Functions And Dysfucntions Of Genomic Regulation DSA Flashcards
What does the central dogma of molecular biology explain?
The flow of genetic info from DNA to RNA to make a functional product,a protein
The central dogma state that the pattern of info that occurs most frequently in our cells is what?
From existing DNA to make new DNA (DNA replication)
From DNA to make new RNA (transcription)
From RNA to make new proteins (translation)
Describe the DNA backbone
Comprises of five C sugar (pentose) molecules bound to a nucleoside (A, C, G or T)
Pentose molecules are also asymmetrically joined to phosphate groups by phosphodiester bones
Phosphate-deoxyribose backbone
Which type of bond stabilizes and forms the double helix structure of DNA?
Hydrogen bonds between complementary nucleotides (G:C or A:T)
How many nucleotide pairs are there per helical turn?
10 nucleotide pairs per helical turn
What are the three forms of DNA?
B, A and Z form
Characteristics of the B form of DNA
10 nucleotide pairs per turn
Right handed
Characteristics of the A form of DNA
11 nucleotides per turn
Right handed
Characteristics of the Z form DNA
Left handed B form
Actively transcribed DNA
The deoxyribonucleotides of DNA are joined by what type of bond?
Covalent phosphodiester bond
Where do the phosphodiester bonds form?
Between the 3’-OH groups of the deoxyribose sugar on one nucleotide with the 5’-phosphate groups on the adjacent molecule
The 5’ end of one strand is base paired with the 3’ end of the other strand. What stabilizes this?
Noncovalent interactions - H bonds
How many hydrogen bonds are between adenine and thymine?
Two
How many hydrogen bonds are between guanine and cytosine?
Three
How does base pairing in the interior of the helix stabilize the interior of the double stranded DNA?
Because stacked bases repel each other due to their hydrophobic nature
What is chromatin?
DNA packaged into a protein-DNA structure which allows it to fit in the nucleus
Consists of very long double stranded DNA molecules, small basic proteins called histones as well as smaller amounts of non-histone proteins and a small quantity of RNA
What nucleosomes?
The fundamental organization upon which the higher order packing of chromatin is built
The core consists of a complex of 8 histone proteins with double stranded DNA wound around it
What are histones?
A heterogenous group of closely related arginine and lysine rich basic proteins which help them bind tightly to the negatively charged sugar phosphate backbone of DNA
Provide for the compaction of DNA
Each nucleosome core consists of what?
Two molecules each of histone H2A, H2B, H3 and H4
What separates each nucleosome?
Link histone H1
What are the three elements of chromosome structure?
Telomeres, centromeres and multiple origins of replication
What are telomeres?
Hexameric DNA repeats found at the ends of chromosomes that serve to protect the chromosome from degradation
What are centromeres?
Serve as handles which allow mitotic spindles to attach to the chromosome during cell division
Also serve as a boundary that separates the two chromosome arms
Describe multiple origin of replication
In order for DNA in chromosomes to replicate a specific nucleotide sequence acts as a DNA replication origin
They are dispersed throughout its length
At the ORC there is an association of sequence specific double stranded DNA binding proteins with a series of direct repeat DNA sequences
What is a gene?
The complete sequence region necessary for generating a functional product/protein
Describe the area that the gene takes up on a DNA strand
The area encompasses promoters and control regions necessary for the transcription, processing and translation
Genes are concentrated in random areas along the genome,with vast expanses of non coding DNA between them
What are the coding regions of the gene called?
Exons
What are the noncoding regions of the gene called?
Introns
What are the four characteristics of DNA replication/synthesis?
