Lecture 5

Question 1

Recall the CENTRAL DOGMA

Answer 1

DNA -> RNA (transcription) -> protein (translation)

ALL cells use this

In Eukaryotes:
-DNA undergoes transcription, pre-mRNA undergoes 5’ capping, RNA splicing, 3’ polyA tail in NUCLEUS; mRNA is exported out of nucleus, translated to protein outside nucleus

In Prokaryotes:
-DNA undergoes transcription - mRNA - translated to protein; NO nucleus

EVERY cell processes information like this

Information processing (how a cell goes from DNA to protein)

Question 2

RNA processing

Answer 2

RNA splicing
5’ cap
3’ PolyA tail
ONLY in eukaryotes

Question 3

Eukaryotes vs Prokaryotes

Answer 3

Eukaryotes are LARGER, possess introns/exons, RNA processing, and nucleus (prokaryotes don’t have those)

Question 4

Product of a gene is NOT always turned into a protein

Answer 4

Cells can regulate how much is made into protein (usuallly at transcription)

Question 5

A cell can express different genes at

Answer 5

Different rates

Question 6

Gene expression

Answer 6

1st step is transcription

Question 7

What determines where RNA polymerase starts transcribing DNA?

Answer 7

Transcription of a gene produces an RNA complementary to one strand of DNA

The promoter

Question 8

Transcription proceeds in a 5’ to 3’ direction using a

Answer 8

3’ to 5’ template

Question 9

Bacterial promoters and terminators have specific

Answer 9

Nucleotide sequences that are recognized by RNA polymerase

Question 10

Transcription in Bacteria

Answer 10

starts on a sequecnce call the Promoter: It is NOT a continuous strand of bases, occurs in segments (UNLIKE replication origin)

Transcription starts at the +1 (this is where the first nucleotide is added

Question 11

In eukaryotes, the promoter is NOT in

Answer 11

RNA

Question 12

Signals in the nucleotide sequence of a gene tell bacterial RNA polymerase

Answer 12

Where to start and stop transcription

Question 13

Sigma Factor

Answer 13

Transcription factor that helps the RNA polymerase (one of the main differences between prokaryotic and eukaryotic)

Recognizes the Promoter

Question 14

Terminator

Answer 14

Where transcription stops

Ends up in molecule of RNA (promoter does NOT)

Question 15

Eukaryotic promoters

Answer 15

Contain sequences that promote the bindings of the general transcription factors

Question 16

TBP binds to the TATA box and bends

Answer 16

The DNA molecule

Question 17

General transcription Factors

Answer 17

found in EVERY single cell and initiate transcription

Question 18

Regulatory Transcription factors

Answer 18

Regulate transcription (activators, repressors)

Vary on cell type

Question 19

Some genes are transcribed using one DNA strand as a template, and others are transcribed from

Answer 19

The other DNA strand

Question 20

How does RNA polymerase differ from DNA polymerase?

Answer 20

DNA is transcribed into RNA by the enzymes RNA POLYMERASE

-Helicase opens the helix in RNA, too; opens as it goes, closes behind it; NO primer for transcription of RNA

Question 21

How do RNA and DNA differ from each other?

Answer 21

The chemical structure of RNA differs slightly from that of DNA
-RNA uses ribose (has one more OH), DNA uses deoxyribose (one less OH)

RNA uses uracil (one less methyl)

DNA uses thymine (one more methyl)

uracil forms a base pair with adenine

Question 22

Messenger RNAs

Answer 22

mRNA

Code for proteins

NOT translated to proteins

Question 23

Ribosomal RNAs

Answer 23

rRNAs

Form the core of the ribosome’s structure and catalyze protein synthesis

Question 24

MicroRNAs

Answer 24

miRNAs

Regulate gene expression by associated with RISC complex then binding to certain mRNA that it carries a message for and destroys that mRNA

Question 25

TransferRNAs

Answer 25

tRNAs Serve as adaptors between mRNA and amino acids during protein synthesis

Question 26

Other noncoding RNAs

Answer 26

Used in RNA splicing, gene regulation, telomere maintenance, and many other processes

Question 27

RNA can fold into structures that are held together by

Answer 27

H bonds

Question 28

How does transcription Proceed?

