Molecular Bio Test 1

What is the flexible region of histone proteins that is the target of post-translational modifications?

histone tail

What is the chemical formula of ribose?

C5H10O5

What is the chemical formula of deoxyribose?

C5H10O4

What are the pyrimidines?

C and T

What are the purines?

G and A

What does dNMP stand for?

deoxyribonucleoside monophosphate

How many nucleotides make up the haploid human genome?

3.2 billion

What is the protein complex involving four different histone proteins (H2A, H2B, H3 and H4)?

histone octamer

how do histone proteins bind to dsDNA?

electrostatic interactions

what is the chromatin structure induced by the addition of linker histone H1 to nucleosomes?

30nm fiber

How much of the human genome codes for proteins?

1.5%

The chemical process used to synthesize oligonucleotides in vitro is called ______________________ chemistry.

phosphoramidite

what is the protein that acts as a barrier to cohesin extrusion and controls loop formation

CTCF

Where does adenine attach to a dATP? What kind of bond is it?

1’ carbon, covalent bond

how many chromosomes are there in the mitochondrial Human genome?

1

What is the class of enzymes that alter the supercoiling of double-stranded DNA?

topoisomerase

What is the biological complex involving chromosomes interacting with proteins?

chromatin

what is the compact chromatin where transcription is often suppressed?

heterochromatin

what is the covalent bond that links one nucleotide to the next in DNA or RNA chains?

phosphodiester bond

what are the chemicals that are capable of inserting themselves between base pairs in DNA?

intercalating agents

what is the physiological form of DNA, the one discovered by Watson and Crick?

B form

what are the base tautomers in DNA?

enol/keto isomers

Which base pairs have 2 hydrogen bonds?

A and T

Which base pairs have 3 hydrogen bonds?

G and C

What is the protein that prevents the two template strands from rehybridizing during DNA replication?

SSDBP

what are common post-translational modifications that targets histone tails and influence chromatin compaction?

phosphorylation, methylation, acetylation

What does amphipathic mean?

molecule has both hydrophilic and hydrophobic parts

Who deciphered the genetic code?

Marshall Nirenberg

What did Erwin Chargaff do?

discovered that total purines = total pyrimidines in DNA

what is the enzyme that synthesizes short RNA primers during DNA replication?

primase

How is Z DNA different from B DNA?

it is left-handed, and the backbone is in a zig-zag pattern

what does an RNA-dependent RNA polymerase do?

copies RNA to RNA - no DNA involved at all

what is the difference between a nucleotide and a nucleoside?

Nucleoside = base + sugar

Nucleotide = base + sugar + 1-3 phosphate groups

what is the small plant that is widely used as a model organism in plant biology and genetics?

Arabidopsis thaliana

what is a Trizol extraction?

a form of organic separation that allows the rapid isolation of cellular RNAs

what is the enzyme that changes chromatin structure locally by moving histones or by modifying amino acids on histone tails?

nucleosome modifying enzyme

What are enhancers?

DNA sequences in eukaryotes that loop the DNA to bring the enhancer-bound complex close to the promoter

What are sigma factors?

protein cofactors in prokaryotes that recognize the -10 and -35 regions to position the polymerase correctly

What do RNA polymerases do?

peel the synthesized RNAs off the DNA template as they move forward

what is the ribozyme involved in the maturation of pre-tRNAs?

RNase P

what is the conserved adenine located near the 3' end of an intron that is essential for the formation of the lariat?

branch site

what is the transcription factor that binds to the TATA box?

TATA binding protein

What RNA molecule acts as a catalyst?

ribozyme

what are the different mRNAs that are generated from identical pre-mRNAs through alternative splicing?

splicing isoforms

what is the transcription factor in prokaryotes?

sigma

what is the template-independent RNA polymerase in charge of the maturation of the 3' end of eukaryotic pre-mRNAs?

poly-A polymerase

what is the group of three nucleobases interacting edge-to-edge by hydrogen bonding in a RNA molecule?

base triple

what are the transcription promoters in prokaryotes?

-35 and -10

Which ribosomal subunit is the peptidyl-transferase center located in?

the large subunit

what is the name of the 2D-RNA structure in which dsRNA is capped by a loop?

hairpin

Can viroids infect humans?

no

What does Rho do?

Rho is a protein that terminates transcription in prokaryotes

what is the name of an internal RNA 2D structure in which the loop of a hairpin motif base pairs with a distant single stranded region?

pseudoknot

what is the name of the analytical chemistry technique in which molecules are placed in a magnetic field and the signal is produced by excitation of their nuclei?

NMR

What is the enzyme that transcribes RNA from DNA or RNA?

RNA polymerase

what is the RNA motif that involves multiple hairpins connected at their base?

multiway junction

what is the lasso-shaped structure adopted by introns during splicing?

lariat

what is the laboratory technique employed to observe the shape of flash-frozen molecules by firing electrons at them?

Cryo-EM

What is 5’ capping?

the addition of m7G onto the 5' end of eukaryotic mRNAs during their synthesis

what is the unicellular eukaryote and well-characterized model organism?

Saccharomyces cerevisiae

what is the multiprotein complex that functions as a transcriptional coactivator in eukaryotes by interacting with transcription factors, activators, and the RNA polymerase?

mediator complex

What does the mi in miRNA stand for?

micro

can several RNA polymerases transcribe the same gene at the same time?

no

what is the complex involving one snRNA and one or several proteins?

snRNP

what is the RNA 2D structure in which a stem is interrupted by an asymmetrical loop?

bulge

what is the active site of the ribosome that is in charge of the polymerization of amino acids?

peptidyl-transferase center

what is the name of non-canonical base pair often found in RNA?

non-Watson-Crick base pairs

what is the first nucleotide in a gene that is used as a template for transcription?

Transcription start site (+1 position)

what non-coding RNAs are part of the spliceosome?

U1, U2, U4, U5, and U6 snRNAs(small nuclear RNA)

When does 5’ capping occur?

immediately as the pre-mRNA emerges from the RNAP

what is the laboratory technique for the investigation of RNA structures that rely on chemicals or enzymes that discriminate paired from unpaired nucleotides?

RNA probing

what is the RNA that catalyzes its own splicing without the help of a spliceosome?

self-splicing intron

what is a permanently established culture derived from various organs or tissues that will proliferate indefinitely given appropriate fresh medium and space?

cell line

what is the collection of biochemical modifications of RNAs that happen in a cell after transcription and that are not directly encoded in the DNA?

epitranscriptome

what is the domain on the RNA polymerase serving as a binding site for numerous pre-mRNA processing enzymes?

RNA polymerase tail

What is alternative splicing?

process where different combinations of exons from a single pre-mRNA are selected and joined to produce multiple distinct mRNA (and protein) isoforms from one gene

What are UP elements?

upstream promoter elements are AT rich DNA elements in prokaryotes that serve as extra binding sites for RNA polymerase