- Semiconservative with respect to parental strand
- Bidirectional with multiple origins of replication
- Primed by short stretches of RNA
- Semidiscontinous with respect to the synthesis of new DNA
Describe the characteristic of DNA replication being semiconservative with respect to the parental strand
When DNA is replicated during the process of cell division one parent or original strand of DNA is distributed to each daughter duplex in combination with a newly organized strand with an anti-parallel orientation
At the end of the process each of the two daughter strands has half new DNA and half old DNA
Describe how the characteristic of DNA replication being bidirectional with multiple origins of replication
DNA replication is bidirectional and starts in several different locations at once
Replication begins at several sites on linear DNA and is completed by the end of DNA synthesis (s phase) of the cell cycle
As replication nears completion bubbles of newly replicated NDA come together forming two new molecules
Explain the characteristic of DNA replication being primed by short stretches of RNA
Replication requires short stretches of RNA for initiation bc DNA polymerases cant initiate synthesis of a complementary strand of DNA on a single stranded template
DNA primase synthesizes short stretches of RNA that are complementary and anti parallel to the DNA template
RNA primer is later removed
Explain the characteristic of DNA replication being semidiscontinuous with respect to the synthesis of new DNA
All DNA polymerases function in the same manner meaning they read a parental strand 3’-5’ and synthesize a complementary strand anitparallel new strand 5’-3’ One strand (leading) is synthesized 5’-3’ and the opposite strand (lagging) is synthesized 5’-3’ but discontinuously
What are DNA helicases?
A class of motor proteins required to unwind short segments of the parental duplex DNA
What is the function of topoisomerases?
Remove the supertwisting of DNA
What do single stranded DNA binding proteins do?
Prevent premature annealing of the single stranded DNA to double stranded DNA
Which proteins function in parental strand separation during replication?
DNA helicase, topoisomerases and ssDNA binding proteins
Which proteins function in DNA synthesis/chain elongation?
DNA primases and DNA polymerases
What is the function of DNA primases during DNA synthesis?
Initiate the synthesis of an RNA molecule essential for priming DNA synthesis on both the leading and lagging strands
What is the function of DNA polymerases during DNA synthesis/chain elongation?
Function as a complex to initiate DNA synthesis and chain elongation by adding new nucleotides
They also have exonuclease activity or proofreading ability that allows them to remove nucleotides that are part of the double helix
What enzyme functions in DNA ligation of replication?
DNA ligase
What is the function of DNA ligase?
Catalyzes the sealing of nicks (breaks) remaining in the DNA after DNA polymerase fills the gaps left by RNA primers
Is required to create the final phosphodiester bond between the adjacent nucleotides on a strand of DNA
Describe the telomere/end of chromosome problem
The telomere shortens with every cell division
The lagging strands of replicated telomeres undergo shortening after the removal of the last RNA primer from the 5’ ends during each successive cycle of cell division
The gap cannot be filled in due to the lack of a primer which leads to shortening of the telomeres
Recognized as part of the normal aging process
What is the telomere maintenance enzyme?
Telomerase which is an RNA-dependent DNA polymerase which adds TTAGGG repeats to the ends of chromosomes
What are the 4 types of RNA?
Ribosomal, transfer, messenger and micro RNA
What is the function of ribosomal RNA and which enzyme produces it?
Structure and function of ribosomes
Produced by RNA polymerase I
What is the function of tRNA and which enzyme produces it?
Carry aa to ribosomes for protein synthesis
RNA polymerase III
What is the function of mRNA and which enzyme produces it?
Carrier of genetic info from genes to ribosomes for protein synthesis
Produced by RNA polymerase II
What is the function of microRNA and which enzyme produces it?
Regulate mRNA stability and downregulate gene expression
Produced by RNA polymerase II
What are the difference regulatory elements in protein coding genes?
Promoter region, splice acceptor and donor sequences (intron) and different regulatory regions
Where are promoters located?
Constantly located just before the coding region
Where are enhancers and response elements located?
Can be anywhere on the genome upstream and downstream and they can be 1000s of bases away from the transcription units located on the same chromosome
What are the three reactions for RNA processing?
Addition of a 5’ cap, addition of a polyA tail and intron removal/splicing
