Flashcards in Central Dogma (DNA Transcription, DNA Translation, DNA Post-Translational Modification ) Deck (66):
What is the monomer unit of DNA composed of?
Deoxyribose sugar+ Base (ATCG)+ Phosphate Backbone
What are the two forms that the DNA monomer can be? (Hint: Endings of the name are different, molecules differ by on component)
Nucleoside (Sugar+ Base)
What is the difference between Ribonucleic Acid and Deoxyribonucleic Acid?
Ribonucleic Acid has an Oxygen attached to the Carbon #2 and Carbon #3.
Deoxyribonucleic Acid has an Oxygen group attached to only Carbon #3
Why is Deoxyribonucleic Acid used for DNA synthesizes opposed to Ribonucleic Acid?
The Hydroxyl Group on the Ribonucleic Acid makes it susceptible to hydrolysis, thereby making it too unstable to make up DNA.
What is the process of making polymers of proteins, nucleotides, and nucleotides?
What does it mean that DNA is synthesized from 5' to 3'?
it means that the the 5' carbon in the first nucleotide is not bound to anything, and the 3' carbon in the last nucleotide is not bound to anything.
How do bases attached to each other?
What are the purines?
Adenine & Guanine
What are the pyrimidines?
Cytosine & Thymine& Uracil
Which are the "2 ringed" bases?
Which are the "1 ringed" bases
What are prokaryotes?
Prokaryotes are single celled organisms with no nucleus or membrane bound specialized organelles. Prokaryotes include bacteria and cyanobacteria.
What are Eukaryotes?
Eukaryotes are organisms with cells that have membrane bound nucleuses.
Is there a difference in the bases in Prokaryotic DNA vs Eukaryotic DNA?
No, they are the same
Is there is a difference in the bases in Prokaryotic RNA vs. Eukaryotic RNA?
No, they are the same
Where is base Uracil found?
In RNA. This is because there no Thymine in RNA
What is the term that means "all the DNA in an organism"?
What is done to DNA in prokaryotes to make sure that that restriction enzymes do not "chop up" the DNA?
DNA is methylated heavily in prokaryotes
What is a protective measure that DNA methylation does to Prokaryotic organism?
Viral DNA is not methylated, so this helps Restriction enzymes to "cut it out"
How is prokaryotic DNA packaged?
DNA Gyrase makes "loops" with the circular DNA in the prokaryotes. This is called Supercoiling.
What is the 1st way that Eukaryotic DNA differs from prokaryotic DNA?
It differs as Prokaryotic DNA assumes a circular form (before supercoiling).
Eukaryotic DNA is linear however.
How is the linear Eukaryotic DNA packaged?
Start from the most basic level to the highest level
1. DNA is packaged around a core of histones (This is called a nucleosome)
2. Nucleosomes are then wrapped around each other (chromatin)
3. Them, chromatin is twisted together (chromosome)
What are sister chromatids?
Identical copy of a chromosome. It is made during DNA replication
Where are sister chromatids attached?
They are attached at the centromere?
Where are homologous chromosomes?
Homologous chromosomes are copies of chromosomes where one is inherited from father and another is inherited from mother
What are the ends linear chromosomes subject to to prevent damage?
They are capped. in the ends of the chromosome, you have single and double stranded DNA with the sequence "TTAGGG" that helps to make the "cap"
What are the ends of chromosomes called?
What is the first step of the central dogma?
transcription (DNA to RNA)
What is the second step of central dogma?
translation (RNA to proteins)
What is the start codon?
What is the ending codon?
What is a trick to remember the end codons?
All start with U, all only have U, A, and G
What are the 4 main categories of mutations that can happen in DNA?
1) Polymerase errors
2) Endogenous damage
3) Exogenous damage
What are the 3 different polymerase mutations that can occur?
1) point mutations (missense, nonsense, silent)
2) small repeats
3) insertions/ deletions (small , frameshift)
What is a point mutation?
