1
Q
physiological roles of nucleotides
A
energy currency (ATP)
signaling molecules (cAMP)
enzyme co-factors (NAD, FAD)
building blocks of nucleic acids
2
Q
physiological roles of nucleic acids
A
genetic information (DNA,RNA)
all stages of protein synthesis (DNA, mRNA, tRNA, rRNA)
3
Q
structural features of Nucleotides
A
building blocks of nucleic acids
ribose sugar
nitrogenous base
phosphate
4
Q
what form is ribose in, in nucleotides
A
cyclized form
beta-D-ribofuranose
5
Q
what sugars do DNA and RNA contain
A
DNA- deoxyribose sugar
RNA - Ribose sugar
6
Q
what is more stable Ribose or deoxyribose
A
deoxyribose
the hydroxyl on ribose makes it m ore susceptible to degradation
7
Q
what Carbon is anomeric on ribose sugars
A
C1
8
Q
what is the difference between RNA and DNA
A
for DNA, 2 carbon of the ribose is in the deoxy form
9
Q
what are the two families of the nitrogenous bases
A
purine and pyrimidines
10
Q
purines
A
Adenine and Guanine
11
Q
pyrimidines
A
cytosine, uracil and thymine
12
Q
how do purines and pyrimidines differ
A
pyrimidines have a single ring and purines have two ring system
13
Q
characteristics of nitrogenous bases
A
planar and relatively non-polar
14
Q
how does the 4th nitrogenous base differ
A
DNA has thymine and RNA has uracil
15
Q
why doesn’t cytosine swap with uracil in RNA
A
if it swapped the amino group in cytosine would screw up DNA repair mechanism if it became uracil
16
Q
why is uracil less stable than thymine
A
it is used in RNA for short term purpose
but has the same function as thymine
17
Q
why i thymine used in DNA and not uracil
A
it is more energetically expensive; needed to maintain DNA structure
18
Q
how do nitrogenous bases attach
A
hydrogen bond donors and acceptors
purine with pyrimidine
19
Q
how do nitrogenous bases link to ribose
A
through N-glycosidic bonds
at the C1 of the sugar
20
Q
where is the N-glycosidic bond in purines and pyrimidines
A
purines- N9 of nitrogenous base
pyrimidines- N1 of nitrogenous bases
21
Q
how do nucleotides and nucleosides differ
A
in whether they are phosphorylated at the C5 position
22
Q
where and how many phosphorylation on nucleotides
A
1-3 phosphates on the 5’ position
one (NMP) two (NDP) three (NTP)
23
Q
what are nucleotides
A
phosphorylated nucleosides
24
Q
what are the three things to look at for nomenclature of nucleotides and nucleosides
A
- which nitrogenous base is present
-whether the sugar is ribose or deoxyribose
-whether there are phosphoryl groups
(suffix of osine from nucleosides; ylate for nucleotides
25
what is an alternate version for naming nucleotides
specify the number and position of the phosphoryl groups
26
how do nucleotides transfer energy
Anhydride linkages in ATP are high energy bonds.
