Cell and Molecular Bio Terms to Know Exam 2

DNA Transposon

Cut and Paste

Retrotransposon

Copy and Pastemechanism of transposition that involves RNA intermediates.

What does DNA transposon code for?

Transposon

Retrotransposon codes for?

reverse transcriptase and integrase enzymes.

tRNA serves as a primer for?

reverse transcriptase

How can Reverse transposon be classified as?

LTR-retrotransposons and non-LTR retrotransposons.

non-LTR retrotransposon has two types:

LINEs and SINEs.

What is the best well known SINE?

Alu sequence

Nucleosome definition

A structural unit of a eukaryotic chromosome, consisting of a segment of DNA wound around a core of histone proteins, playing a crucial role in the organization and regulation of DNA.

The two types of chromatin

are euchromatin and heterochromatin.

Thickness of euchromatin

around 10nm thick

Thickness of a heterochromatin

approximately 30nm thick

Is euchromatin transcriptionally active or inactive?

Euchromatin is transcriptionally active

Is heterochromatin transcriptionally active or inactive?

Heterochromatin is transcriptionally inactive.

Is euchromatin hyperacetylated or hypermethylated?

hyperacetylated in order to loosening the chromatin structure and allow for gene expression.

Is heterochromatin hyperacetylated or hypermethylated?

hypermethylated to maintain a compact chromatin structure, preventing gene expression.

What mediates acetylation?

Histone AceTylase (HAT)

What mediates methylation?

Histone Methyltransferase (HMT)

What is Epigenetics?

chemical modification in histone to regulate transcription activity

What are some nonhistone proteins that help chromosome packing?

HMT, HDAC, HP1, scaffold protein and condensin

What are some nonhistone proteins that chromosome unpacking?

HAT

What are some DNA sequences that control transcription?

promoter, enhancer, and proximal element

Lac operon plays a role in?

lactose metabolism

In the presence of lactose, the operon is?

on; which means the transcription is on

In the absence of lactose, the transcription is?

off

Why does lactose inhibit Lac repressor?

to initiate transcription

if both lactose and CAP present, how does it affects transcription rate?

the transcription rate hits its maximum state

3 DNA sequences that control transcription

promotor, proximal elements, and enhancer

RNA polymerase II activation is initiated by?

phosphorylation of CTD (C terminal Domain) of the protein

RNA polymerase I catalyzes what?

the production of rRNA

RNA polymerase II catalyzes?

catalyzes the production of mRNA, snRNA, siRNA, and miRNA

RNA polymerase III catalyzes?

The production of tRNA

WHat is Antiposhperine antibody

antibody to be used for the localization of activated RNA polymerase II

What are some molecular methods to identify and characterize DNA sequences that control transcription?

Site directed mutagenesis, sequence scrambling mutations, 5’-deletion series assay, and DNase I footprinting assay

Killing two birds with one stone type of method to find DNA sequence and transcription factors involved in transcription?

DNase I footprinting

Name some reporter genes that can be used to measure the level of transcription

GFP, RFP, LacZ, luciferase, Thymidine kinase, alkaline phosphatase

What are some motifs involved in controlling gene transcription?

Zinc finger, leucine zipper, and basic helix-loop-helix motif

What does the Glucocorticoid receptor, the transcription factor, do?

It reveals nuclear localization signal to enter the nucleus as it binds to glucocorticoid and charperon proteins like HSP70

What does transcription dimerization increase?

It increases the binding affinity to DNA elements (promotor, enhancer, and proximal elements) and increase transcription control options (or outcomes)

RNA polymerase I catalyzes?

The formation of rRNA

RNA polymerase III catalyzes?

The formation of tRNA

tRNA gene’s 2 promoters are located where and what are their functions?

tRNA gene's 2 promoters are located in its own coding sequence: play dual functions-1) as promotors, they recruit transcription factors and RNA polymerase III, and 2) they serve as coding sequence that specifies the structure of tRNA.

Transcription result in the production of what?

pre-mRNA, pre-tRNA, and pre-rRNA in the nucleus

All biological pathways, including RNA processing, RNA editing, nuclear exit, translation, protein degradation and mRNA degradation, are considered what type of control?

Posttranscriptional Control, the most diverse and efficient mechanism of gene expression

RNA processing occurs where?

in the nucleus

5' capping pre-mRNA involves three chemical modification at 5’end of pre-mRNA

addition of methylated guanine, 5’-5’ triphosphate linkage, and methylation of several sugars at 5’ end

pre-mRNA undergoes what three step processing to form mature mRNA

5’ capping, 3’ poly adenylation. and alternative splicing

What are the purposes of 5’ capping

protection from exonuclease, necessary for nuclear exit, and promotion of translation

3’ poly adenylation is completed by what and what is the purpose

poly A polymerase and the purpose is the same as the purpose of 5’ capping

Is splicing a universal event and what is its purpose

Splicing is universal event in eukaryotic cells and the purpose is to promote protein diversity

Who discovered splicing mechanism

Philip Sharp

Splicing is catalyzed by what and what are the steps

Splicing is catalyzed by RNA itself via 2 transesterification step: so RNA that catalyze this process is called ribozyme

Ribozyme activity will be promoted by what?

U1, U2, U4, U5, U6 snRNP complex

each snRNP consists of what

each snRNP consists of a snRNA and its cognate protein

what does snRNA directly interact with?

snRNA directly interacts with intron sequence

Best example of RNA editing

best example is C to U change by cytosine deaminase

What is the consequence of CAA to UAA change in apoB mRNA

cause the production of a version (apoB48) of apoB100

Overall what is the impact of RNA editing

increase of protein biodiversity

In human uv squid how often does RNA editing happen

in human in rarely (less than 10%) but in squid majority of genes undergo RNA editing

What processes take place in the nucleus

Transcription, RNA processing and RNA editing

Where do rRNA processing and ribosome formation occur

in the nucleolus

What is snRNP and does it do

snRNA+Riboprotien and it assists in alternative splicing

What is mRNP and does it do

mRNA and Riboprotein: assist nuclear exit process of mRNA

What is rRNP and does it do

rRNA + Riboprotein: assist rRNA processing