Bio 1A Lecture 21

Front 1

what is transcription?

Back 1

is the process in which genetic information stored in a strand of DNA is copied into a strand of RNA. The sequence of the four bases in DNA is preserved in the sequence of the four bases in RNA.

Front 2

>[molecular components of transcription] what does the messenger RNA do

Back 2

it is the carrier of information from DNA to the cell's protein-synthesizing machinery

Front 3

an enzymes called an _____ pries the two strands of DNA apart and hooks together the RNA nucleotides as they base-pair along the DNA template

Back 3

RNA polymerase

Front 4

RNA polymerase assemble a polynucleotide in its ___what direction___

Back 4

5'--->3' direction

Front 5

Can RNA polymerases able to start a chain from scratch?

Back 5

yes, unlike DNA, RNA polymerase don't need a primer

Front 6

The DNA where RNA polymerase attaches and initiates transcription is known as the _____

Back 6

promoter

Front 7

the stretch of DNA that is transcribed into an RNA molecule is called _____

Back 7

a transcription unit

Front 8

Eukaryotes have three types of RNA polymerase in thier nuclui they are

Back 8

numbered I, II, and III

Front 9

which one is used for mRNA synthesis

Back 9

RNA polymerase II

Front 10

[synthesis of an RNA transcript] there are three stages of transcription what are they

Back 10

1. initiation
2. elongation
3. termination

Front 11

[initiation] the promoter of a gene includes a ________ point. what does it do?

Back 11

transcription starting point (the nucleotides where RNA synthesis actually begins)

**the promoter determines which of the two strands of DNA helix will be used as the templates.

Front 12

In eukaryotes a collection of proteins called ______ mediate the binding of RNA polymerase and the initiation of transcription

Back 12

Transcription factors

Front 13

the completed assembly of transcription factors and RNA polymerase II bound to the promoter is called a _____

Back 13

transcription initiation complex

Front 14

waht is a crucial promoter DNA sequence called

Back 14

TATA box

Front 15

what happens in elongation?

Back 15

RNA polymerse moves along the DNA and continues to add nucleotides (to the double helix) to the 3' end of the growing RNA

Front 16

Termination of transcription: describe the process/mechanism

Back 16

the pre-mRNA is cleaved from the growing RNA chain while polymerase II continues to transcribe the DNA. The polymerase transcribes a sequuence on the DNA called polyadenylation signal (AAUAAA) in the pre-mRNA. Then from the AAUAAA signal, proteins associated with the growing RNA transcript cut it free from the polymerase, releasing the pre-mRNA.

Front 17

When is transcription is terminated

Back 17

when the polymerase eventually falls off the DNA, it (pre-mRNA) is then modified during RNA processing.

Front 18

[Eukaryotic cells modify pre-RNA after transcription: alteration of mRNA ends] Each end of a pre-mRNA is modified in a certain way. Describes how the 5' end and 3' end is transcribed (or capped off)

Back 18

the 5' end is first transcribed-- it is capped off with a modified form of guanine (G) nucleotide after transcription (first 20-40 nucleotides) forming a 5' cap

At the 3' end, an enzyme adds 50 to 250 adenine (A) nucleotides, forming a poly-A tail.

Front 19

Why is the poly A tail adrolytic ennd 5' cap important (what is its function)?

Back 19

1. facilitate the export of the mature mRNA from the nucleus
2. help protect the mRNA from degradation by hydrolytic enzymes
3. once the mRNA reaches the cytoplasm, both structures help ribosomes attach to the 5' end of the mRNA

Front 20

que suture

Back 20

sagital

Front 21

[the central Dogma of molecular biology] what is the process of DNA to protein

Back 21

DNA (templates for its own replication)----->goes through transcription using RNA polymerase makeing---> RNA----> translation (the act of synthesizing proteins from the the information of RNA----> proteins

Front 22

[prokaryotes transcription] the act of transcription produces a mRNA that encodes more than_____

Back 22

one protein (or genes)

Front 23

in RNA splicing the ____ are cut out from the molecule and the _____ joined together, forming an mRNA molecue with a _______ coding sequence

Back 23

introns; exon; continuous

Front 24

how is pre-mRNA carried out?