-the energy released from hydrolysis of these bonds drives many biochemical energy
-can use other molecules but still use phosphate bond for energy
27
how do nucleotides work in transduction of signals
cyclic AMP is formed from ATP in a reaction catalyzed by adenylyl cyclase
-cAMP is common intracellular messenger produced in response to hormones
-caffeine causes increase in cAMP levels in the cell
28
what joins nucleotides in nucleic acids
phosphodiester bonds
29
phosphodiester bonds in nucleic acids
nucleotides form linear nucleic strands through 5'-3' phosphodiester linkages
-identical in DNA and RNA
-identical independent of nucleotides being joined
-
30
what is the back bone of nucleic acids
the strand of sugars linked by phosphodiester bridges
31
how does the charge of phosphodiester bonds affect shape
each link creates negative charge
-fully extended repel each other
-form hydrogen bonds, extremely polar
-forms the double helix and position bases on the inside
32
what is the direction of nucleic acid starnds
sequences are presented 5' -> 3'
33
network effect in nucleic acids
the more you sequence the more valuable they become
34
what uniquely characterizes a nucleic acid
the sequences of bases
35
how does RNA differ from DNA
contains ribose rather than deoxyribose
contains uracil rather than thymine
36
how many strands does RNA have
single stranded but can adopt complex three dimensional structures
37
function of rRNA
an integral part of ribosomes
most abundant RNA
38
function of tRNA
carrya ctivated amino acids to ribosomes for protein synthesis
39
function of mRNA
code for proteins; contain triplet codons that specify the amino acid sequence of a protein
40
miRNA function
short oligonucleotides
function in transcriptional and post-translation regulation of gene expression
41
differential stabilities of DNA and RNA
the 2' hydroxyl group of RNA increases its susceptibility to base hydrolysis at the phosphodiester linkage
-the greater stability of DNA is consistent with its role as a long-term information storage molecule
42
basics of double helix (6)
two helical DNA strands coiled around a common axis forming a right-handed double helix
-run in opposite directions
-complimentary to each other
=sugar phosphate backbones are on the outside of the helix; bases on the inside
-base pairs are perpendicular to helix axis
-purine with pyrimidine for constant diameter
43
what bases pair with each other
A-T
G-C
44
what is the specificity of Watson-Crick base pairing largely determined by
hydrogen bonding
45
Chargaffs rule
A+G = C+G
number of purines equals number of pyrimidines in duplex DNA
46
how many hydrogen bonds between G and C
and between A and T
G-C = 3
A-T =2
47
how does the hydrophobic effect stabilize the double helix
burying purine and pyrimidine rings in the interior of the helix
48
how does stacking interactions stabilize the double helix
stacked base pairs form van der Waals contact
strong interactions when stacked
49
how do hydrogen bonds stabilize the double helix
hydrogen bonding between base pairs
50
how does charge-charge interactions stabilize the double helix
electrostatic repulsion of negatively charged phosphate groups decreased by cations (Mg) and cationic proteins
51
how do many proteins bind DNA
in a sequence-specific fashion
(restriction enzymes, transcription factors)
52
what are the grooves in DNA
major - deep and wide
minor- shallow and narrow
53
what do major grooves do
makes base pairs accessible to interactions with other molecules
DNA-binding proteins can use these interactions to read a specific sequence
54
restriction endonucleases
recognize and cleave specific DNA sequences
bacterial defense mechanism against viral invasion
55
how do host cells protect DNA
by covalent modifications of bases at the restriction site
(eg. methylation)
56
what do the names of restriction enzymes reflect
origins
57
where do restriction enzymes cut
at palindrome sequences
58
what else can restriction enzymes be used for
molecular scissors for manipulation of DNA
59
how does DNA fingerprinting work
treating DNA from different individuals with restriction enzymes will break DNA into pieces
-due to differences in genome sequences, DNA from different people will break down into a different number of fragments and fragment sizes
-highly variable regions give restriction fragments that are as unique as fingerprints and can be used to identify individuals in a large population
60
complimentary strands in duplex DNA
duplex DNA contains 2 complimentary, anti-parallel strands
-because strands are complimentary, the sequence of one strand determines the sequence of the other strand
61
what is the complimentary nature of DNA important for
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 DNA duplexes will be identical
62
denaturation
complete separation of double stranded DNA by heat or chemical agents
63
annealing
reforming the double strnaded helix from single strands
64
melting point of DNA
temperature at which half the DNA has become single stranded
