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What are bacterial terminator sequences?

-rHo dependent

rho factor used

-rHo independent

inverted repeat sequences transcribed form hairpin loops



Most bacterial transcripts are said to be collinear, what does this mean?

DNA directly encodes them. 

one-to-one correspondence between of bases between the gene and the mRNA transcribed from the gene



What are homologs?

genes related to a second gene by descent from a common ancestral DNA sequence


What singles the beginning of DNA replication?

Helicase bindind to DNA and breaking the hydrogen bonds between the two strands to separate them. 


Who discovered transposable elements?

Barbara McClintock 


What are class 2 TEs?

-aka DNA transposons

-complete/autonomous TEs

-encode the protein transposase, required for insertion and excision

-never use RNA intermediaries



What interferes with L1 activity?

siRNAs interfere with L1 activity and are derived from the 5' UTR of L1 LTRs


What is the Medaka fish example of?

Example of how TEs affect gene regulatory regions and phenotypes

Tol2 transposon either hops out of fish cleanly (results in albinoism) or takes with it genetic material (pigment alterations). 


How were full length cDNA sequences selected for?

-Biotin capping the 5' end 

-Washing the cDNAs with an RNA digestign enzyme like RNase I

-Only cDNAs with biotin cap (full cDNAs) could be recovered



Beta-thalassemia is a result of ___

an insertion (point) mutation


What is eukaryotic termination?

-for RNA pol 1:

similar to Rho-dependent termination of bacteria

-for RNA pol 2:

complex, mRNA  might be synthesized well beyond coding region.

cleaved by a complex and then adenylated

for RNA pol 3:

similar to Rho-independent termination


What is the difference in bacterial/ eukaryotic promoters?

Bacteria- 3 elements

pribnow box (TATAA site)

consensus sequence TTGCCA

upstream element (AT-rich)


Eukaryotes- 7 elements

enhancer sequences (bind with activators to alter DNA structure and facilitate RNA pol 2 binding

need transcription factor

TATA box



In humans, what are the only active class of transposons (jumping genes)

The non-LTR class of retrotransposons (class 1 TEs)



What are nonautonomous TEs?

-TEs that require another TE to move

-They either lack the gene for transcriptase or retrotransposase, so must borrow from a nearby TE

-ex: McClintock's DS element


one form of leukemia is caused by ____

translocation (chromosomal) mutation


What characterizes class 2 TEs?

-inverted repeats on their ends to be recognized by transposase (ex: ACGCTA, TAGCGT)

-short direct repeats that flank inverted repeats and play a role in insertion. They are footprints left behind and sometimes alter gene expression. They are not actually part of TE, because they're left behind


What were the genetic crosses that McClintock performed?

What was the hypothesis of phenotype of the resulting progeny?

What actully occurred?

What was the conclusion?

C'C'bzbz- - x CCBzBzDsDs

To yield heterozygots:



all progeny would be colorless


many kernels were colorless but some cells were purple or brown resulting in spots/streaks of color


A breakage at the Ds locus caused some cels to lose the C' and Bz that would yield colorless or brown phenotypes. Depending on when the breakage occured during development, there was more or less spotting


What are autonomous TEs?

-TEs that can move on their own

-ex: McClintock's AC elements


What are the minor/major grooves of the DNA double helix? What is their role?

Major/minor groove: caused by the asymmetric spacing of the antiparallel helix backbone

Their Role: role in binding of proteins that regulate gene transcription


Besides epigenetic silencing, how do TEs silence themselves?

siRNA, allows TEs to mediate their own silencing

siRNA: prevent transposition. double stranded RNA


How do siRNAs interefere with L1 activity?

5' UTR of L1 promoter encodes a sense promoter that transcribes L1 gene and an antisense promoter that transcribes an antisense RNA

The result is homologous sequence and hybridization and a double stranded RNA that can serve as a substrate for RNAi. 


some cancers are caused by ____

insertion (chromosomal) mutation


                                                                                                        What differentiates DNA from RNA?

DNA doesn't have a 2' OH group on the sugar molecule


Who is Kornberg?

-enzymologist and nobel prize winner

-described DNA replication as a tape recording of instructions for completing a task 

-discovered that DNA polymerase catalyzes DNA synthesis by mixing necessary ingredients for e-coli DNA synthesis in a test tube


How were okazaki fragments discovered?