Answer 28

TO begin transcription, eukaryotic RNA polymerase II requires a set of general transcription factors: - TATA and TFIID recognize promoter - Recruit TFIIB - TFIIB binds, recruits TFIIE and TFIIH and RNA polymerase II - TFIIH breaks H-bonds and acts as a helicase (does NOT stay the whole time like helicase does in DNA) - DNA melts, transcription factors dissociate

Question 29

RNA polymerase I

Answer 29

most rRNA genes

Question 30

RNA polymerase II

Answer 30

All protein-coding genes, miRNA, plus genes for other noncoding RNAs (e.g. those of teh spliceosomes)

Question 31

RNA polymerase III

Answer 31

tRNA genes, 5S rRNA gene, genes for many other small RNAs

Question 32

Eukaryotic vs. Prokaryotic Initiation

Answer 32

Eukaryotic -TATA, TBP, TFIID recognize promoter, recruit TFIIB, binds to promoter, recruits TFIIE, TFIIH, polymerase II, TFIIH unwinds helix (closes right behind), DNA melts, transcription factors dissacoiate Prokaryotic: -Sigma factor binds to RNA polymerase, RNA polymerase binds to promoter at start site, begins RNA synthesis, sigma factor is released, polymerase calmps firmly on DNA, RNA synthesis terminated at stop site, polymerase and completed RNA released

Question 33

Phosphorylation of the tail of RNA polymerase II allows RNA-processing proteins to

Answer 33

Assemble

Question 34

TFIIH functions

Answer 34

1) Helicase 2) Phosphorylation - Melt DNA, open up, phosphorylate Phosphorylation acts as a docking site ONLY RNA polymerase II does this (other proteins not made by RNA polymerase II do NOT have a cap)

Question 35

Eukaryotic mRNA molecules are modified by capping and polyadenylation

Answer 35

Capping: Occurs on 5' ends, message is capped BEFORE trancription is even done Tail: Poly-A tail is added at the EN of transcription (after message is completed)

Question 36

Major function of PolyA tail and 5' cap

Answer 36

1) Stabilizes message/prevents being eaten by nucleases | 2) Translate; helps DNA to realize that these are processed and don't need to be destroyed

Question 37

There is ALWAYS s string of sequences at BOTH ends that are

Answer 37

NOncoding (start codon is NEVER right at the end)

Question 38

Special nucleotide sequences in a premRNA transcript signal the beginning and the end of an intron

Answer 38

pre-mRNA hasn't been fully processed There are very soncerved sequences that tell us where these sections are Start codon is NEVER at the end, always separated by UTR

Question 39

An intron in a pre-mRNA molecule forms a branched structure during RNA splicing

Answer 39

Red "A" 100% conserved base; any mutations are fatal 3' ydroxyl group attacks 5' end Lariat (bundle of introns that results from 3' hydroxyl attacking 5' end) will be degraded so you can reuse the bases

Question 40

Splicing is carried out by a collection of RNA-protein complexes called

Answer 40

snRNPs RNA portion of snRNP base-pairs with sequences that signal splicing It is the RNA that recognizes sequences in the introns Active site created by two things (U2 and U6) Excised intron in the form of a lariat Exon junction complex

Question 41

Small nuclear ribonucleic proteins:

Answer 41

RNA protein complexes

Question 42

Spliceosome

Answer 42

One of largest complexes in cell Binds at ends to bring together

Question 43

Some pre-mRNAs undergo alternative splicing to produce different mRNAs and proteins from the same

Answer 43

Gene We can alternatively splice messages (splice 2 out, get completely different protein) 90% of proteins are alternatively spliced Mix and match

Question 44

Most protein-coding human genes are broken into multiple

Answer 44

Exons and introns Prokaryotes do NOT have introns and exons Drosophila gene: 38000 different genes (record for alternative splicing)

Question 45

Eukaryotic and bacterial genes are organized

Answer 45

Differently

Question 46

A specialized set of RNA binding proteins signals that a complete mRNA is ready for export to the

Answer 46

Cytosol Ribosomes are out in the cytoplasm Will bind to proteins (proteins tell the cell message hass been processed) Transport through nuclear pore => protein exchange (switch out for translation initiation factors)

Question 47

When a message is processed, it associates with a bunch of proteins that tell the cell if the information has been processed

Answer 47

Transported through nuclear pore Protein exchange in nuclear pore