplex DNA

A

pyrimidines

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44
Q

what are the A-T and G-C hydrogen bonded pairs like

A

they are planar and have the dame dimentions

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45
Q

what base pairs are more stable? G-C or A-T

A

G-C=3H bonds so more stable
A-T only have 2H bonds

46
Q

what weak forces help to stabilize the double helix

A

-hydrophobic effects
-stacking interacrtions
-hydrogen bonds
-charge-charge interactions

47
Q

what does the hydrophobic effects do in a double helix

A

they bury purine and pyrimidine rings in the interior of the helix

48
Q

what do the stacking interactions do in a double helix

A

stacked base pairs form van der waals contacts

49
Q

where do hydrogen bonds from in the double helix

A

between base pairs

50
Q

how do charged charges interactions work in the double helix

A

electrostatic repulsion of neg charged phosphate groups os decreased by cations (e.g. Mg2+) and cationic proteins

51
Q

a double helix has two grooves of uneven width what are these

A

major groove and minor groove

52
Q

within each groove base pairs are—-and are——-

A

exposed and are accessible to interactions with other molecules

53
Q

how do DNA binding proteins read specific sequences

A

because within each groove base pairs are exposed and can interact with other molecules. through these interactions DNA binding proteins can “read” specific sequences

54
Q

how much of of our genome represents genes

A

and very small precent

55
Q

what does restriction endonuclease do

A

it recognizes and cleaves specific DNA sequences

56
Q

how do bacteria protect themselves against viral invasions

A

-using restriction endonuclease
-the host cell protects there own DNA by covalent modifications of bases at the restriction site (e.g methylation)

57
Q

what does the name of restriction enzyme reflect

A

the origins i.g…
-BamHI is the first restriction enzyme characterized from bacillus amyloliquefaciens strain H
- EcoRV is the fifth restriction enzyme characterized form Esherichia coli strain R

58
Q

what sequence do restriction enzymes cut at

A

palindrome sequence

59
Q

what can using restriction enzymes do when used as “molecular scissors”

A

manipulation of DNA

60
Q

what does treating DNA from different individuals with restriction enzymes do to the DNA

A

it breaks it into pieces

61
Q

how do different peoples DNA react to restriction enzymes

A

due to difference in genome sequences DNA from different people will break down into a different number of fragments and fragments of different sizes

62
Q

duplex DNA contains two complementary…

A

anti parallel strands

63
Q

in duplex DNA because the strands are complementary…

A

they sequence of one strand determines the sequence of the other strand

64
Q

what is the complementary nature of the DNA strand important for

A

-replication and repair
-as the nucleotide sequence of one strand determines the sequence of the other each strand can be used as a template to produce the other
-resulting two DNA duplexes will be identical

65
Q

what is denaturation

A

the complex separation of double stranded DNA by heat of chemical agents

66
Q

denaturation of DNA is a ____ process

A

cooperative

67
Q

what is annealing

A

reforming the double stranded helix form single strands

68
Q

what is the melting point for denaturalization of DNA/what does it reflect

A

-the temperature at which half the DNA has become single stranded
-it reflects the sequence compositions; the higher the GC content the higher the Tm

69
Q

what are the primary enzymes for synthesizing nucleic acids

A

DNA and RNA polymerases

70
Q

what are substrates for the synthesis of nucleic acids

A

nucleotide triphosphate

71
Q

what direction does polymerase synthesize nucleic acids

A

-all polymerases synthesize nucleic acids in the 5’ to 3’ direction

72
Q

what way are incoming residues added during the synthesis of nucleic acids

A

incoming residues are added to the 3’ end of the growing strand

73
Q

how are incoming residues selected in the synthesis of nucleic acids

A

they are selected to be complementary to the template strand

74
Q

what is polymerase chain reaction

A

it takes advantage of the ability for each DNA strand to serve as a template for production of a complementary strand

75
Q

what does polymerase chain reaction use to make new DNA

A

heat stable enzymes

76
Q

what does PCR allow for

A

exponential amplification of short regions of DNA very quickly

77
Q

what did PCR revolutionize

A

molecular biology, diagnostics and forensics

78
Q

the amount of eukaryotic DNA necessitates its packaged into…

A

higher order structures

79
Q

what does a first level of DNA packaging involve for packing of eukaryotic DNA

A

formation of nucleosomes

80
Q

what are nucleosome “beads” for packing of eukaryotic DNA

A

that are DNA-histone complexes on a “string” of double-stranded DNA

81
Q

what are histones

A

-DNA packaging proteins
-they are highly conserved and positively charged
-there is 5 histone proteins

82
Q

what are the 5 histone proteins

A

H1, H2A, H2B, H3 and H4

83
Q

which of the 5 histone proteins represent the core for packing of eukaryotic DNA

A

H2A, H2B, H3, H4

84
Q

what region does histone H1 bind for packing of eukaryotic DNA

A

the region of linker DNA

85
Q

histones are reversibly modified to regulate…

A

there interaction with DNA

86
Q

what is a gene

A

a segment of DNA containing information for production of a functional biological product (like a protein)

87
Q

how can the size of a gene be estimated

A

from the size of the corresponding protein

88
Q

what does 3 nucleotides=

A

3 nucleotides= 1 codon= 1 amino acid

89
Q

where are genes contained

A

within the chromosome

90
Q

how many chromosomes do virus and bacterias have

A

they have a single chromosome

91
Q

how many chromosomes do eukaryotes have

A

they will have multiple

92
Q

what is the genome of a bacteria like

A

-millions of base pairs
-closed circular genome
-no interruptions (intons)
-have additional genetic information in the form of plasmids

93
Q

what are plasmids

A

-non chromosomal DNA
-many encode information for resistance to antibiotics
-they may be isolated and manipulated

94
Q

in eukaryotes billions of ___ divided among numerous____

A

nucleotides, chromosomes

95
Q

do all organisms have the same number of chromosomes

A

no they have different numbers

96
Q

each chromosome has a characteristic…

A

set of genes

97
Q

what shape are eukaryotic chromosomes what problems does this bring

A

-they are linear
-presents problem for replication ends of chromosomes

98
Q

what do ends of chromosomes containing repeating sequences called

A

telomers

99
Q

can stomatic cells be imortal

A

no. only cancer cells

100
Q

in eukaryotes what are genes interrupted by non-coding regions

A

introns

101
Q

what organelles may contain additional DNA distinct from the nucleus

A

the mitochondria and the chloroplast

102
Q

because the mitochondria and chloroplast can contain additional DNA what does this inducate

A

that these at one point were separate organisms

103
Q

most eukaryotic genes interrupted by…

A

non coding intervening sequences (introns)

104
Q

what do exons contain

A

protein coding information

105
Q

how can introns vary

A

in size, number and position

106
Q

are introns on mRNA during translation

A

no they are removed prior to translation

107
Q

what is one functional advantage of introns

A

that multiple mRNAs of different sequences can be generated from a single gene

108
Q

what do conventional genetics suggest about inheritance

A

that individuals inherit genetic material which they pass to their offspring; that we are carriers rather then editors of genetic info

109
Q

what does epigenetic refer to

A

the functionally relevant changes to the genome that do not involve a change in the nucleotide sequence

110
Q

in response to environmental influences how else can our genetic material be modified

A

-it can be covalent modified
-modifications can include methylation of cytosine residues

111
Q

can the covalent modifications of DNA be heritable

A

yes it can be passed to offspring

112
Q

what does epigenetics do

A

the changes can alter patterns of gene expression (and phenotypes) without altering the underlying DNA sequence

BMSC 200 (10 decks)

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