A single base pair change
What is a missense mutation?
When the codon for an amino acid changes by one b.p and codes for another amino acid
What is a nonsense mutation?
When the codon for an amino acid changes by one base pair and codes for a stop codon
What is a silent mutation?
A silent mutation is when the codon for an amino acid changes by one base pair and codes for the original amino acid.
What are insertions/deletions?
When one base pair is added or subtracted from as sequence.
What do these insertions and deletions cause?
They cause frameshift mutations to occur.
Define Endogenous damage and exogenous damage
Endogenous damage to DNA means damage to DNA that originates within the host itself
Exogenous damage is damage that is outside the host
What other group of errors can endogenous damage cause?
Endogenous damage can cause polymerase errors.
What are the 3 types of endogenous damage that can occur?
1) DNA Oxidation
2) Base crosslinking
3) Physical Damage
What are the 3 types of endogenous damage that can occur?
1) UV radiation
2) X-Ray damage
3) Chemical damage
What does UV radiation cause?
It causes pyrimidine dimers to forms
What does X-ray radiation cause?
It causes the DNA to break completely
What is a transposon?
A set of DNA that can "jump around"
What is a transposon composed of?
A transposon is composed of 2 inverted repeat sequences with a transposase coding gene in-between it.
How does a transposon work?
A transposon first encodes its transposase sequence that codes for a transposase. then the transposase cuts out the transposon, and the transposon inserts itself in a new area of a chromosome.
What are the two types of gene regions that a transposon can insert itself into? What effects would this have?
1) It can insert itself into an intergenic region, where it would cause no harm
2) it can also insert itself into a coding region, where it can cause harm, as this region is translated.
What are the three types of transposons? And what are they composed of?
1) Simple transposon (inverted repeats+transposase coding sequence in the middle)
2) Complex transposon(inverted repeats+transposase coding sequence+genes in the middle)
3) Composite transposon (two transposons+ central region in the middle)
What are two issues that can occur with composite transposon?
The two issues are that can occur with a composite transposon is deletion of a chromosomal area, or inversion of a chromosomal area.
Describe how composite transposon can cause deletions?
Composite transposon can cause there to be deletions if the inverse transposons are going in opposite directions
How can composite transposons cause inversions?
If the inverse transposons are going in the same direction, then there will be an inversion
How can transposons cause amplification to occur in a chromosome?
The transposon replicates itself before inserting itself into a separate part of the same chromosome.
What are the repair pathways associated with polymerase errors ?
1) Mismatch repair pathway (happens after replication
2) Nucleotide excision repair (happens before replication)
Do transposons have repair pathways?
Describe mismatch repair pathway
1) After replication, a mismatched base is detected. Then, it is replaced with the right base
(the new strand is detected as it is not methylated like the old template strand)
Describe nucleotide excision repair pathway
2) Before replication, the wrong base pair is detected. That segment is excised out, and a new strand is put in.
What other types of mutations can nucleotide excision repair fix?
It can repair mutations caused by endogenous and exogenous damage
What is an another way to repair endogenous damage?
Homologous end joining and non-homologous end-joining
What kind of mutations does homologous and non-homologous end-joining fix?
They fix double stranded breaks that can be caused by endogenous and exogenous damage.
Describe homologous end-joining:
Homologous end-joining cuts the individual strands until one of the strand is longer than the other on each broken strand.
Then a sister chromatid strand is used to find the identical template that was broken in the damaged DNA strand.
This template is then used to re-create the broken and "chewed up" strand. Then, afterwards, you have both of the finished strand, and they re pair and you have a fixed strand.
Describe non-homologous end-joining:
Non-homologous end-joining is when the ends of both chromosomes are destroyed until the damaged part ends, and then joined at two random points.
It does not require a sister chromatid.
What are 2 problems with non-homologous end-joining?
1) mutagenic, as you lose bases in the process
2) translocations, can cause two different parts chromosomes to attach to another.