-Pulse chase experiment

- DNA exposed to isotopic-nucleotides (pulse) and then regular nucleotides for varying periods of time (chase)

-short chases resulted in most radioactivity in "slow" DNA

-increasing length of chases resulted in radioactivity increase in "fast" DNA but not "slow" DNA

-shows that in short period of time okazaki fragments form but with more time they elongate as DNA replication continues


What are class 1 TEs? How do they differ from class 2 TEs?

-aka retrotransposons

-move through the action of RNA intermediaries

-do not encode RNA transcriptase, rather produce RNA transcripts and rely on reverse transcriptase enzymes to reverse transcribe RNA into DNA, which is inserted into target site


What are chemical mutations?

Free radicals (oxidizing agents) may modify nucleotides

Example: Dioxin intercalates between base pairs, disrupting DNA helix integrity 

Example: benzo[a]pyrene induces lesions at guanine sites in P53, lung cancer!


Why are RNA primers required at the origin of replication?

Because DNA can't bind de novo and can only add deoxyribonucleotides to the 3' OH group of an existing chain 


Human chromosomes range from _ o _ in length

50 to 250 million base pairs


What are transposons?

-Jumping genes

-DNA sequences that move from one location on the genome to another


What are the essential chemical ingredients in PCR?

- DNA polymerase


-essential salts (like Mg)

-DNA template

primers with exposed 3' OH groups 


What is the central dogma of molecular biology?

DNA->RNA-> proteins

First step transcription

Second step translation


Cri-du-chat syndrome is caused by ___

deletion (chromosomal) mutation


What is an example of a mutation "hot spot"?

regions of DNA with large numbers of trinucleotide repeats. 

This could lead to DNA polymerase slippage and alteration of the repeat sequence 


What is the length of a turn of DNA?

What is the width of the DNA double helix?

How many bases are in 1 turn?

length: 3.4 nm (34 A)

width: 2 nm (20 A)

1 turn: 10 nucleotide bases


What is the Ames test?

Test to determine if a chemical compound or any of the digested material derived from it is a mutagen 


What is a protein domain?

a region tha can adopt a 3D structure


What are two families of non-LTR retrotransposons?

-Line1 (L1) (LONG! LESS!)

-6 kb in length

-less copies in humans but longer so 15-17% of human genome




-only a few hundred nucleotides

-more copies in humans


What is cDNA?

complimentary DNA synthesized from mRNA using reverse transcriptase



What is the role of DNA polymerase I?

Removes the RNA primer after DNA polymerase III has begnun and replaces it with nucleotides


What are two ways in which sequences are fixed

proofreading- correction during replication

mismatch repair-correction after replication


What is the role of DNA polymerase III?

does most of the elongation work 

adds nucleotides one by one to the 3' end of a growing single strand 


In what direction does DNA synthesis occur?

5' to 3' direction ONLY


What are the bonds that link the backbone of DNA and what are they made up of?

Phosphodiester bonds of the DNA backbone are made up of 5 carbon sugars and phosphate groups


What is a protein motif?

-short, conserved region of a protein

-10 to 20 contiguous residues



What are the sequences at the start and end of splice sites?

Start: GU



What adds new nucleotides to an DNA strand during DNA replication?

DNA polymerase


What are the two types of class 1 TEs?

Class 1 TEs: retotransposons

Type 1: LTR retrotransposons

-Have long terminal repeats on both ends

Type 2: non-LTR retrotransposons

-do not have long terminal repeats at both ends


What are orthologs?

genes in different species that evolved from a common ancestral gene


What results in sickle-cell anemia?

A point mutation in a nucleotide converts the sixth amino acid from glutamic acid into valine 


How is genetic information encoded in DNA?

genetic information is encoded in the sequence of bases attached to the 1' carbon of the sugar molecule of the DNA backbone


What are connected to the carbons of the sugar molecule in DNA?

1' carbon: OH group is replaced by nucleotide bases

2': in RNA, has an OH group. In DNA, it does not

3': a phosphate group attaches here

4': attached to the 5' carbon

5' carbon: 5' phosphate group 


What is an example of environmental mutation?