Back 24

particles called small nuclear ribonucleoproteins (snRNPs-- located in the nucleus) contains a small nuclear RNA (snRNA) where they join with additional proteins to form splicesome. the spliceosome interacts w/ certain sites along an intron, releasing the intron and joining together the exons.

Front 25

what is ribozymion?

Back 25

ribozymes is an RNA molecules that function as enzymes

**the introns RNA functions as a ribozyme and catalyzes its own excision.

Front 26

[the funtional and evolutionary importance of introns] introns play a ____ roles in the cell

Back 26

regulatory

**contains sequence that control gene activity in some way

Front 27

the present of introns in a gene may facilitate____? how does it facilitate evolution

Back 27

the evolution of new and potentially useful proteins--- known as exon shffling.
**introns increase the probability of potentially beneficial crossing over b/w the exons of alleles.

Front 28

in prokaryotes an mRNA will usually go through how many open reading frame (OPF1)?

Back 28

usaully wil go through 1 OPF and up to 10 reading frame

**OPF are genes

Front 29

In ecoli the averge mRNA includes how many ORF?

Back 29

2

Front 30

Transcription always starts at a ____ and proceeds through the gene making RNA. Transcription procees in the same chemical direction as ____ and ends at the _____ sequence where it stos mRNA polymerase.

Back 30

promoter
DNA 5'-->3'
Terminator sequence

Front 31

[prokaryotes] ther are two parts to the promoter what are they?

Back 31

-35 and -10 sequence

Front 32

what does -35 and -10 refers to?

Back 32

it refers to the distance in base pair **from the first base of DNA that is copy to RNA

** -10 = 10 Bases pair upstream

Front 33

what is upstream and downstream

Back 33

downstream is the region toward the 3' end of the strand and upstream is the regions toward the 5' end

Front 34

transcription and translation of mRNA move in what directions? what about the copied template strand?

Back 34

**transcription/translation moves downstream 5'--->3' and the template copies move in upstream 3'--->5'

Front 35

-35 is recognized by a protien called ______. and what is its purpose

Back 35

sigma factor--- which are regulatory proteins ---> which helps RNA polymerease to identified which genes to transcribe and at what time

Front 36

Baterial RNA polymerase--- is discovered by Mike Chamberlin. It is made up of 4 diff. subunits what are they?

Back 36

**2 big subunits called the alpha
**and one copy of each of the Beta (B and B')

*alpha is the largest size and B is smaller

Front 37

these four polypeptide made up of the ____

Back 37

core enzyme

Front 38

sigma factore is a _____ subnit and it has many varieties

Back 38

regulatory

ex:
**sigma 70 transcribe most genes
**sigma (heat shock)-- a stress that bacterial exhibit. In order to deal with this stress they have to turn on a bunch of diff. genes
**sigma sporulation

Front 39

Key factors of sigma factors is that they provide ___

Back 39

specifity to particular promoter by recognizing variant -35

Front 40

RNA polymerase recognize ____

Back 40

-10

Front 41

What makes RNA special? name 4 things

Back 41

1. a 2' hydroxyl on the sugar ribose
***the 2'OH is what makes RNA unstable

2. use uracil instead of thymine

3. does not require primer for transcription

4. synthesis in 5'-->3' direction same as DNA

Front 42

there are three steps to transcription: describe elongation

Back 42

RNA recognize the -10 bp and binds forming a Close Promoter Complex

**close means DNA double helix is still base pair to itself

Front 43

elongation

Back 43

formation of open promoter comlex---> the melting of the promoters

**melts a region that is over 17 bp

Front 44

what does it means to be 17 bp

Back 44

10 bp/term
so almost two terms of a helix
**RNA polymerase starts to synthesize RNA

Front 45

[how do you figure out where a protein binds DNA?] proteins that interact w/ DNA can interact at____.

