Molecular Biology - Ch 21

Front 1

RNA Polymerase

Back 1

Catalyzes the synthesis of RNA using DNA as a template

Front 2

Sigma factor

Back 2

Subunit of prokaryotic RNA polymerase that promotes binding of RNA polymerase to promoters

Front 3

RNA Synthesis - Process

Back 3

RNA Polymerase binds to a DNA promoter sequence, which triggers unwinding of the DNA double helix
Uaing one of the two strands as a template, RNA Polymerase initiates the synthesis of an RNA chain
RNA Polymerase moves along the DNA chain, elongating the RNA chain by polymerizing nucleotides
Termination signal is reached, RNA molecule is released and RNA polymerase dissociates from the DNA template

Front 4

Four Stages of RNA transcription

Back 4

Binding
Initiation
Elongation
Termination

Front 5

Promoter Site

Back 5

a specific sequence of several dozen base pairs that dtermines where RNA synthesis starts and which DNA strand is to serve as the template strand

Front 6

Concensus sequence

Back 6

the sequence that reflects the most common choice of base or amino acid at each position. Areas of particularly good agreement often represent conserved functional domains.

Front 7

mRNA

Back 7

RNA copied from gene (DNA), used to synthesize protein

Front 8

rRNA

Back 8

Ribosomal RNA - forms the core of the ribosome

Front 9

tRNA

Back 9

Transfer RNA - "translates" the coded base sequence of mRNA and brings appropriate amino acids to the ribosome

Front 10

RNA Polymerase - function

Back 10

Makes RNA from DNA template strand

Front 11

No proofreading during _______

Back 11

No proofreading during _transcription_

Front 12

Genetic Code

Back 12

Rules governing the relationship between the nucleotide base sequence of DNA molecules and the linear order of amino acids in protein molecules

Front 13

Reverse Transcriptase

Back 13

Creates DNA from RNA - found in retroviruses

Front 14

Genes - definition

Back 14

Functional units of DNA that code for the amino acid sequence of one or more polypeptide chains, or alternatively, for one of several types of RNA that perform functions other than specifying amino acid sequence of polypeptide chains

Front 15

Triplet Code

Back 15

Three base pairs in double-stranded DNA are required to specify each amino acid in a polypeptide

Front 16

Wild Type

Back 16

"Normal", i.e. not mutant

Front 17

Mutagen

Back 17

Mutation-inducing agent

Front 18

Frameshift Mutation

Back 18

insert/deletion of a base pair that throws the sequence of triplets out of phase. Can be corrected when an equal number of base pairs are deleted/inserted in close proximity to the original frameshift

Front 19

Degenerate Code

Back 19

Term used to describe the genetic code; that is, a given amino acid can be specified by more than one triplet code

Front 20

Nonoverlapping

Back 20

Describes that each nucleotide is part of one, and only one, triplet code.

Front 21

Template Strand

Back 21

Strand of DNA that serves as a template for mRNA formation during transcription

Front 22

Coding Strand

Back 22

The Strand of DNA that is unused during transcription. Identical to new mRNA strand, except that Ts are replaced with Us in mRNA

Front 23

Codon

Back 23

Nucleotide triplets in mRNA, they are the actual coding units read by the translational machinery during protein synthesis

Front 24

mRNA molecules are synthesized in the _'->_' direction and are translated starting at the _' end

Back 24

mRNA molecules are synthesized in the 5'->3' direction and are translated starting at the 5' end

Front 25

Codons are written in the _' to _' order

Back 25

Codons are written in the 5' to 3' order

Front 26

Start codon

Back 26

initiates the process of protein synthesis

Front 27

Stop codons

Back 27

Instruct the cell to terminate synthesis of the polypeptide chain

Front 28

Start Codon - sequence

Back 28

AUG

Front 29

Stop Codon - Sequences

Back 29

UAA
UAG
UGA

Front 30

Genetic Code is Unambiguous:

