Gene Expression Flashcards
DNA to RNA
Transcription
DNA for the synthesis of another identical DNA.
Replication
RNA to protein or AA
Translation
RNA to DNA because of retro virus
Reverse transcription
Largely dictates the physical observable characteristic of an organism which is known as phenotype
Genotype
Characteristic of an organism
Phenotype
Refers to a change in the DNA
Mutation
Result from different kinds of mutation
Disease
DNA structure
Double helix
2 anti parallel strand
Bond that keeps the 2 anti parallel strands together
H bond
Stacked at the center of the DNA
Base
Back bone of DNA
Sugar and phosphate
3 form of DNA
B
A
Z
Tall and slender
It is where enzymes will attach during replication and transcription
Right handed
B form
Form seen in a solution with higher salt concentration or with alcohol added
Short and stout
A form
Longer than B form
Seem to zigzag
Z form
A molecule made up of repeating sub units
Polymer nucleotides
Nucleotides linked by
Phophodiester bond
Each nucleotide is made up of?
Bases
Deoxyribose
Phosphate
H bonded with each other
Attached to the sugar
Bases
Attached to the PO4
Deoxyribose
Sugar
Has 5 carbon
Deoxyribose
Used to distinguish it from the carbons of the base
Primes
Attachment of bases by glycosidic bond
C1
Contains a hydroxyl functional group 3’ ends
C3
Contains hydroxyl group
Called the 5’ end of the sugar
Always contain a PO4
C5
Mitochondria
Prokaryotic DNA bacteria
Closed circular
Eukaryotic DNA
Linear
Linear DNA ends are referred to as
Telomeres
Telomeres shorten after each round of
Replication
Linker part of the DNA
Linker histone
Associates with the linker part of the DNA
H1
Will form the octameric core
H2A
Nucleosome
H4
Size of DNA that wounds around Histone
150 bp
Size of linker DNA
50bp
DNA that is further compacted
Nucleosome
Is the nucleosome
30 nm fiber
30 nm fiber will be packaged into a lampbush or test tube brush appearance
700 nm scaffold
Packaging ratio during interphase
1000
Packaging ratio during mitosis
10,000
The lampbrush in turn will be packaged into a
Chromosome
Central part of the chromosome
Centromere
Ends of linear chromosome
Telomere
1 chromosome =
1 DNA molecule
In the nucleus of human cell, it contains how many molecules of DNA
46
Refers to all the DNA present in human cell
Genome
DNA present in the nucleus
Nuclear genome
DNA present in the mitochondria
Mitochondrial genome
Portion of the nuclear DNA that can be potentially transcribed into RNA
Gene sequences 30%
The remaining 70% of nuclear genome do not code for anything. They are just there as
Spacers
Gene sequences 30%
10 % codes for protein
90% codes for RNA
Apparent when the chromosome is stained
Extragenic DNA
Usually contain active genes
Referred as euchromatin
Light staining areas
Usually contain junk DNA
Referred as heterochromatin
Dark staining areas
DNA polymerization proceeds in
5’ to3’ direction
DNA polymerization, complementary DNA acts as
Template
DNA polymerization, acts as co factor
Magnesium
Enzyme that catalyze the synthesis of phosphodiester bond
DNA polymerase
It will determine the sequence of the new strand
Template
Bond formation between P and OH and cleavage of the diphosphate
Nucleophillic attack
The oxygen would launch a nucleophillic attack as a result there is formation of
Phosphodiester bond
Why do we say that the DNA grows in the 5’ to 3’ direction?
You can always add only in the 3’ end
Synthesize primers?
Primase
To provide 3’OH to initiate DNA synthesis
Primers
Without primers
DNA polymerase cant start its activity
Responsible for removal of primers
Take over DNAsynthesis by inserting 5’ to 3’ polymerase function
DNA polymerase 1
Utilizes energy from ATP
Synthesize a phosphodiesterbond to make it a one continous strand without breaks
Ligase
Unwinding and primer formation
Initiation
Formation of daughter DNA strands
Elongation
Will separate the 2 strands
Helicase
Keeps the 2 strand apart from each other
Single strand binding protein
Primary responsible for the synthesis of leading strand
DNA polymerase 3
Synthesis of leading strand
Requires primers
5’to3’ direction
Synthesis is continous
DNA grows towards the direction of the replication pork
Synthesis of the lagging strand
Requires multiple primers
5’ to 3’
Discontinuous resulting to the formation of okazaki fragments
DNA goes away from the replication fork
Enzyme responsible for initial synthesis of the okazaki fragment
DNA polymerase 3
Remove primers
DNA polymerase 1
Connect adjacent okazaki fragments after the primers have been taken out
Ligase
Mechanism that make sure that the replication porks meet at the other end simultaneously
Termination utilization substance
Difference between eukaryotic and prokaryotic DNA replication
Prokaryotic- single origin
- DNA polymerase 2 creates both strands
- supercoiling
Eukaryotic- multiple origin
- DNA polymerase alpha for leading strand and delta for lagging strand
- supercoiling and telomere shortening
Problem associated primarily with prokaryotic replication
Supercoiling
Solution for supercoiling
Topoisomerase
Problem associated with linear DNA replication
Telomere shortening
Because there is no 3’ for OH no attachment site
Solution for telomere shortening
Telomerase
How do we solved that 3 overhand
T loop, dahil sa telomerase
It synthesize DNA utilizing an RNA template
hTRT human telomerase
New strand is longer than the original one. Extra sequences have been introduced.
