EXAM 4 - Chapter 12, Gene Expression at Molecular Level Flashcards
In the early 1900’s…
Gregor Mendel’s work published in 1865 on genetics was rediscovered and finally understood
A British Physician in 1908 by the name of….was..
Archibald Garrod, who was studying the inheritance of disease Alkaptonuria
Garrod proposed…
a link between genes and the production of enzymes
By 1908 biochemists understood…
that metabolic pathways consisted of a series of enzymes, each one converting one chemical into another
they were linked series of reaction in which enzymes were involved
Garrod…
applied Mendel’s theory on genes to the pathway for the breakdown of Phenylalanine and the disease to Alkaptonuria
He made the connection that…
if the gene is broken/affected, enzyme cannot respond
Garrod knew that Alkaptonuria…
was inherited and proposed the disease was caused when an individual inherited recessive, defective genes from both parents
Garrod was the FIRST to…
link genes with enzyme production
Garrod termed the defective genes…and…
inborn errors of metabolism and began field of Human or Medical Genetics
He is considered the father of…
human or medical genetics
_________ saw Garrods work while….
Beadle and Tatum saw his work while wokring on the nutritional needs of a mold Neurospora
Beadle and Tatum exposed mold to…
x rays to produce mutations
After exposing molds to xrays they…
isolated a number of mutant strains which could not produce certain nutrients
They were working on…
inheritance or genetics of these mutant strains, in other words, could mutant pass mutant strains to next generation
they were intentionally trying to break parts in pathways
The metabolic pathway for ______ production was known to…
Arginine, be controlled by three enzymes
They had several strains of Neurospora which…
could not produce Arginine
Is starts with the precurser molecule then…
enzyme 1 produces OMITHINE -> enzyme 2 produces CITRULLIN -> enzyme 3 produces ARGININE
By seeing the products they could…
isolate which enzyme is blocked and broken and therefore which gene was mutated
They found that….
different strains had different mutations (in genes) which all prevented arginine synthesis, but at DIFFERENT STEPS in pathways
They (Beadle and Tatum) first proposed that…. which become known as…
each gene controlled a separate enzyme, “ONE GENE ONE ENZYME” theory
The one gene one enzyme theory…
has been modified over time because of a few exceptions that were found
Exception #1
Genes do control the production of enzymes, but not all genes code for enzymes
Exception #2
Not all enzymes consist of a single polypeptide
Some multimeric enzymes are formed by the product of multiple genes, each producing a separate polypeptide which combine to form mature/complete enzyme
One Gene - One Polypeptide
Exception #3
Some genes are alternatively spliced to produce multiple proteins, or versions of a proteins
so some genes produce multiple proteins
This is why 20,000 genes code for about 2 million proteins, because they can be spliced
The Central Dogma of biology:
traces the path of information flow within cells
Cycle is…
DNA (transcription) -> mRNA (translation) -> polypeptide (protein)
______ comes first, before _____
transcription, before translation
In transcription only..
one half will be copied
It goes from double helix to..
single mRNA
Transcription is also called
DNA-Directed RNA Synthesis
The one molecule/enzyme concerned with Transcription is
RNA Polymerase
The promoter is…
The region of gene where RNA Polymerase attached to transcribe the gene
Gene is the…
region of DNA linked to production of polypeptides
Transcription occurs on…
the template strand only
Transcription occurs on..
one gene only (one at a time)
First RNA Polymerase…
attached to DNA at promoter and denatures (unwinds) DNA
In Eukaryotes…
a variety of proteins are involved in the attachment process
These variety of proteins are called…
Initiation and Transcription factors
RNA Polymerase…
unwinds then winds it back
The second step is _____ ….then the enzyme _______…
Ribonucleoside Triphosphates (ribose sugar and 3 phosphates) line up opposite DNA template strand and then RNA polymerase connects them together in the 5 to 3 direction
Template strand is running….so…
3 to 5, so built in 5 to 3, adding new nucleotides at the 3 end
Ribonucleoside triphosphates are…
precursors for transcription
What happens to ribonucleoside triphosphate is…
removal of pyrophosphate (2 phosphates) and polymerization of nucleotide to 3 end of the growing RNA chain
Three types of RNA are
mRNA, rRNA, tRNA
mRNA…
carries info (message) from DNA to ribosome
rRNA…
they are a component of ribosomes
tRNA…
“escorts” (i.e. transfers) amino acids to the ribosomes
All three of these…*
are all TRANSCRIBED in the same way
_______ occurs in a variety of different ways in RNAs
termination
The final product…..is not…
Primary Transcript (Pre-RNA) is NOT the final product
So the main three steps of Transcription are…
- INITIATION - (RNA Polymerase binds to promoter and starts to unwind DNA strands
- ELONGATION - Ribonucleoside Triphosphates line up opposite DNA template strand and RNA Polymerase connects them together in 5 to 3
- TERMINATION - final product (Primary Transcript/pre-RNA) is not final product
Within a single chromosome..