UV mutations induce hydrolysis of cytosine causes it to mispair to adenine

(creates a C-T fingerprint type mutation)

UV also induces covalent bonds between adjacent pyrimidines


What were some other discoverys by McClintock?`

-Additional discoveries showed an element Ac that was necessary for phenotypic effects of Ds

-McClintock had trouble mapping Ac and Ds, noting that they changed locations



T/F: Scientists have identified a polymerase that can add nucleotides to the 5' end



Why is maize ideal for genetic analysis?

Each kernel is a unique embryo so many different phenotypes can be scored on a single ear of corn 


How were TEs discovered?

-Barabara McClintock

-Studying maize

-studying phenotypic system of maize (triploid endosperm  that is the colored protein coating and diploid zygote

-Four maize genes studied: C' (dom, colored inhibitor)/ C (rec, color shown), Bz (dom, color purple)/ bz (rec, color brown), Ds (location on Ch9 where breakage occurs), As (unknown factor that impacts Ds expression)

Ds observed due to unexpected phenotypes in maize genetic crosses


What is the difference between purines and pyrimidines?

Purines: composed of two rings (guanine and adenine)

pyrimidines: composed of one ring (thymine and cytosine)


What is a single-nucleotide polymorphism?

A single base pair alteration that is common in populations

Basically, any location where at least two sequences are found and are prevalent in at least 1% of population


How are complimentary bases connected?

Complimentary nucleotides are hydrogen bonded to each other. 


Where does translation occur?

When does it begin?

In ribosomes

Once initiation factor proteins bind to small subunit of ribosome

Methionine carrying tRNA binds to mRNA near AUG start

Methionine is the first amino acid encoded in any new protein 

methionine not removed in MK case


cystic fibrosis is a result of ___

deletion (point) mutation


Optiz Kaveggia syndrome is a result of _____

An insertion (chromosomal mutation)


What is the role of DNA ligase

seals the bond between two adjacent nucleotides. 

This "nick" is due to removal of RNA primer and left behind by DNA polymerase I and RNase H. 


Which complimentary nucleotides form 2 hydrogen bonds and which complimentary nucleotides form 3?

2 hydrogen bonds: AT

3 hydrogen bonds: GC (hence why they form a stronger bond)


What is topoisomerase?

reduces torsional strain caused by DNA unwinding


What are two types of sponatenous mutations?

1. deamination

loss of an amino group in a nucleotide

typically if cytosine, repair mechanism fixes this unless cytosine is methylated. Then it is read as a thymine

(CpG islands frequent targets for methylation and mutation)

2. depurination

purine is removed so polymerase can't determine what nucleotide to add to new strand. 

generally polymerase adds an adenine (sometimes guanine)


What is the result of an expanding trinucleotide repeat?

The normal number of repeated trinucleotides is expanded

results in fragile X, huntington's disease


What catalyzes splice reactions and what type of reactions are involved?


transesterification bonsd guanine and adenine

3' and 5' end of intron connected via transesterification as well 


What is a transversion mutation?






What is DNA cloning?

-DNA clonin involves the cloning of expressed DNA genes via a reversal of the central dogma of molecular biology


-An mRNA transcript is transcribed into DNA via reverse transcriptase 


What is the difference between a non-sense and a mis-sense mutation?

non-sense: changes AA sequence to premature stop codon

mis-sense: changes AA sequence


What are the differences between eukaryotic and prokaryotic replication?


-many replication origins

-DNA organized into nucleosomes with histones

-different set of polymerases (polymerasa beta and polymerase gamma instead of polymerase III)

-13 polymerases discovered to date

-chromosomes are linear

-gap in newly synthesized DNA ends protected by telomeres



-single replication origin (oriC)

-chromosomes are circular


where does the splicing process occur?

in spliceosomes in nucleus ?


What experimental evidence proved the existence of reverse transcriptase?

1. The DNA polymerase only incorporated deoxyribonucleotides, not ribonucleotides, into its product.

2. The product itself "behaved" like DNA--in other words, it was sensitive to treatment by deoxyribonucleases but not ribonucleases.

3. The RNA itself was the template, as shown by the fact that treatment of virions with ribonucleases destroyed the ability of the polymerase to incorporate radioactively labeled nucleotides.


