Examen final de Genética

is a segment of DNA used to make a functional product– either an RNA or a polypeptide

is the first step in gene expression, literally means the act or processof making a copy, the term refers to copying a DNA sequence into an RNA sequence

site for RNA polymerase binding; signals the beginning of transcription.

site for binding of regulatory proteins that influence the rate of transcription. Regulatory sequences can be found in a variety of locations.

translation begins near this site in the mRNA. In eukaryotes,the ribosome scans them RNA for a start codon.

in the mRNA determines the sequence of amino acidsin a polypeptide.

which means it encodes two or more polypeptides

is the template strand

to the template strand

is the coding strand or the sense strand as well as the non-template strand

is identical to the RNA transcript except for the substitution of uracilin RNA for thymine in DNA

recognize the promoter and regulatory sequences to control transcription

occurs in three stages:Initiation Elongation Termination

The promoter functions as a recognition site for transcription factors. The transcription factor(s) enables RNA polymerase to bind to the promoter. Following binding, theDNA is denatured into a bubble known as the open complex.

RNA polymerase slides along the DNA in an opencomplex to synthesize RNA.

A terminator is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA.

which are transcribed into mRNA Final functional products are polypeptides

are not translated

DNA sequences that “promote” gene expression they direct the exact location for the initiation of transcription typically located just upstream of the site where transcription of a gene actually begins bases in a promoter sequence are numbered in relation to the transcription start site

RNA polymerase holoenzyme is composed of:Core enzyme Sigma factor These subunits play distinct functional roles

The RNA polymerase holoenzyme binds loosely tothe DNAIt then scans along the DNA, until it encounters apromoter regionWhen it does, the sigma factor recognizes boththe –35 and –10 regionsA region within the sigma factor that contains ahelix-turn-helix structure is involved in a tighterbinding to the DNA

The binding of the RNA polymerase to the promoterforms the closed complexThen, the open complex is formed when theTATAAT box in the -10 region is unwoundA short RNA strand is made within the opencomplexThe sigma factor is released at this point

The core enzyme slides down the DNA to synthesize an RNA strand The DNA strand used as a template for RNAsynthesis is termed the template or antisense strandThe opposite DNA strand is called the coding strand

Behind the open complex, the DNA rewinds back into a double helix

• TranscriptionTermination is the end of RNA synthesisTermination occurs
• when the short RNA-DNAhybrid of the open complex is forced toseparate
• releasing the newly made RNA as wellas the RNA polymerase

– rho-dependent termination• Requires a protein known as r (rho)– rho-independent termination• Does not require r (rho)

the basic features very similar to bacteria• gene transcription in eukaryotes is more complex• more complex cells (organelles)• higher cellular complexity means more genes encoding proteins are needed • Multicellularity adds another level of regulation–express genes only in the correct cells at the proper time

• RNA pol I
• RNA pol II
• RNA pol III

Transcribes all rRNA genes (except for the 5S rRNA)

Transcribes all structural genes
synthesizes all mRNAs
Transcribes some snRNA genes

Transcribes all tRNA genes and the 5S rRNA gene

Regulatory elements
TATA box
Transcriptional start siteS

consists of the “TATA box” and “transcriptional start site”• determining the start point for transcription– The core promoter by itself produces a low level of transcription or basal transcription

short DNA sequences that affect the binding of RNA polymerase to the promoter

bind to these regulatory elements and influence the rate of transcription

RNA polymerase II
Five different proteins called general transcription factors (GTFs)
A protein complex called mediator

• Pre-mRNAs are modified by cleavage near their 3’end with subsequent attachment of a string of adenines• Transcription terminates 500 to 2000 nucleotides downstream from the polyA signal

The sequence of DNA in the coding strand corresponds to the sequence of nucleotides in the mRNA• The sequence of codons in the mRNA provides the instructions for the sequence of amino acids in the polypeptide• eukaryotic structural genes reveal that they are not always colinear with their functional mRNAs

– Introns are later removed or excised– Exons are connected together or spliced

For example• Trimming of rRNA and tRNA transcripts• 5’ Capping and 3’ polyA tailing of mRNA transcripts

cleave a covalent bond between two nucleotides at one end of a strand

can cleave bonds within a strand

of the mRNA codons into amino acid sequences leads to the synthesis of proteins

are termed structural genes
These are transcribed into messenger RNA (mRNA)

First to propose (at the beginning of the 20th century) a relationship between genes and protein production
Garrod studied patients who had defects in their ability to metabolize certain compounds