different strands of the double stranded DNA form the template strand
(Can be bottom or top strand)
RNAs are all…
post-transcriptionally modified in a variety of ways
There are ____ types of modification
8 TYPES
The 8 types are…
1.) Addition of 5’ 7-methyl Guanosine Cap
2.) Addition of a Poly-A Tail
3.) Splicing
4.) Pre-RNA may be cut into more than 1 RNA
5.) Removal of nucleotides from 5/3 end
6.) Addition of CCA to 3’ end
7.) Chemical modification of bases
8.) RNA Editing
1.) Addition of 5’ 7-methyl Guanosine Cap occurs in…and its function is…
mRNA ONLY
Allows mRNA to exit nucleus and bind to ribosome
2.) Addition of Poly-A tail occurs in…function..
mRNA ONLY
Allow mRNA to be exported from nucleus and persist in cytosol
3.) There are…
two types of splicing
3.) Splicing A is
removal of introns (intervening regions) can occur to ANY TYPE OF RNA by action of SPLYCEOSOMES which is a complex of RNA and proteins
The exon…
is expressive, this is the part than turns into a protein
The intron..
is intervening, non-exon region
3.) Result of Splicing A is…
removal of introns results in RNA Transcript much shorter than corresponding gene (DNA)
3.) Spicing B is…
Since not all exons always included in final mRNA
If different combinations of exons are used to produce different RNAs, different proteins are produced in different cells or tissues FROM THE SAME GENE
so some exons spliced out, different number of exons = different everything
3.) ______always comes before _____
intron splicing…alternative splicing
4.) The Pre-RNA may be cut into more than one RNA occurs in…its function…
ALL RNAs, but ALWAYS occurs in rRNA
After introns cut out, can be left with separate pieces, that why it can be so diverse
5.) Removal of nucleotides from 5 and/or 3 end occurs in….and…
ALL RNAs
just simply removing nucleotides
6.) The addition of CCA to 3 end occurs in…and..
ONLY tRNA
if it doesnt already have a cap it adds, the CCA is an amino acid attachment site
7.) Chemical modification of bases occurs in…and…
tRNA ONLY
Reactions happening on pre-RNA to change bases, change into weird bases that can affect other things, shown as weird shapes or different letters other than the normal A,C,G,T,U
8.) RNA Editing is…
process by which one or more nucleotides in an RNA can be changed, added, or removed
8.) Two kinds of editing are
Substitution Editing, Insertion/Deletion Editing
8.) In substitution editing…
one nucleotide is substituted for another
enzymes modify or change one base into another
Cytidine deaminase converts C in RNA to U
Adenosine deaminase converts A to I, which ribosomes translates as a G
8.) In insertion/deletion editing…
uses guide RNAs produced by separate genes to bind and indentify the RNA molecles where a nucleotide will be added or removed
8.) RNA editing…(2)
has been found in all three major types of RNA
Error in RNA editing can cause mental disorders such as schozophrenia
MEMORIZE ONLINE TABLE
MEMORIZE ONLINE TABLE
Translation is…
the second step, comes after transcription
The 3 letters codes made after transcription called…
codons
The bottom amino acids made after translation have…
anticodons on tail that match with the codon
_________ are used for translation..
all three RNAs (mRNA, rRNA, tRNA)
mRNA in translation…
carries the information
tRNA in translation…
brings the amino acids (transfers from cytoplasm to ribosome)
rRNA in translation…
is a component of ribosomes
other enzymes used during translation are ________ and the purpose of them is…
Aminoacyl-tRNA Synthetase….are also used to “load” amino acids onto corresponding tRNA molecules
Makes sure the right amino acids get on/become the right RNA
Triplet Code:
3 bases make up a codon
A codon is…
a sequence of 3 bases in mRNA which code for an amino acid
Transfer RNA (tRNA)…
speak both nucleotide and amino acid language
The start codon is…and…
AUG, it is initiation/start codon, it marks the point where translation begins
The codons that stop translation…
are called the terminators, which stop translation rather than insert an amino acid
They are UAA, UAG, UGA
The genetic code is…since…
degenerate (redundant) since most amino acids are represented by more than one codon
2D shape of tRNA is…
3 leaf clover
The stem of 2D shape is…
the acceptor stem - amino acid is attached to the 3’ end of tRNA
connected with H bonds
3D shape of tRNA is
L-shaped, anticodon on one end and then the 3’ single stranded region on the other end (acceptor stem)
The ______ is across from the acceptor stem on tRNA and it…
anticodon loop, pairs with the codon on mRNA
Aminoacyl-tRNA Synthetases….
loads proper amino acid onto tRNA using energy from ATP
First, Aminoacyl-tRNA Synthetases…
binds ATP and the specific amino acid recognized by that activating enzyme
the energy from ATP is transferred to amino acid as AMP (breaks off pyrophosphate to make AMP, and AMP holds onto amino acid)
Then….