How do TEs drive the evolution of genomes?

-help repair double-strand breaks

-exon shuffling

-translocation of gene sequences



What is gene amplication?

An example of copy number variants 

It's a result of the number of tandem copies of a locus being increased

in some breast cancers 


Transposable elements make up how much of human and maize genome

-50% of human genome

-90% of maize genome


What is meme?

searching for common motifs in unaligned sequence


What epigenetic defense mechanisms can silence TEs?

chromatin remodeling

chromatin becomes so constricted in some areas that transcription factors can't bind

DNA methylation (heterochromatin)

In Maize for example: wild-type sequences are methylated. In mutated maize, transposons are transcribed. 


Used in gene regulation: cause histone modification and DNA methylation, bind to mRNA



What is exon shuffling? Why does it occur?

Exon shuffling occurs becaue TEs do not always excise perfectly from sequence. The result is that two previously unrelated exons are are juxtaposed, potentially creating new gene products





What is oriC?

The replication origin

a base-pair sequence of nucleotides


What is a transition mutation?

Mutation of purine to purine or pyrmidine to pyrmidine


T->C (pyrimidine)

A-> G (purine)


What are the 3 types of RNA  polymerases?

In eukaryotes:

RNA Pol 1: ribosomal RNAs

RNA Pol 2: responsible for mRNA synthesis from template DNA

RNA Pol 3: responsible for small RNA, tRNA synthesis


Role of RNA primase?

inserts starter of RNA nucleotides at trancription start site

also attaches RNA primers to lagging strand to yield okazaki fragments


What is the role of RNase H?

Removes the RNA primer after DNA polymerase III has begnun and replaces it with nucleotides


What is the usefulness of cDNA libraries?

can be used to identify genes that are expressed differently in different types of tissues or different stages of development

cDNA libraries give a snapshot of gene activity since only  genes that are expressed and transcribed into mRNA can be cloned


What is prosite?

a database of protein patterns that can be searched by either regular expression patterns orsequence profiles


What is phi blast

searching a specific protein sequence pattern with local alignments surrounding the match 


What is the difference between the 5' and 3' end of the DNA double helix?

5' end: has a free 3' phosphate group (negatively charged)

3' end: has a hydroxyl group on the 3' carbon of the sugar


How does replication of the lagging strand occur?

RNA primase creates an RNA primer with 3' OH so that DNA replication can begin. 

DNA polymerase III adds deoxynucleotides in the 5' to 3' direction following the 3' end of the primer

DNA polymerase I replaces DNA polymerase III and replaces RNA with DNA after exonuclease removes RNA primer

DNA ligase binds 3' OH of growing strand with 5' phosphate of the existing strand by eliciting formation of a phosphodiester bond. 


What are paralogs?

genes related by diplication within a genome 


What is the difference between the leading and lagging strand?

DNA polymerase can only add new nucleotides to a free 3' end of a growing chain. 

Leading strand: replication occurs continuously in the 5' to 3' direction

lagging strand: to provide a 3' OH, RNA primase attaches to the DNA and synthesizes a short RNA primer. DNA polymerase III then adds deoxynucleotides to the 3' end of the primer. DNA polymerase I replaces the RNA with DNA. The enzyme DNA ligase forms a phosphodiester bond betwen the 3' OH of the growing strand and the 5' phosphate in front of it. 


What is the role of SSBPs?

singal stranded binding proteins keep separated DNA strands from reattaching 


What do jumping genes do?


-May result in mutation when they insert into a gene

-Example: L1 into Factor VIII results in hemophilia

-Example 2: L1 in APC genes in colon cancer

-L1 transposes in mammalian somatic cells, which could play a role in disease development. 


Where does helicase split the DNA molecule apart?

At the start of the replication fork, typically areas rich in A and T because they're only connected by two hydrogen bonds 


What are the 4 steps to replication?

1. initiation

2. unwinding

3. primer synthesis

4. elongation



What is a silenced TE?

Why are some TEs silenced?

-Silenced TE: does not produce a phenotypic effect (opposed to L1, most TEs appear to be like this)

-Inactive due to:

  • mutations that affect ability to move around chromosomes
  • kept inactive by epigenetic defense mechanisms