Replication slippage example huntingtons disease
Change in nucleotide sequence
Mutation by UV light
Happens on the 3rd base of the codon
Usually codes for the same amino acid
Least dangerous
Silent mutation
Change in the base, change in the amino acid
Missense mutation
Sickle cell anemia
Amino acids become stop codon
Nonsense mutation
Most severe
Opposite of nonsense mutation
Stop codon to an amino acid
Readthrough mutation
Type of mutation
Substitution
Deletion
Insertion
A deletion mutation can result to frameshift with removal of
1,2 or 4 amino acids
No frameshift if the removal of 3 bases or any multiples of 3
Consequences of mutation
Disease
Silent- if mutation happen in the spacer DNA
Evolution
DNA repair system
Base excision
Nucleotide excision
Mismatch repair
Damage base
AP site
Recognize AP site and remove its base
DNA glycosylase
Removes AP site and neighboring nucleotides
AP endonuclease
Involved in removing damaged nucleotides
UvrA
UvrB
UvrC
Mismatch repair is very expensive. Enzyme involve
Helicase 2
SSB protein
DNa polymerase 3
Ligase
Synthesis of RNA utilizing DNA as the template
Transcription
Not all forms of DNA can be transcribed, only certain stretches and this called
Gene
Enzyme used in transcription
RNA polymerase
Synthesis of RNA 3 major steps
Initiation
Elongation
Termination
Works to inhibit the RNA polymerase
Rifampisin
Initial binding site for RNA polymerase
Promoter region
Parts of the gene that being transcribed
Promoter region
Informative sequence
Terminator sequence
Other name for promoter region
Tata box
Pribnow box
GC box
Hogness box
This is the actual transcription site, ito talaga yung itatranscribe
Informative region
2 strand from DNA
Template
Coding strand
When the RNA polymerase has reached this region of the gene, transcription has to end
Terminator sequence
Allows hairpin loop formation on mRNA
GC rich region
RNA polymerase with sigma factor locate promoter region
Closed promoter complex
RNA polymerase will also act as helicase, the 2 strand separated is now called
Open promoter complex
When RNA polymerase locate the first base it will now
Start synthesize RNA
While the polymerase unwinds the DNA, after the DNA has been used as template, there is an
Automatic rewinding
In the RNA, the sequence will be CG,CG,CG which has what is known as
Self complimentarity
Remember, in the terminator sequence, the sequence is
GC,GC,GC
There will be hair pin loop formation
Poly A for DNA
Poly U for RNA
Alternative ending, a protein which comes in and separates the RNA from DNA template
Rho Factor
Transcription in eukaryote
3 types of RNA polymerase
Not just promoter region
RNA Is not ready for use
Transcription and translation not coupled together
Eukaryotic transcription
Code for RNA and protein as well
These are sequence that are transcribe and translate
Exons
Eukaryotic transcription
Code for RNA but do not code for protein.
Transcribe but not translate
Introns
Eukaryotic transcription
Types of RNA polymerase
RNAP 1,2,3
Eukaryotic transcription
Transcribe all ribosomal RNA with the exception of 5S
RNAP 1
Eukaryotic transcription
Transcribes mRNA
RNAP 2
Eukaryotic transcription
Transcribe tRNA including 5S
RNAP 3
This will render the gene silent and cannot be expressed
Methylation of CpG islands
Example of how activators and repressors work together to control expression of the lactase gene
Lac operon
DNA is released so that it is not anymore lightly packed
Acetylation of nucleosome
Smallest
Adaptor molecule
T loop
tRNA
Complimentary to the codon in mRNA
Anti codon loop
Where amino acids are artached
Acceptor arm
Largest
Most abundant
Found in ribosome
Ginger like
rRNA
Has P site, A site and mRNA bunding site
Small ribosomal sub unit
The one where it has the enzyme peptidyl tranferase
Large ribosomal sub unit
tRNA
RNA
AA
P site
M ribosomal binding site
A site
The synthesis of protein utilizing as mRNA as template
Begins at the start codon and ends when the stop codon reached
Translation
Template that determines the sequence of the amino acids
mRNA
The one that brings the amino acid there
tRNA
It is where it will all.
It is ribosomes catalyzes peptide bond formation
rRNA
