Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry and Molecular Genetics > Chapter 8 Exam 2 > Flashcards

Chapter 8 Exam 2 Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

What is a gene?

A

a segment of a DNA molecule that contains the
information required for the synthesis of a functional biological
product, whether protein or RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are ribosomal RNAs?

A

components of ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are messenger RNA’s?

A

intermediates in protein synthesis
-portion of cellular RNA
carrying the genetic information from DNA to the
ribosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are transfer RNA’s?

A

adapter molecules that translate the information in mRNA into a specific amino acid sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are noncoding RNA’s?

A

wide variety of functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the three components of nucleotides?

A

a nitrogenous base
(pyrimidine or purine)
– a pentose sugar
– 1+ phosphates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is a nucleoside?

A

the molecules without a phosphate group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How do nucleotides bond?

A

N-β-glycosyl bond = covalently joins the 1′ carbon of the pentose
to the base (at N-1 of pyrimidines and N-9 of purines)
– formed by removal of the elements of water
the phosphate is esterified to the 5′ carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the deoxyribonucleotides?

A

structural units of DNA
– also called deoxyribonucleoside 5′-monophosphates,
deoxynucleotides, and deoxynucleoside triphosphates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the names of cAMP and cGMP?

A

adenosine 3′,5′-cyclic
monophosphate (cAMP)
* guanosine 3′,5′-cyclic
monophosphate (cGMP)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is a phosphodiester linkage?

A

covalent bond that joins
successive nucleotides of both
DNA and RNA
– between the 5′-phosphate
group of one nucleotide unit
and the 3′-hydroxyl group of
the next nucleotide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does Hydrolysis of DNA and RNA happen?

A

under alkaline conditions:
– RNA is rapidly hydrolyzed due to the presence of 2′-hydroxyl
groups
– DNA is not rapidly hydrolyzed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the schematic representation of nucleotide sequences?

A

phosphate groups symbolized by ℗
* deoxyribose symbolized by a vertical line, from C-1′ at the top to C-5′
at the bottom
* lines connecting nucleotides drawn diagonally from C-3′ to C-5′
can also be written as:
– pA-C-G-T-AOH
– pApCpGpTpA
– pACGTA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is an oligonucleotide?

A

short (typically < 50 nucleotides)
nucleic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is a polynucleotide?

A

longer nucleic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the properties of nucleic acids that affect structure?

A

weakly basic compounds
* aromatic molecules
* because most bonds in the
ring have partial double-bond
character:
– pyrimidines are planar
– purines have a slight
pucker

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are tautomers?

A

Free pyrimidine and purine bases may exist as tautomers
may exist in readily
interconverted forms
called tautomers- Uracil
– lactam
– lactim
– double lactim
(lactam)predominates at
pH 7.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the absorption spectra of common nucleotides?

A

all nucleotide
bases absorb UV
light
* strong absorption
near 260 nm
AMP-15,400
GMP-11,700
UMP-9,900
dTMP-9,200
CMP- 7,500

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How are nucleotides solubile?

A

hydrophobic and relatively insoluble in pH 7.0 water
– leads to stacking interactions (van der Waals and dipole-
dipole)
* charged and more soluble at acidic or alkaline pH values
Stacking of bases helps minimize contact with water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How many base pairs are there per turn and how does the phosphodiester bond run?

A

per helical turn:
– 10.5 bp
– 36 Å (3.6 nm)
antiparallel = 3′ ,5′ -
phosphodiester bonds run in
opposite directions
– ultimately confirmed by x-
ray analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is complementary in DNA structure?

A

Antiparallel Polynucleotides Chains are
Complementary
double-helical DNA strands are
complementary:
– when A occurs in one chain, T is
found in the other
– when G occurs in one chain, C is
found in the other
* hydrogen bonding does not contribute
significantly to stability of the structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How is DNA double helix stabilized?

A

the double helix is stabilized by:
– metal cations that shield the negative charges of
backbone phosphates
– base stacking interactions between successive base
pairs
* successive G≡C or C≡G are stronger than
successive A=T or T=A
* duplexes with higher G≡C context are more stable

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is the first step in DNA replication?

A

Step 1: preexisting or
“parent” strands
become separated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the second step in DNA replication?

A

Step 2: each “parent”
strand serves as a
template for the
biosynthesis of a
complementary
“daughter strand”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What do structural variations in DNA reflect?

A

-different possible
conformations of the
deoxyribose
– rotation about the
contiguous bonds making
up the
phosphodeoxyribose
backbone
– free rotation about the C-
1′–N-glycosyl bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What are the three DNA conformations?

A

B-form DNA = the Watson-Crick structure
– most stable for a random-sequence DNA molecule under
physiological conditions
* A-form DNA = right-handed double helix with a wider helix, 11
bp/turn, and a tilted plane
– favored in solutions devoid of water
* Z-form DNA = left-handed helix with 12 bp/turn and a backbone with
a zig-zag appearance
– appears more slender and elongated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is a palindrome?

A

region of DNA
that is identical when read
either forward or backward
– applied to regions of DNA
with inverted repeats

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is a mirror repeat?

