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149 terms

Molecular Biology Test 1

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DNA's strand arrangement
anti-parallel
DNA strands are connected by what type of bonds?
hydrogen bonds
Guanine and cytosine are connected by how many hydrogen bonds
3
Adenonine and thymine are connected by how many hydrogen bonds
2
Which is more stable: more GCs or more ATs
GC
DNA's structure type
double helix
In a normal DNA molecule the two DNA strands make a full twist every..
10.4 base pairs
If a molecule has more twists, the strands coil around each other this is called
positive supercoiling
If a molecule has fewer twists, the strands coil around each other this is called
negative supercoiling
DNA super coiling is monitored and adjusted by?
topoisomerases
True or False: Prokaryotes also have topoisomerases
true
Type 1 topoisiomerases funtion
make a break in one of the the DNA strands
type 2 topoisomerases function
make a break in both of the DNA strands
In DNA recombination different...
DNA molecules are combined
Homologous recombination
between homologous DNA seqments
Non-homologous recombination
between non-related DNA segments
2 examples of when homologous recombination occurs
DNA repair, crossing over
Examples of Non-homologous recombination
recombinant DNA, DNA repair, antibody formation, transposition
VDJ recombination is an example of
non-homologous recombination
VDJ recombination occurs during
B cell development
D in VDJ stands for what
heavy strand
Define transposition
a segment of DNA moves to another lovation in the genome
is transpostion non-homologous recombination
yes
The segment of DNA that moves to another location is called the
transposon
In prokaryotes transposition can form
antibiotic genes
Define translocation
unwanted exchange of DNA between non-homologous chromosomes
Eukaryotic DNA molecules are wrapped around what
histone proteins
Histone proteins allows
condensing of DNA, regulation of the rate at which DNA is used for gene expression
DNA length is about
3-6 feet
Epigentic changes include
histone phosphorylation and histone acetylation
Both phosphorylation and acetylation result in what type of charge
neutral
resulting charge from epigentic changes cause what
less interaction between DNA(-charged) histone(now N), this opens up chromatin
Opening of chromatin allows for
more access for gene transcription
DNA methylation occurs in both
eukaryotes and prokaryotes
DNA methyltransferase transfers..
a methyl group from S-adenosyl methionine to the cytosines in CpG combinations
In each replication fork the two DNA strands are separted by
Helicase
Helicase breaks what type of bonds
hydrogen bonds
What binds and hold the separated strands made by helicase apart
single stranded DNA binding proteins (SSB)
What unwinds the DNA while it is being separated
topoisomerase 1
The nucleotide sequence of the template strand is read in what direction
3' to 5'
The new DNA strand is synthesized in what direction
5' to 3'
What functional group must be present for DNA polymerase to work
Hydroxyl group (-OH)
T or F: DNA polymerase is able to proofread
T
T or F: RNA polymerase is able to proofread
F
In what direction does DNA polymerase proofread
3' to 5'
What strand does DNA synthesis occur continously?
Leading strand, 5' to 3'
What strand does DNA synthesis occur in fragments
lagging stand
What's the name of the fragments formed from lagging strand
Okazaki frament
DNA polymerase requires what to start synthesis of new strand
RNA primer
Why is an RNA primer need for DNA polymerase?
Because D polymerase requires a free hydroxyl group to start
T or F: each okazaki fragment starts off with an RNA primer
T
RNA hybridase's function
removal of RNA primer after DNA synthesis is complete
RNA hybridase is a type of..
ribonuclease
Telomeres defined
repeating DNA sequences of DNA at the end of eukaryotic chromosomes
Telomeres function
serve as buffers to prevent loss of genetic information during replication
T or F: Telomeres are found in prokaryotes
F
Telomerase function
adds DNA to telomeres
Telomerase uses what as a template and therefore can be considered a..
RNA molecule as template, a type of Reverse transcriptase
Spontaneous hydrolysis
cleavage of the glycosyl bond connecting the bases to the DNA backbone
UV light causes what to form in DNA
cyclobutane pyrimidine Dimers between neighboring nucleotides
Cylobutane pyrimidine Dimers causes what to happen to DNA
kinks in it's structure
Replication of UV-damaged DNA can cause
mutations
Cytosine dimers are especially dangerous because they often cause the incoporation of what
adenine instead of guanine
Oxidative stress occurs when
formation of reactive oxygen species exceeds removal
Oxidative stress can cause (3)
single and double strand breaks, base oxidation
2 types of Chemical DNA damage
alkylating agents, intercalating agents
Alklylating agents cause
addition of alkyl groups to DNA bases
Intercalating agents action
wedge between bases in the DNA strands
Nucleotide excision repair action
an oligonucleotide is excised
Nucleotide excision repair is for
UV damage and chemcial adducts
Base excision repair action
one base is excised
Base excision repair is for
spontaneuos hydrolysis, base oxidation and single stranded breaks
DNA recombination repairs what
double stranded breaks
Cell cycle stages in order
M, Go, G1, S, G2
Cell Cycle checkpoints and when they occur
G1, G2, M, they all occur right after their phase, eg G1 occurs after G1 has been completed not before
Cell cyclle regulation occurs by
cyclin-dependent kinases (Cdk)
A Cdk is active only when
bound to its specific cyclin
Quiescent cells
cells that are stable in Go and can reeenter cell cycle
senescent cells
cells that are damaged in Go and can NOT reenter cell cycle
Can only pass M phase checkpoint if this is formed properly
mitotic spindles
Cyclin-dependent kinases induce cell cycle progression via
phosphoylation of the retinoblastoma protein
The retinoblastoma protein's action
inhibits cell cycle by inhibiting transcription factors of the E2F family, inhibited by phosphorylation
Retinoblastoma is considered what type of gene
tumor supression gene
Cyclin levels are regulated by
growth factors
_______ are proteins in the extracellular space that determine cell survival and proliferation after bind to their receptor on the surface of a target cell
growth factors
Growth factor activates____, which activates____ causing____
Ras, Cyclin D, cell cyle progression
Ras is considered what type of gene
protooncogene
Know the mitosis phases and what happens in each
...