Back 45

specific or non specific sites

Front 46

what is one method to find exactly to where the DNA binds.

Back 46

DNA fingerprinting

Front 47

[continue on elongate transcription]

Unlike DNA, transcription hapens how fast? RNA polymerase?

Back 47

**transcription---> 60 nucleotide/second

**RNA polymerase--> 1000 nucleotides/second

Front 48

why is RNA polymerase slower than DNA polymerase?

Back 48

there is a helixcase in DNA-- an enzyme infornt of DNA polymorase that is burning ATP to unwind the strand. Whereas RNA polymerase have no helixcase to help it unwind and in addition is melting DNA, also b/c it's mking a RNA Longer and longer (adding extra bagage)

Front 49

[Termination] what happen

Back 49

transcription goes past the termination sequence. Then a terminator is made in the RNA and is the interaction with the RNA in the terminator protein that cuase RNA polymerase to stop

Front 50

what is rho protein

Back 50

a protein that recognizes terminator and causes RNA polymerase to stop

Front 51

how are prokaryotes and eukaryotes differ and similar in transcription?

Back 51

**initiation and elongation are similar to eukaryotes and pro. but termination is differ.

**in prokaryotes the RNA transcript is immediately usable as mRNA, whereas in eukaryote, it must first undergo processing to become mRNA

Front 52

Eukaryotes have 3 diff RNA polymerase what r they

Back 52

RNA polymerase 1,2,3

Front 53

in Eukaryotes all messenger RNA is made by what? rRNA? and tRNA

Back 53

mRNA--> RNA plymerase 1
rRNA---> 2
tRNA---->3

Front 54

[more new collection of noncoding RNA] What are they?

Back 54

micro RNA (mRNA)---> made by RNA poly. 2

small nuclear RNA (snRNA)--> RNA poly. 2 and 3

small interfering RNA (siRNA)

Front 55

eukaryotic RNA are large enzymes made of ____ subunits and interact with hundreds of proteins at the promoter sites

Back 55

12-13 subunits

**some RNA shared subunits w/ each other
**some are specific RNA polymerase

Front 56

[making ribosomal RNA (rRNA)] why do we have many rRNA copies ( >100)

Back 56

**you need a lot of ribosome and each of the ribosome have to have its own complement RNA

Front 57

gene is trascribed together in a transcript about ____ kb long. we need to make three diff. RNAs for ribosome what are they

Back 57

5.8s, 18s, and 28s --->mature structural RNAs of ribosome

Front 58

[making Eukaryotic mRNAs]
The primary transcript is changed in two ways what are they? (5'cap and 3' poly A describes them)

Back 58

5' cap--- is the 3'5' phophosdiester addition of rGTP to 5' base of mRNA

**it is there to stabilize the message against ribonucleous

**3' end of gene---> 3' AAAA (poly A)
--poly A is added by an enzyme called poly A polymerase (which is nontemplated extension of 3' end)
**contributes to the stability of message

Front 59

[RNA splicing: comes in two forms]
(1) RNA of the ribosome is an enzyme that...

Back 59

catalyst itself and process out the intron and stich the primary transcript back togehter again

Front 60

the intron is looped out known as the

Back 60

"lariat" excised intron w/ expose 3'OH

Front 61

[RNA splicing form 2] the non-splicing is more common: most genes have there introns remove by ____, which use ____ and ____ to recognize the junctions of exon and introns.

Back 61

splicing factors
proteins and RNA

Front 62

these RNA splicing factors assemble into ____ that process the intron out

Back 62

splicesosome

Front 63

There is an alternative splicing. what is that?

Back 63

in which you splice the 1st exon to the 3rd exon skipping a few exons and introns or splices the 1st to the 4th