A

sequence
when the inverted repeat
occurs within each individual
strand

29
Q

How do hairpin and cruciform structures form?

A

form from the self-
complementarity within each strand

30
Q

What is Hoogsteen positions?

A

N-7, O6, and N6 of purines
– participate in the hydrogen bonding with a third DNA strand

31
Q

What is Hoogsteen pairing?

A

the non-Watson-Crick pairing
* triplex DNAs = form from Hoogsteen pairing

32
Q

What are tetraplex DNA’s?

A

occur
when four DNA strands
pair
– occur readily only for
DNA sequences with
a very high proportion
of G residues
– G tetraplex = very
stable

33
Q

What is transcription?

A

Process by which mRNA’s are formed on a DNA template

34
Q

In mRNA what is monocistronic and polycistronic?

A
  • monocistronic = codes for only one polypeptide
    – most mRNAs in eukaryotes
  • polycistronic = codes for 2+ different polypeptides
    – occurs in bacteria and archaea
    Gene has noncoding RNA on both sides
35
Q

What is the complex three-dimesional structure of mRNA?

A
  • mRNA is always single-stranded
    – right-handed helical conformation
    – dominated by base-stacking
    interactions
  • strongest between two purines
    – can base pair with complementary
    regions of DNA or RNA
  • paired strands are antiparallel
36
Q

What is a secondary structure of RNA’s?

A
  • structure of complementary
    RNA strands is an A-form
    right-handed double helix
  • breaks caused by
    mismatched or unmatched
    bases result in bulges or
    internal loops
  • internal loops form between
    palindromic sequences
37
Q

What is the most common type of secondary structure in RNA?

A

Hairpins are the most common type of secondary structure

38
Q

Why does DNA play a role as a repository of genetic information?

A

The Role of DNA as a Repository of Genetic
Information
* depends in part on its inherent stability
* chemical transformations are generally very slow in the
absence of enzyme catalysts
* carcinogenesis and aging may be linked to slowly
accumulating, irreversible DNA alternations

39
Q

When does denaturation or melting occur with double-helical DNA or RNA?

A

denaturation, or melting, of
the double helix:
– due to pH extremes or
high temperatures
– disrupts hydrogen
bonds and base-
stacking interactions

40
Q

What does anneal mean in regard to DNA

A

process by which
two strands spontaneously
rewind when temperature or
pH is returned to its normal
range
– two-step process

41
Q

What is the hypochromic effect?

A

the observed decrease in the absorption of UV light when complementary strands are paired

42
Q

What is the hyperchromic effect?

A

the observed increase in the absorption of UV light when a double-stranded nucleic acid is denatured

43
Q

What does monitoring UV absorption at certain wavelengths tell us?

A

monitoring UV absorption at 260 nm can detect the transition from
double-stranded to single-stranded DNA
* Free solution of nucleotides has more absorption of UV lights with a
similar quantity of nucleotides in chain form due to stacking.
* Absorption spectrum: free nucleotides> denaturing DNA >double
helical DNA

44
Q

How does heat affect DNA denaturation?

A

denaturation temperature, tm =
temperature at which ½ of DNA is
present as separated single
strands
– increases with content of G≡C
base pairs

45
Q

What are bubbles?

A

partially denatured DNA
* denatured
regions form
bubbles
* often rich in
A=T base
pairs

46
Q

How does denaturation affect RNA?

A

Denaturation of Double-Stranded RNA and RNA-DNA Hybrids
* RNA duplexes are more stable to heat denaturation than DNA duplexes (at least 20 degree higher), with a comparable sequence, assuming that the strands in each molecule are perfectly
complementary
* RNA-DNA hybrid stability is generally intermediate

47
Q

What affect does nonenzymatic transformations have on nucleotides and nucleic acids?

A

The rate of spontaneous alterations is generally very slow,
* but they are physiologically significant because of the cell’s very low
tolerance for changes in its genetic information.
* Mutations = alterations in DNA structure that produce permanent
changes in the genetic information encoded
– linked to aging and carcinogenesis

48
Q

What is deamination?

A

spontaneous loss of
exocyclic amino groups

49
Q

How does deamination occur and how often?

A

deamination of cytosine to uracil:
– 1 of every 107 cytidine residues in
24 hours
– = ~100 events/day
– recognized as foreign in DNA and
removed
– almost certainly,
– Why? DNA contains thymine rather
than uracil
* Deamination of adenine and guanine
occurs at about 1/100th of this rate.
* 5’ Methyl cytosine -> Thymine = hot spot
for mutation

50
Q

What is depurination?

A

hydrolysis of the N-β-
glycosyl bond between the base and
the pentose

51
Q

What does depurination cause?

A

creates an AP (apurinic,
apyrimidinic) site or abasic site
– more common with purines
– 10,000 per mammalian cell are
lost from DNA in 24 hours under
typical cellular conditions

52
Q

How does radiation affect DNA?