reflects sequences composition; the higher the GC content the higher the melting point
65
is denaturation of DNA cooperative or non-cooperative
cooperative
66
what are the primary enzymes for synthesis of nucleic acids
RNA and DNA polymerase
67
what is the substrate for nucleic acid synthesis
nucleotide triphosphate
68
what direction do polymerases synthesis nucleic acids
5' to 3'
69
incoming residues and where they are added
selected to be complimentary to the template strand added to the 3' end of the growing strand
70
polymerase chain reaction
takes advantage of the ability for each DNA strand to serve as a template for production of a complimentary strand
71
what does PCR use to make new DNA
heat-stable enzymes
72
what does PCR allow for
exponential amplification of short regions of DNA very quickly
73
what does the amount of eukaryotic DNA do
necessitates its packaging into higher order structures
74
what does the first level of DNA packaging involve
formation of nucleosomes
75
nucleosomes
DNA-histone complexes on a string of double stranded DNA
76
histones
packaging proteins
highly conserved and positively charged
77
what are the five histone proteins
H1, H2A, H2B, H3, H4
78
what are nucleosomes composed of
two molecules of each H2A, H2B, H4, H3 and 146 base pairs of DNA
79
what is H1 do
binds the region of linker DNA
80
how are histones modified
reversibly to regulate their interaction with DNA
81
a gene
segment of DNA containing the information for production of a functional biological product
82
how may the size of a gene be estimated
from the size of the corresponding protein
3 nucleotides= 1 codon = 1 amino acids
83
where are genes contained
within the chromosomes
84
how do eukaryotic, virus and bacterial chromosomes differ
viruses and bacteria have a single chromosome
eukaryotes have multiple chromosomes
85
bacterial genome
millions of base pairs
closed, circular genome
no internal interruption (introns)
contains all the information required to produce every protein required by the bacteria
86
what else do bacteria have for genetic info
plastids
-non-chromosomal DNA
-many plastids encode information for resistance to antibiotics
-may be isolated and manipulated
87
eukaryotic genome
billions of nucleotides divided among multiple chromsomes
-different organisms have different amount of chromosomes
-each chromosomes has a characteristic set of genes
-linear, makes problem for replicating the ends of chromosomes
-contain telomers
-interrupted region - introns
some organelles contain additional DNA
88
introns
non-coding intervening sequences
vary in size, number and position
removed from mRNA prior to translation
89
exons
contain protein-coding information
90
what is a functional advantage of introns
multiple mRNA's of different sequences can be generated from a single gene
91
epigenetics
in response to environmental influences, our genetic material can be covalently modified
-modifications include methylation of cytosine residues
these modifications are inheritable
92
what does epigenetics refer to
functionally relevant changes to the genome that do not involve change in nucleotide sequence
-changes can alter patterns of gene expression without altering the underlying sequence
93
what can comparing genomes from different species provide
insight into phenotypic differences
ex. genome sequencing of healthy people vs people with a disease can provide insight into genetic basis of that disease
94
what do genomic approaches enable in medecine
better prediction, understanding and treatment of disease
-personalized medecine
95
denaturation of DNA is _____
cooperative
96
true or false
disruption of the duplex requires breakage of phosphodiester bonds
false
97
true or false
the watson-crick base pairs are perpendicular to the axis of the helix
true
98
true or false
the nitrogenous bases of opposing strands associate through watson-crick base pairs
true
99
true or false
disruption of the duplex requires breakage of hydrogen bonds
true
100
true or false
the nucleotides within each strand are linked through phosphodiester bonds
true
101
epigenetics refers too
heritable changes in gene expression that do not involve changes to underlying DNA sequence
102
a nucleic acid sample has a composition of 30%A, 25%C, 20%G and 25% U, what is most likely the conclusion
the sample is likely single stranded RNA
103
in both DNA and RNA, the phosphodiester bonds link which carbons of the ribose rings
3' and 5'
104
bacterial and human genomes are structurally similar in that they both:
are made from double-stranded DNA
105
which nitrogenous base is found within DNA but not RNA
thymine
BMSC 200
flashcards
Decks in class (10)
# Cards
-
Module 1: Foundations24
-
Module 2: Water46
-
Module 3: Amino Acids, Peptides, and Proteins0
-
Module 4: The Three Dimensional Structure of Proteins87
-
Module 5: Hemoglobin and Myoglobin85
-
Module 6: Enzymes127
-
Module 7: Carbohydrates80
-
Module 8: Lipids68
-
Module 9: Biological Membrane and Transport97
-
Module 10: Nucleic Acids105
