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

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