exam 4 genetics review

Transcription

The process of making mRNA from DNA

Translation

Process of making protein from mRNA

Template strand

RNA is transcribed from one DNA strand

Nontemplate strand

Strand usually not transcribed

Ribosomal RNA

Cell type: prokaryotic and eukaryotic

Location of function in eukaryotic cells: Cytoplasm

Function: structural and functional components of the ribosome

Messenger RNA (mRNA)

Cell type: prokaryotic and eukaryotic

Location of function in eukaryotic cells: nucleus and cytoplasm

Function: carries genetic code for proteins

Transfer RNA (tRNA)

Cell type: prokaryotic and eukaryotic

Location of function in eukaryotic cells: Cytoplasm

Function: helps incorporate amino acids into polypeptide chain

The transcription unit

A promoter

RNA-coding sequence

Terminator

3 stages of transcription

Initiation, elongation, termination

Initiation

In which the transcription apparatus assembles

Elongation

In which DNA is threaded through RNA polymerase

Termination

The recognition of the end of the transcription unit

Promoter

Sequences that determine the location of the gene of where to start the process, does not transcribe RNA but has info of where to start polymerzation

Active transcription

Christmas tree like structure

Multiple RNA polymerases

transcribe the same gene simultaneously

Bacterial RNA polymerase

Five subunits made up of the core enzyme:

Two copies of α

Single copy of β

Single copy of β’

Stabilizing enzyme: ω

The sigma factor

Binding to the promoter when transcription starts

Bacterial promoters

Consensus sequences (an example)

Consensus sequences

Sequences that possess considerable similarity

-10 consensus: 10 by upstream of the start site

Pribnow box

5’ TATAAT 3’

3’ ATATTA 5’

-35 consensus sequence: TTGACA

What step of transcription does this represent?

Elongation

Rho-dependent termination

Uses rho factor

Does not require primer

Rho-independent termination

Hairpin structure formed by inverted repeats, followed by a string of uracil’s

Does not need helicase

Promoters of eukaryotic transcription

Basal transcription apparatus

Transcriptional activator proteins

RNA polymerase II

Consensus sequences of RNA splicing

5’ : GU A/G AGU: 5’ splice site

3’ : CAGG

Spliceosome

Five RNA molecules + 300 proteins

Determines where the 5’ and 3’ consensus sequences are and splice them

(Eukaryotic) transcription by RNA polymerase II

Terminated when an exonuclease enzyme

• attaches to the cleaved 5’ end of the RNA

• Moves down the RNA

• Reaches the polymerase enzyme

3 primary regions of mature mRNA

5’ untranslated→ the protein-coding region→ the 3’ translated region

Proteins

Nothing more than chain of amino acids just as DNA is a chain of nucleic acids

Triplets of codons

Sets of three DNA bases

(Why there are silent mutations)

All protein starts with the amino acid…

Methionine (AUG start codon)

Translational termination

Translation is ended once we come upon a stop codon

Translation

We land on the 5’ end of mRNA, scan for the first AUG start building a chain of amino acids until we reach a stop codon

Ribosome

The site of translation and allows information contained within mRNA to be used to make of amino acids

• lands on the 5’ end of the mRNA and scans until it finds the first AUG

Each nucleotide have three things in common

A phosphate group, five carbon sugar (called ribose), a base

Phosphodiester bond

The bond holding nucleotide together

Protein synthesis

Requires the ribosome

• mRNA are scanned for the first AUG; this lines up the ribosome

• Then a tRNA recognizes the codon on one end and results an amino acid with the other

Structural genes

Proteins used in metabolism, biosynthesis, play a structural role

Regulatory genes

That regulatory protein (or RNA molecule) that somehow interact with DNA to alter the expression of other genes

Regulatory protein often directly bind to DNA to promote of inhibit gene expression

Constitutive genes

Genes that don’t need regulation and are always on

(DNA binding proteins) Domains

~ 60-90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA

(DNA binding proteins) motif

within the binding domain, a simple structure that fits into the major groove of the DNA