the specific tRNA recognized by the synthetase is bound and the amino acid is transferred from the AMP to the tRNA
AMP is there to give energy and help hold things, once transferred, AMP is released
Finally…
the tRNA, charged with the appropriate amino acid is released, as is the enzyme (in an unaltered state) and the AMP
enzymes are not changed during course of reactions
This whole process above is how…
join together the correct amino acid with tRNA with the correct codon
This whole process happens in…
cytoplasm, or rough ER, wherever there are ribosomes
Structure of ribosomes
large and small subunits each constrcuted of one or more rRNA and 20-50 proteins
Sedimentation rates…
based on mass, density, and shape, CANT BE ADDED SIMPLY
The ribosome subunits…
can be apart, but during translation they come together during process
Eukaryotic ribosomes are…
larger
Self assembly in ribosomes mean…
the rRNAs and proteins come together naturally, enzymes and charges involved in building small and large subunits
The parts of the ribosome…
3 positions to hold tRNAs:
- A site - holds new RNA **(EXCEPT FOR FIRST, THE FIRST GOES INTO THE SECOND P SITE)
- P site - hold tRNA with polypeptide chain
- E site - holds empty tRNA to exit the ribosome
large subunit on top, small on bottom
A site, anticodon matches with codon right at that moment
P site, holds what has been built so far
RIGHT TO LEFT, A-P-E
RNA Directed Polypeptide synthesis (Translation) step #1:
Small ribosomal subunit attaches to 5’ end of mRNA (not yet connected to large subunit)
ribosomal binding sequence matches with 3 codons on the ribosome, this is so they can bind
RNA Directed Polypeptide synthesis (Translation) step #2:
First tRNA attaches to small subunit P site
RNA Directed Polypeptide synthesis (Translation) step #3:
Large ribosomal subunit attaches to form the complete ribosome
RNA Directed Polypeptide synthesis (Translation) step #4:
One first aminoacyl-tRNA has attached to P-site, second aminoacyl-tRNA attaches at A-site of ribosome, matching the 2nd codon on the mRNA
matches codon of mRNA to anticodon on tRNA
the mRNA-ribosome-tRNA complex positions the amino acids so they are adjacent to one another
RNA Directed Polypeptide synthesis (Translation) step #5:
Peptidyl Transferase catalyzes a peptide bond between first two amino acids by transferring (backwards) the 1st amino acid from the 1st tRNA to the 2ns amino acid on the 2ns tRNA
RNA Directed Polypeptide synthesis (Translation) step #6:
Translocation moves the ribosome toward the 3’ end, to the right, to the next codon with the release of the 1st tRNA from the exit (E) site
first amino acid is alreayd attached to the 2nd, both are attached to the second tRNA (in the P site)
mRNA is relatively stable, but ribosome moves (5 to 3)
when ribosome moves to the right, tRNA is moved down from A to P to E
RNA Directed Polypeptide synthesis (Translation) step #7:
The 3rd aminoacyl-tRNA anitocodn attaches to the A-site of the ribosome accoding to the 3rd mRNA codon
RNA Directed Polypeptide synthesis (Translation) step #8:
Peptidyl transferase catalyzes the next peptide bond, ribosome translocates in the 3’ direction once more
tRNA in P site passes all amino aids to the tRNA in A site, then moves out and another one can come in
RNA Directed Polypeptide synthesis (Translation) step #9:
Repeat steps 6-8
anticodon is on…codon is on..
ANTICODON on tRNA
CODON on mRNA
RNA Directed Polypeptide synthesis (Translation) step #10:
Upon reaching a termination (stop) codon, a releasing protein attaches to the A-site instead of an aminoacyl tRNA
releasing facotr binds to A-site and causes release of last tRNA and polypeptide
Two ribosomal subunits are released from the mRNA and are recycled to same the same or another mRNA to translate
mRNA is translated my…
numerous ribosomes AT THE SAME TIME, once first ribosome clears the 5’ end, the next attaches
all translating different parts at same time
A Polysome is…
one mRNA and all the multiple ribosomes translating it at the same time
Once synthesized…
(or during synthesis), proteins with transit sequences may be exported to various organelles
Post-Translational Modifications of proteins can me…(3 types)
- proteolysis
- glycosylation
- phosphorylation
Proteolysis
cleaving or cutting polypeptide allow the fragments to fold into different shapes
Glycosylation
add sugars, important for targeting and recognition
Phosphorylation
added phosphate groups alter the shape of the protein
Example of glycosylation is
Glycoprotein synthesis
Role of ER in Glycoprotein synthesis…
signal sequence - causes the ribsosome to be transported to the ER (co-translational sorting)
Once completed…
the eventual glycoprotein is released into lumen of ER and the ribosomal subunits are released to the cytoplasm
