Genetics Final New Material

Central Dogma

Explained the way in which the information encoded in the DNA was expressed in the cell

Francis Crick

Who proposed the central dogma and wobble hypothesis?

codon

Sequence of three bases that specifies a single amino acid

unambiguous, redundant, specific start/stop signals, no punctuation, nearly universal

5 characteristics of the genetic code

wobble hypothesis

\-The base at the 5' end of the anticodon (complementary to the base at the 3' end of the codon, i.e. the third letter) is not as constrained as the other two

\-Therefore, certain tRNA molecules can pair with more than one codon

AUG

What is the start codon?

nonsense

What type of codons are stop codons?

missense mutations

mutations that change the amino acid coded

nonsense mutations

mutations that change sense codon to nonsense and prematurely stop translation

Transcription

The process of synthesizing an RNA copy of a section of DNA

template strand

The DNA strand that is copied by RNA polymerase

complementary

The nontemplate strand is _____ to the template strand

gene

In transcription, template and nontemplate strands are _____ specific

DNA template, Ribonucleose Triphosphates, RNA polymerase, Mg++

What does transcription require?

primer

unlike DNA replication, transcription does not require ____

5’, 3’

RNA is synthesized from __ to __

3’, 5’

RNA polymerase moves along the template from __ to __

initiation, elongation, termination

What are the 3 stages of transcription?

core enzyme

responsible for polymerization activity during initiation

holoenzyme and sigma

What is needed in addition to the core enzyme to ensure transcription begins at the correct location?

promoter

A specific regulatory nucleotide sequence in the DNA to which RNA polymerase binds in order to initiate of transcription

upstream

opposite of the transcription start site to the direction RNA polymerase moves

RNA polymerase initiates transcription randomly

what happens if sigma is absent?

\-10 region and -35 region

What are the 2 critical conserved sequences in ecoli promoter?

downstream

Base pair substitutions or deletions in critical conserved regions results in either diminished or enhanced transcription of the gene _______ from them

cis

Promoter sequences are **_____ acting** regulatory sequences

consensus sequence

\-The most prevalent sequence at a specific location

\-Identified by sequencing the same region of a large number of genes and identifying the most common nucleotide at each position

yes

Do cis-acting regulatory sequences need to be directly adjacent to the parts of the DNA that they are regulating?

holoenzyme, open promoter complex, template

In initiation…

•The _______ binds to the promoter

•The DNA double helix opens up and an **____________** is formed

•This exposes the _________

ribonucleoside triphosphate

The first _______________, complementary to the nucleotide at the transcription start site, is brought in and bound to the template

5’ to 3’ phosphodiester

what type of bonds are formed between nucleotides

8nt

Since the first few attempts at polymerization tend to be abortive, at what length is the dna/rna hybrid typically stable?

sigma

what is released from the holoenzyme once the stable 8nt length is reached?

core enzyme, 5’ to 3’, unwound

In Elongation…

•The _________ slides along the DNA and catalyzes the denaturation of the two DNA strands

•RNA polymerization takes place in the _______ direction

•A short stretch of DNA is kept ________ as transcription continues

10-12

within the unwound region, how many bp of RNA are H-bonded to the DNA in a RNA-DNA hybrid?

specific DNA sequences, stops, released, released

Termination…

•Indicated by ___________ which signal that:

•RNA synthesis ____

•RNA molecule is _________ from the DNA

•RNA pol is _________ from the DNA

rho-independent and rho-dependent

what are the 2 kinds of termination signals in prokaryotes?

rho independent terminators

* Sequence w/ two-fold symmetry followed by series of around 6 AT bp
* Causes hairpin loop ->stalls RNA pol

rho dependent terminators

* Still have 2 fold symmetry
* Lack AT string
* So RNA wont fall off after hairpin loop
* Need accessory Rho to pull RNA pol off

polycistronic RNA

RNA that consists of more than one gene, only in prokaryotes

Monocistronic RNA

RNA that consists of only one gene, all eukaryotic RNA

prokaryotic because there is no nuclear envelope

In which type of cell can transcription and translation occur at the same time, why?

chromatin remodeling, 3 different RNA polymerases, more complex regulation, RNA polymerases don’t bind to “naked” promoters

What are some differences in eukaryotic vs prokaryotic transcription?

core promoter elements, proximal promoter elements, enhancers, silencers

What are the 4 major classes of cis acting elements in eukaryotes?

core promoter elements

* \~-40 to \~+40
* Determine where RNA polymerase binds and where transcription is initiated
* Not responsible for differential gene expression
* Contain some initiator element, tata box, BRE (B recognition element)

proximal promoter elements

* Within 100 nt upstream of +1
* Effect efficiency with which RNA pol binds
* Increase basal level of transcription
* Ex: GC and CAAT boxes
* Mutations in these sequences drastically reduce transcription

enhancer and silencer elements

* Turn genes on and off when they are needed
* Responsible for tissue specific/temporal patterns of expression
* Act at a distance to modular transcription
* Can be thousands of bp up or downstream of +1

by binding to proteins

how are cis-acting elements turned on and off

by the transcription factors bound to them.