Back 30

Every codon has one and only one meaning

Front 31

All organisms, i.e. prokaryotes, eukaryotes & viruses all use the same _____ _____

Back 31

Genetic code (except mitochondria)

Front 32

Central Dogma

Back 32

DNA->RNA->Protein

Front 33

Transcription

Back 33

Transfer of nucleic information from DNA->RNA

Front 34

Template strand

Back 34

Strand of DNA the RNA complements

Front 35

Translation

Back 35

Protein synthesis involving a "language change" from the nucleotide sequence of RNA to the amino acid sequence of a polypeptide chain

Front 36

Upstream

Back 36

Toward the 5' end; Opposite direction of transcription

Front 37

Downstream

Back 37

Toward the 3' end; Along the direction of transcription

Front 38

Startpoint

Back 38

Point where Transcription beings. Almost always a Purine, often an adenine

Front 39

-10 & -35 Sequences

Back 39

Promoter sequences upstream from the startpoint

Front 40

During Initiation, the DNA strand qith the promoter sequence determines which way the ________ is facing

Back 40

During Initiation, the DNA strand qith the promoter sequence determines which way the _RNA Polymerase_ is facing

Front 41

During Initiation, after the first 2 NTPs become hydrogen bonded to the complementary bases on the template strand, RNA Polymerase catalyzes the formation of _________ between the ______ and the ____

Back 41

During Initiation, after the first 2 NTPs become hydrogen bonded to the complementary bases on the template strand, RNA Polymerase catalyzes the formation of a _phosphodiester bond_ between the _3' of the first NTP_ and the _5' of the second_

Front 42

During Elongation, RNA Polymerase moves along the template strand in a _' to _' direction

Back 42

During Elongation, RNA Polymerase moves along the template strand in a 3' to 5' direction

Front 43

During Elongation, RNA Polymerase unwinds DNA and synthesize RNA in a _' to _' direction

Back 43

During Elongation, RNA Polymerase unwinds DNA and synthesize RNA in a 5' to 3' direction

Front 44

At Transcription Termination, ______ releases both the ______ and _________ and rebinds _______

Back 44

At Transcription Termination, _RNA Polymerase_ releases both the _DNA_ and _new RNA_ and rebinds _sigma factor_

Front 45

Transcription in Eukaryotic cells differs from Prokaryotes . . .

Back 45

Three different (more) RNA Polymerases transcribe nuclear DNA

Binding of eukaryotic RNA Polymerases to DNA requires additional transcription factors, some of which must bind to the promoter and initiate replication

Many protein-protein interactions involved in initiation

Much processing of RNA

RNA cleavage is more important than the site where transcription is terminated

Front 46

RNA Polymerase I

Back 46

Responsible for synthesizing RNA molecules that serve as a precursor for 3 of 4 types of rRNA. Found in the nucleolus of eukaryotes

Front 47

RNA Polymerase II

Back 47

Found in the nucleoplasm. Synthesizes precursors to mRNA

Front 48

RNA polymerase III

Back 48

Nucleoplasmic enzyme that synthesizes small RNAs

Front 49

Structurally, RNA polymerases are ______

Back 49

Structurally, RNA polymerases are _similar_

Front 50

The promoter used by RNA Polymerase I has two parts:

Back 50

Core Promoter
Upstream Control Element

Front 51

Core Promoter

Back 51

Smallest set of DNA sequences able to direct the accurate initiation of transcription by RNA polymerase

Front 52

RNA Polymerase has _ types of DNA sequences in core promoter function:

Back 52

4:
- Inr; A short Initiator sequence surrounding the transcription startpoint
- TATA box, located upstream from the startpoint
-TFIIB recognition Element (BRE) located slightly upstream from the TATA box
- Downstream promoter element (DPE)

Front 53

Two general types of core promoters:

Back 53

- TATA-driven promoters (Inr & TATA & maybe BRE)
- DPE-driven promoters (Inr & DPE)

Front 54

In contrast to RNA Polymerase I & II, RNA Polymerase III uses ______ that are entirely ________ of the transcription unit's startpoint

Back 54

In contrast to RNA Polymerase I & II, RNA Polymerase III uses _promoters_ that are entirely _downstream_ of the transcription unit's startpoint

Front 55

Promoter Elements for RNA Polymerase II Include . . .