A
  • UV light causes:
    – cyclobutane pyrimidine
    dimers
    – 6-4 photoproduct
  • ionizing radiation (x-rays and
    gamma rays) causes:
    – ring opening
    – base fragmentation
    – breaks in the covalent
    backbone of nucleic
    acids
53
Q

How does reactive chemicals affect DNA?

A

DNA Damage by Reactive Chemicals
* nitrous acid precursors = deaminating agents
* alkylating agents = generate modified nucleotides nonenzymatically

54
Q

What can alkylating agents do to DNA bases?

A

Alkylating Agents Can Alter Certain Bases of DNA
* can methylate
guanine to O6-
methyl-guanine,
which cannot
base-pair with
cytosine

55
Q

What does oxidative damage do to DNA?

A
  • reactive oxygen species (hydrogen peroxide, hydroxyl
    radicals, superoxide radical) damage DNA
  • hydroxyl radicals are responsible for most oxidative DNA
    damage
  • cells have an elaborate defense system to destroy
    reactive oxygen species
  • Catalase, Superoxide dismutase, antioxidant enzymes.
56
Q

When does DNA methylation occur?

A
  • A and C are methylated more
    frequently than G and T
  • all known DNA methylases use S-
    adenosylmethionine as a methyl
    group donor
  • In eukaryotes, 5% of cytidine
    residues are methylated
    – most common at CpG
    sequences
    – affects DNA metabolism and
    gene expression
57
Q

How has the chemical synthesis of DNA been automated?

A

chemical synthesis
of DNA by the
phosphoramidite
method is highly
efficient

58
Q

What is polymerase chain reaction? What does it rely on and what does it add to preexisting strands?

A

polymerase chain reaction (PCR) = method of amplifying DNA segments of interest
– relies on DNA polymerases (enzymes that synthesize DNA from deoxyribonucleotides
(dNTPs) using a DNA template)
– DNA polymerases add nucleotides to the 3′ ends of preexisting strands called primers

59
Q

What are some uses of PCR?

A
  • PCR can detect and amplify just one DNA molecule in
    almost any sample type
  • Uses of PCR:
    – cloning of rare, undegraded DNA segments from 40,000+ years ago
    – tracing evolution
    – potent tool in forensic medicine
    – detecting viral infections and cancers before they cause symptoms
    – prenatal diagnosis of genetic diseases
60
Q

What is Sanger sequencing?

A
  • Sanger sequencing = dideoxy chain-
    termination sequencing
  • nucleotide analogs called
    dideoxynucleoside triphosphates (ddNTPs) interrupt synthesis
    -Still uses polymerase and primers, used to determine long DNA strands
  • each of the
    four ddNTPs is labeled with a different colored fluorescent tag
61
Q

How is DNA sequencing technologies advancing?

A
  • “next-gen” sequencing:
    1. reversible terminator sequencing
    – developed by Illumina
    – uses four different modified deoxynucleotides (A, T,
    G, and C), each with a particular fluorescent label
    and a 3′ blocking group
    2. single-molecule real time (SMRT) sequencing
62
Q

What is SMRT sequencing?

A
  • SMRT (single-molecule
    real time) sequencing =
    technology allowing read
    lengths averages up to
    30,000-40,000 bp
  • lower throughput, higher
    cost, and higher error rate
    than the Illumina
    approach.
63
Q

What is sequencing depth?

A
  • sequencing depth = the
    number of times that a
    particular nucleotide in a
    genome is sequenced, on
    average
64
Q

What are contigs?

A
  • contigs = long, contiguous
    sequences that are
    assembled from overlaps
65
Q

How do nucleotides carry chemical energy?

A
  • hydrolysis of nucleoside
    triphosphates provides
    chemical energy
    – ATP is the most
    widely used
66
Q

How does hydrolysis of nucleoside phosphates produce energy?

A
  • when coupled to a reaction with a positive free-energy change, ATP
    hydrolysis shifts the equilibrium to favor product formation
    – hydrolysis of the ester linkage yields ~14 kJ/mol (under standard
    conditions)
    – hydrolysis of each anhydride bond yields ~30 kJ/mol
67
Q

How are adenine nucleotides components of enzyme cofactors?

A
  • adenosine does not
    participate directly in the
    primary function, but its
    removal reduces cofactor
    activities
  • nucleotide-binding fold =
    single protein domain that
    binds adenosine
68
Q

What are nucleotide regulatory molecules?

A
  • second messengers = compounds produced
    inside the cell following the interaction of
    extracellular chemical signals with receptors
    – often a nucleotide, like adenosine 3′,5′-
    cyclic monophosphate (cyclic AMP, or
    cAMP)
  • ppGpp = produced in bacteria during amino
    acid starvation to inhibit the synthesis of the
    rRNA and tRNA molecules
69
Q

What is another function of adenine nucleotides?

A

Adenine Nucleotides also Serve as Signals
* ATP and ADP serve as:
– neurotransmitters in a variety of signaling pathways
– signals for receptors that mediate pain sensation
– blood clotting signals
– ATP binds P2x receptors on the postsynaptic cell
– Extracellular ADP binds P2Y receptors in sensitive
cell types

Biochemistry and Molecular Genetics (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions