Bio II exam 4

Gene Expression

The process by which DNA directs protein synthesis, includes two stages

Transcription and translation

The two stages of gene expression

How does the DNA inherited by an organism lead to specific traits?

Dictating the synthesis of proteins and of RNA molecules involved in protein synthesis

Proteins

The link between genotype and phenotype

Genes

Receptor proteins are encoded by ______

Humans have

>400 olfactory receptor genes, but 3-7 million olfactory nerves

Olfactory nerve

Sensory nerve responsible for your sense of smell

Each olfactory neuron expresses

One olfactory receptor gene

Olfactory nerves must choose

One gene to express and to silence the rest

Each receptor has a specific

shape

Odorants must have a matching shape to be able to

bind

When matching molecules bind

the neuron fires a signal to the brain

Each neuron expresses one receptor type, so

It only responds to specific odorants

julia is poopy

yes

One gene-one enzyme hypothesis

each gene encodes a specific enzyme that controls a single, specific chemical reaction within an organism

One gene-one protein hypothesis

Each gene is responsible for the production of a specific enzyme that controls a particular metabolic step

Many proteins are composed of several

Polypeptides

Each polypeptide has its own

Gene

Sometimes RNA is the

end-product

A DNA sequence that is expressed to form a functional product

Either RNA or polypeptide

The central dogma of molecular biology

DNA → RNA → Protein

Expresssion

Transcription and translation of a gene

Transcription

Copying a gene encoded in DNA into an mRNa version

Translation

Building a protein from the instructions encoded on mRNA

Crick and Brenner experiments

Took synthetic RNA or mRNA and deleted one base to see what would happen, repeated the experiment but deleted three bases

Codon

The set of 3 nucleotides that specifies a particular amino acid

Reading frame

The series of nucleotides read in sets of 3 (codon)

Only one reading frame is correct for

Encoding the correct sequence of amino acids

Transcription proceeds through

Initiation, elongation, and termination

Initiation

RNA polymerase identifies where to begin transcription

Elongation

RNA nucleotides are added to the 3’ end of the new RNA

Termination

RNA polymerase stops transcription when it encounters terminators in the DNA sequence

A double helix has

Two antiparallel strands

The template strand is determined by

The promoter (not by which strand is on top)

Promoter

a specific region of DNA located upstream of a gene that acts as the binding site for RNA polymerase and transcription factors to initiate transcription

Different genes on the same chromosome can

Use different strands as a template

The mRNA mirrors the

Non-template strand (T→U)

The transcription bubble

a molecular structure formed during DNA transcription when a small portion of the DNA double helix is unwound by RNA polymerase

Speed of transcription

~40-50 nucleotides/second

Multiple RNAP’s can transcribe

the same gene simultaneously

The growing RNA trans peels way as

RNAP moves forward

The growing RNA does not stay paired to

the DNA template

Three strands, one rule:

mRNA sequence = coding strand (T→ U)

RNA polymerase pries the ____ strands apart and joins together the complementary _____ nucleotides only in the ____ direction

DNA, RNA, 5’ to 3’

RNA polymerase assemble _____ only in the _____ direction

polynucleotides, 5’ to 3’

Transcription starts at the

Promoter

The promoter is located

Upstream of the transcription start site

Transcription factors bind ____ and mediate the binding of _____

First, RNA polymerase

Transcription initiation complex

The complemented assembly of transcription factors and RNA polymerase II bound to a promoter

RNA polymerase I

Pol I resides in the nucleolus, transcribing ribosomal

RNA Polymerase II

Pol II functions in the nucleoplasm to transcribe messenger RNA (mRNA) and most small nuclear RNAs

Pribnow box

(5’-TATAAT-3’) Conserved DNA sequence found in prokaryotic promoters

Pribnow box location

10 base pairs upstream from transcription start

Both the prokaryotes (TATAAT) and eukaryotes (TATA) have

High AT content (easier to separate strands)

AT content

the percentage of adenine (A) and thymine (T) bases in a DNA molecule

As RNA polymerase moves along the DNA it

untwists the double helix, 10 to 20 bases at a time (txn bubble)

Multiple RNA polymerases may be transcribing

A gene at a given time

Transcription termination mechanisms differ in

Bacteria and eukaryotes

Bacteria transcription termination

RNAP stops at the end of the terminator and the mRNA can be translated without further modification

Eukaryote transcription termination

RNAP transcribes a polyadenylation signal sequence; the RNA transcript is released 10-35 nucleotides past this polyadenylation sequence

Prokaryotic transcription

Transcription and translation are often coupled, occurring at the same time

In bacteria, transcription and translation can take place

simultaneously

In eukaryotes, the nuclear envelope separates

Transcription and translation

TXN and TLN take place in

different parts of the cell

mRNA must be processes before being

Translated

RNA slicing

Large portions of the RNA molecule are removed and the remaining portions reconnected

Noncoding regions (intervening sequences)

Introns

Exons are usually translated into

Amino acid sequences

The process of splicing

The introns are cut out from the molecule and the exons are joined together

Exon

a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence

Alternative RNA splicing

Same primary transcript → different mRNA

Alternative RNA splicing depends on

Which segments are treated as exons and which as introns

Spliceosomes

a large, dynamic ribonucleoprotein complex in the eukaryotic nucleus that removes non-coding introns from pre-mRNA and joins exons to create mature mRNA

Spliceosomes consist of

Proteins and small RNA’s

Not all enzymes are

proteins

Ribozymes

RNA molecules that function as enzymes

Types of ribozymes

Spliceosomes and ribosomes

In some organisms, RNA is

Self-splicing

The introns can catalyze their own

Splicing

Eukaryotic cells modify RNA after

transcription

Pre-mRNA is modified

5’ cap, 3’ end gets a poly-A tail

The pre-mRNA modifications share several functions

They seem to facilitate the export of mRNA, they protect mRNA from hydrolytic enzymes, they help ribosomes attach to the 5’ end

RNAP does not stop after the chosen OR, it keeps transcribing into ________

Downstream genes

Downstream transcripts lack a

5’ cap

Downstream transcripts cannot leave the

nucleus (so not protein is made from them)

Mechanism 2

The same promoter fires in both directions, the sense transcript becomes the chosen OR’s mRNA, the antisense transcript suppresses the upstream OR - preventing it from being expressed

Antisense transcript

a long non-coding RNA

Result of mechanism 2

One receptor, one neuron, one clear signal

Translation proceeds through

Initiation, elongation, termination

Initiation

mRNA, tRAN and ribosome come together

Elongation

trRAN’s bring amino acids to the ribosome for incorporation into the polypeptide

Termination

Ribosome encounters a stop codon and releases polypeptide