Helix-turn-helix

Location: bacterial regulatory proteins; related motifs in eukaryotic proteins

Characteristics: two alpha helices

Binding site: major groove

Helix-loop-helix

Location: eukaryotic proteins

Characteristics: two alpha helices separated by a loop of amino acids

Binding site: major groove

Zinc finger

Location: eukaryotic regulatory and other proteins

Characteristics: loop of amino acids with zinc at base

Binding site: major groove

A lot of un-transcribed genomic DNA

Made up of regulatory elements

Positive regulation

Naturally gene is off- something must be done to turn it on (activation)

Negative control

Naturally gene is on- something must be done to turn it off (repression)

Operon

Cluster genes of similar function together

Lac operon

Three clustered genes clustered together under control of one promoter

Regulator gene

DNA sequence encoding products that affect the operon function but are not part of the operon (able to bind to DNA & make protein)

Inducible operon

Kept off and must be altered to express

repressible operon

kept on and must be turned off

negative inducible operon

the gene’s natural, unregulated state is on

the regulator is usually made however, so the gene is continually kept off

when signal is received the gene is needed, the repressor is not made or in-activated allowing the gene to expressed

negative repressible operon

also a repressor, natural unregulated state is on

usually not made, so the gene is continuously expressed

when signal is not received the gene is not needed, the repressor is made or activated allowing the gene to repress

positive inducible

natural condition: off

an activator

not usually made so the gene is continually off

when signal is received, the gene is needed, the activator is made or activated allowing the gene to be expressed

positive repressible operon

an activator

naturally off

usually made so the gene in continually expressed

when signal is received the gene is not needed, the activator is no longer made or in-activated allowing the gene to be turned off

all living cells need carbon building block and energy

glucose is the easiest and energetically cheapest sugar to digest

if you offer bacteria glucose and lactose

it will choose glucose (ATP)

If there is no glucose for bacteria to choose

it will choose lactose instead (if offered)

how bacteria make the choice at the molecular level if lactose and glucose are around, keep lac operon off (don’t express)

• a negative inducible operon

• lactose metabolism

• structural genes:

  • lac Z

  • lac Y

  • lac A

regulation of the lac operon

inducer: allolactose

• lac I

• lac P

• lac O

Lac Z

encodes B-galactosidases (breaks down into monomers)

lac Y

encoding permease (transports lactose to enter)

lac A

encoding transacetylase

lac I

repressor encoding gene

lac P

operon promoter

lac O

operon operator

allolactose

breaks down galactose→ glucose & lactose

when there is no lactose around

Lac I is sitting on the operator of the lac operon, blocking the RNA polymerase enzyme from transcribing these genes

the operon is repressed, but wants to be on

steps when lactose enters the environment

• little bit of the permase is expressed

• allows some to enter the cell

• the little bit of B-galactosidase converts some of the lactose to allolactose

• allolactose binds to lac I, forcing it to change shape

• since shape = function, Lac I can not bind to DNA anymore

triptofan (Trp)

amino acid, keeps gene off when it’s there

makes singular mRNA

Trp characteristics

a negative repressible operon

five structural genes (trp E, D, C, B, A)

Trp E, D, C, B, A

five enzymes together convert chorismate to tryptophan

the trp operon is regulated by

transcription attenuation

the attenuator sequence

in the 5’— region of the leader sequence and can make the ribosome stall

the attenuator, which is part of the leader determines

if transcription will be attenuated at the end of the leader or, if transcription will continue into the genes for Trp synthesis

the leader (after operator)

is 162 nucleotides long includes 1-4 segments

if segments 3 and 4 base pair (transcriptional attenuation)

they form a hairpin structure that is the attenuation signal

if segments 2 and 3 base-pair (transcriptional attenuation)

transcription proceeds and the trp synthetic enzymes are made

somatic mutations

mutations in the DNA of any of your cells except your gametes (random not heritable)

germ line mutation

mutation in the DNA of the gametes

transition (base substitutions)

purine (A or G) changes to other purine (double ring

or pyrimidine (C or T) becomes the other pyrimidine (single ring)

transversion (base substitution)

when purines become pyrimidines or vis versa

expanding nucleotides repeats

the number of copies of a set of nucleotide repeats increases, creating repeating sequence

insertion

addition of one or more nucleotides

deletion

deletion of one or more nucleotides