He proposed that a relationship exists between the inheritance of the trait and the inheritance of a defective enzyme
He described the disease as an inborn error of metabolism

Translation relies on the genetic code
The genetic information is coded within mRNA in groups of three nucleotides known as codons

start codon

termination, or stop, codons

has a directionality that parallels the 5’ to 3’ orientation of mRNA

that may be found in polypeptides

hydrophobic

hydrophilic

Primary
Secondary
Tertiary
Quaternary

is its amino acid sequence

secondary structures

• α helix
  
• β sheet

The short regions of secondary structure in a protein fold into a three-dimensional tertiary structure
This is the final conformation of proteins that are composed of a single polypeptide
Structure determined by hydrophobic and ionic interactions as well as hydrogen bonds and Van der Waals interactions

Proteins made up of two or more polypeptides have aquaternary structure
This is formed when the various polypeptides associate with one another to make a functional protein

A category of proteins are enzymes
Accelerate chemical reactions within a cell
Can be divided into two main categories
Anabolic enzymes  Synthesize molecules and macromolecules
Catabolic enzymes  Break down large molecules into small ones
Important in generating cellular energy

tRNAs play a direct role in the recognition of codons in the mRNA
In particular, the hypothesis proposed that tRNAhas two functions
1. Recognizing a 3-base codon in mRNA
2. Carrying an amino acid that is specific for that codon

the anticodonin tRNA binds to a complementary codon in mRNA

a cloverleaf pattern
It contains
Three stem-loop structures
A few variable sites
An acceptor stem with a 3’ single strand region

aminoacyl-tRNA synthetases

Amino acid, tRNA and ATP (for energy)

“second genetic code”

the ribosome

Found in their cytoplasm

One type is found in the cytoplasm
The other is found in organelles
Mitochondria ; Chloroplasts

the large and small subunits

Peptidyl site (P site)
Aminoacyl site (A site)
Exit site (E site)

The mRNA, initiator tRNA, and ribosomal subunits associate to form an initiation complex
This process requires three Initiation Factors
The initiator tRNA recognizes the start codon in mRNA
In bacteria, this tRNA is designated tRNAfmet
It carries a methionine that has been covalently modified to N-formylmethionine
The start codon is AUG

a ribosomal-binding site or Shine-Dalgarno sequence
This is complementary to a sequence in the 16S rRNA

During this stage, amino acids are added to the polypeptide chain, one at a time

The final stage occurs when a stop codon is reached in the mRNA
In most species there are three stop or nonsense codons
UAG
UAA
UGA
These codons are not recognized by tRNAs, but by proteins called release factors
Indeed, the 3-D structure of release factors mimicsthat of tRNAs

three release factors

release factor
eRF, which recognizes all three stop codons

Bacteria lack a nucleus
Therefore, both transcription and translation occur in the cytoplasm

refers to the ability of cells to control their level of gene expression

are unregulated and have constant levels of expression

Conserves energy
proteins produced only when neededAccurate gene expression
Ensures genes expressed in appropriate cell type and at the correct stage in development

used to respond to changes in the environment

All of the organism’s cells contain the same genome but express different proteomes

Most commonly occurs at the level of transcription Or control rate mRNA translated Or regulated at protein or post-translation level

Transcriptional regulation commonRNA processingTranslationPost-translation

Involves regulatory transcription factors
Bind to DNA near a promoter and affect transcription of one or more nearby genes
Repressors inhibit transcriptionNegative control
Activators increase the rate of transcriptionPositive control

in bacteria is a cluster of genes under transcriptional control of one promoterRegulatory region called operator

In E. coli contains several genes for lactose metabolism
lacP - promoter
3 structural geneslacZ – β-galactosidase
Allolactose important in lac operon regulationlacY – lactose permeaselacA – galactosidase transacetylase

Lac repressor binds to nucleotides of lacoperator site preventing RNA polymerase from transcribing lacZ, lacY and lacARNA polymerase can not move forward

Allolactose is a small effector moleculeallolactose molecules binding to lacrepressor prevents repressor from bindingProcess called induction and lac operon is inducible

when CAP is not bound

enhances RNA polymerase binding which increases transcription

In E. coli, encodes enzymes required to make amino acid tryptophan
Regulated by a repressor protein encoded by trpR gene
Binding of repressor to trp operator site inhibits transcription

DNA methylase attaches methyl groups
Common in some eukaryotes but not all
In mammals, 5% of DNA is methylated
Usually inhibits transcription
Unmethylated areas are correlated with active genes