How do eukaryotic RNA polymerases recognize promoters?

general transcription factors

* Bind to core promoter elements
* Bind to all promoters recognized by rna pol II
* Must always be bound for transcription to occur

specific transcription factors

* Transcriptional activators &  repressors
* Bind to specific sequences 
* Regulate expression of specific genes and tissue specific/temporal patterns of gene regulation

transcriptional activators

•Bind to proximal promoters and/or enhancers and thereby promote RNA polymerase binding

transcriptional repressors

•Inhibits transcription by blocking the binding of activators or general transcription factors

eukaryotic

What type of RNA is processed following transcription?

5’ capping, poly A tail addition, splicing

what does the processing of mRNA include?

5’ capping

* Occurs early during rna synthesis (chain \~25 nt)
* involves addition of 7-methlyguanosine residue
* By 5’ to ‘5 triphosphate bond
* Essential for…
* Subsequent processing
* Transport to cytoplasm
* Attachment to ribosome

Protection to degradation

creates a 5’ to 5’ bond that can’t be broken

how does 5’ capping help prevent degradation?

poly A tail addition

* Genes transcribed by RNA pol II don’t have specific termination signal, most have polyadenylation signal


* Cleavage at polyadenylation site
* Addition of adenylic acid residues by poly A polymerase
* Essential for…
* Transport to cytoplasm
* Protection from degradation

exons

coding/expressed sequences

introns

•Noncoding (intervening) sequences

•Must be removed from the pre-mRNA

splicing

* Eukaryotic transcripts contain long sequences of noncoding RNA
* Removes introns and brings exons together

I and II

which groups of introns are self splicing?

no

are nuclear pre-mRNA introns self splicing?

5’ -GU, 3’ -AG, A branch

Nuclear pre-mRNA introns…

* Usually begin w/ ___ and end w/ __
* Include _______ site

Lariet

what model is used to describe nuclear pre-mRNA splicing

spliceosomes

Where does splicing occur?

alternative splicing

What is assembling exons and introns in different orginizations to generate different products called?

coding for proteins

How do genes determine phenotype?

rRNA, mRNA, tRNA

what 3 forms of RNA are required for translation?

5’ leader sequence, coding sequence, 3’ trailer sequnce

3 main parts of mRNA

5’ leader sequence

•Indicates where synthesis should begin

•Binds to ribosome

Shine Dalgarno sequence

•part of 5’ leader sequence

Upstream of start codon

•Complementary to a sequence in the 16S rRNA

closed loop

what kind of translation process do eukaryotes use?

coding sequence

•Determines the amino acid sequence of the protein

3’ trailer sequence

* None of the bases are translated into amino acids
* Messenger RNA binds to ribosomes in order to be translated

ribosome

•Composed of ribosomal proteins and three (prokaryotes) or four (eukaryotes) rRNA molecules

mRNA binding site and A, P, and E tRNA binding sites

What are the 4 ribosome binding sites?

A, A, P, E

•Appropriate amino acid-tRNA complex binds to the _____ site

•Peptide bond is formed between the amino acid in the __ site and the polypeptide attached to a tRNA in the ________ site

•The tRNA that is no longer carrying a polypeptide leaves by the ____ site

tRNA

•Carry amino acids to the ribosomes where they are matched to the transcribed message on the mRNA

cloverleaf, secondary structure

What is the shape of tRNA and what level of structure is this due to?

anticodon loop

•Sequence which recognizes the codon

•Bases are complementary to the bases of the codon for the amino acid carried by the tRNA

3’ end

•Amino acid attachment site of tRNA

•Always ends with **–CCA**

G

What does the 5’ end of tRNA always end in

**Charging** or **Aminoacylation**

•Each amino acid is attached by a high-energy bond to a tRNA molecule specific for that amino acid

•Bond is derived from ATP, the cleavage of which drives peptide bond formation

generation of an activated amino acid and generation of the charged tRNA

What are the 2 steps of charging?

when it doesn’t have an amino acid attached.

When is tRNA considered uncharged?

32, 20

•There are \~_ different tRNAs but only ___ different aminoacyl tRNA synthetases

isoaccepting tRNAs

Different tRNA molecules that carry the same amino acid

peptide bonds

Translation involves the synthesis of _______ between charged amino acids

peptidyl transferase

•Catalyzes formation of a **peptide bond** between the two amino acids attached to the two adjacent tRNAs

•The energy of the charged tRNA is converted into a peptide bond

5’ to 3’

translation occurs __ to

amino, carboxyl

Polypeptides are synthesized from _____ to ____

polyribosomes or polysomes

•Multiple ribosomes all attached to and translating the same mRNA

initiation, elongation, termination

3 stages of translation

30S, 5’

In initiation in prokaryotes, the __ sub-unit binds to the ___ end of the mRNA

translocation

During elongation, what occurs after the formation of the peptide bond?

genome, chromosome, gene

what are the 3 categories of mutation?

genome mutations

\-mutations that affect the number of chromosomes in a cell