Meiosis you start with one diploid cell and get how many haploid cells
4
At the start of Meiosis 2 how many haploid cells do you have
2
_____ are normal genes that supress cell division or promote apoptosis
Tumor supressor genes
Normal genes that promote cell division or reduce apoptosis
proto-oncogene
Human papilloma virus(HPV) requires what to replicate
proliferating cells
HPV proteins E6 and E7 inhibit
p53 and Rb to induce cell proliferation, both of which are tumor supression genes
Stochastic cancer model says
that all cells that the ability to proliferate infinitely
Cancer stem cell model says
only the cancer stem cells have the ability to undergo multiple cell divisions, hierarchically organized
RNA bases are connected by what type of bonds
phosphodiester bonds
RNA sequences are written
5" to 3"
RNA's structure, only exception
single stranded, excpet microRNA is double stranded
T or F: RNA does not fold in on themselves due to hydrogen bonding
F, RNA does fold in on itself
___ are enzymes that degrade RNA
ribonucleases
Endoribonucleases function
cleave phosphodiester bonds with an RNA molecule
Exoribonulceases function
cleave nucleotides from the end of an RNA molecule
What is the main cause of the low stability of RNA molecules
ribonucleases
Alternate name for coding RNA
messenger RNA (mRNA)
Coding RNA carries
the information for the synthesis of a protein
Non-coding RNA function
many functions other than coding for a protein, wow that's mind blowing
microRNA's actions
together with the RISC complex, it binds to complementary sequences in mRNA
Once miRNA binds..
the mRNA is no longer transcribed but is now degraded
Small interfering RNA alternate name
silencing RNA
siRNA's action
can block and break down mRNAs by binding to the RISC complex
___strand is used as a template to synthesize RNA
Template
What synthesizes the RNA
RNA polymerase
What strand is used to report the sequence of a gene
Coding strand
Transcription factors that regulate the expression of a gene bind...
to its promoter which is located upstream (to the 5' end) of the coding strand
What promoter sequence do transcription factors start with
TFIID
TFIID binds to
TATA box
transcription factors form a complex with RNA polymerase called
transcription initiation complex
RNA polymerase forms a phosphodiester bond where
between the 3' OH-group of the last nucleotide and the innermost phospho atom of the new nucleoside triphosphate
RNA synthesis occurs in which direction
5' to 3'
What energy source is used to add the cap?
GTP
What end is the cap added to?
5' end
What is added to the 3' end
a poly-adenosine tail
RNA splicing's actions
Splice out introns and combine exons
What are introns
noncoding segments
what are exons
coding segments
Alternative splicing
one precursor mRNA can lead to different mature mRNA molecules, which causes different proteins to form
Reverse transcriptases action
synthesize a DNA molecule using an RNA molecule as a template
an example of reverse transcriptase
telomerase
Regulation of mRNA stability depends on (3)
enzymes that degrade mRNA, MicroRNA, siRNA
40-50% of all gene expression regulations occurs by
mRNA degradation
What regress the translation from the mRNAs and redirect the mRNAs either back for translation or to P-bodies for degradation
stress granules
P-bodies contain how many factors and for what
50 factors all involved in degradation
P-bodies include (5)
decapping enzymes, deadenylating enzymes, ribonucleases, miRNA, RISC
general transcription factors plus RNA polymerase II is called what
transcription initiation complex
Other Transcription factors determine what
which gene and when the trasncription initiation complex is formed
2 "other" transcription factors
cell-specific and inducible
CAAT and GC are what
Transcription factors
___are a class of transcription factors that are activated by steroid and thyroid hormones
nuclear receptors
Nuclear receptors actions
bind to hormone response elements in the DNA to induce gene transcription
___are proteins that enhance gene expression but do not induce it
activators
Activators bind where
to an enhancer element in the DNA
T or F: enhancer elements can be close to or far away from promoter
T
___are proteins that silence DNA transcription
repressors
Repressors bind with what in DNA
silencer
A silence can overlap with (2)
an activator binding site(enhancer) or a trasncription start site
DNA methylation causes what to be methylated
CpG regions
CpG regions being methylated causes what
Methyl-CpG- binding proteins to bind to them and thus the transcription complex can longer be formed
2 types of treatments based on epigentics
Inhibitors of histone deacetylase, DNA demethylating agents