Back 55

Promoter Elements for RNA Polymerase II Include . . . the TATA Box and the Startpoint

Front 56

General Transcription Factor - Definition

Back 56

A protein that is always required for an RNA Polymerase molecule to bind to its promoter and initiate protein synthesis. They bind to promoters in a defined order. starting with TFIID

Front 57

General Transcription Factor - Function

Back 57

GTFs assemble on promoters that produce mRNA

Front 58

TFIID binds to ____, and a subunit of TFIID called ____ binds directly to DNA

Back 58

TFIID binds to _TATA Box_, and a subunit of TFIID called _TBP_ binds directly to DNA

Front 59

Pre-Initiation complex

Back 59

Group of Transcription Factors that initiate binding

Front 60

RNA Processing

Back 60

Final chemical modifications made to produce a final RNA product. This typically involves removal of portios of nucleotides, methylation and/or passage from nucleus to cytoplasm

Front 61

Primary Transcript

Back 61

RNA product *before* RNA Processing

Front 62

Hairpin Loops

Back 62

folds in secondary structure in tRNA due to base-pairing between complementary sequences located in different regions

Front 63

Cloverleaf Structure

Back 63

2-D structure of tRNA

Front 64

Processing of pre-tRNA - process

Back 64

- a short leader sequence of 16 nucleotides is removed from the 5' end
- At the 3' end, the two terminal nucleotides are removed and replaced with trinucleotide CCA, common in al all tRNA
- Nucleotides are chemically modified during tRNA processin, methylation of bases and sugars
- internal nucleotides are sometimes excised

Front 65

RNA capping

Back 65

Addition of 7-methylguanosine to the 5' end of mRNA to protect from nuclease and help position the mRNA on the ribosome

Front 66

Polyadenylation

Back 66

an enzyme cuts off the G/U rich 3' end of the mRNA downstream from a AAUAAA and adds a poly-tail. This protects the 3' end, makes it more stable, and signals it for export

Front 67

Introns

Back 67

Intervening sequences within primary transcript that do not appear in the mature, functional mRNA.

Front 68

Eukaryotic genes are interrupted by long stretches of __________ (_____) that are not represented in either the functional _____ or its ______ product

Back 68

Eukaryotic genes are interrupted by long stretches of _nucleotides_ (_introns_) that are not represented in either the functional _mRNA_ or its _protein_ product

Front 69

Exons

Back 69

Expressed sequences of DNA

Front 70

cDNA

Back 70

complementary DNA, made by transcribing a gene's mRNA with reverse transcriptase

Front 71

RNA Splicing

Back 71

The entire process of removing introns and rejoining exons

Front 72

snRNA

Back 72

small nuclear - a protein and an RNA

Front 73

snRNPs

Back 73

small nuclear RiboNucleoproteins - RNA-protein complex

Front 74

spliceosome - Function

Back 74

Catalyzes Intron removal

Front 75

Spliceosome - formation

Back 75

RNA-protein complex; a complex of snRNPs

Front 76

Intron removal by spliceosome - Process

Back 76

- snRNP U1 binds to 5' splice site of pre-mRNA (one end of the intron)
- snRNP U2 binds to a branch-point sequence (the other end of the intron)
- A group of snNRPs join in to form spliceosome
- the pre-mRNA strand is cleaved at the 5' splice site and the released end of the intron is covalently bound to the 3' branch point sequence., creating a looped structure called a lariat
- 3' splice site is cleaved, exons are joined and excised lariat is degraded

Front 77

exon shuffling

Back 77

Genetic recombination between introns of different genes that produces genes containing new combinations of exons

Front 78

Relationship between exons and domains

Back 78

exons often code for different domains of a protein