The double stranded parent DNA molecule unwinds into ______ ______ ______ of DNA.
2 single strands
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Once the strands get unwind, each parent strand will act as a ______ to synthesize a new daughter strand
template
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Semiconservative Replication Model
Type of DNA replication in which the replicated double helix consists of one old strand, derived from the parental molecule, and one newly made strand.
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Half of the DNA in the newly synthesized DNA molecule belongs to the ______ and the other half is still ______
parent; conserved
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5'
PO4
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3'
OH
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Erwin Chargaff's Rule
A=T and G=C
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Replication begin at...
origins of replication
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Origins of Replication
sites where the replication of a DNA molecule begins; where 2 parental DNA strands are separated
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Replication Bubble
a region of DNA, in front of the replication fork, where helicase has unwound the double helix
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How many origins of replication do eukaryotes have?
few hundred to thousands
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Replication proceeds in ______ ______ from each origin
both directions
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Helicases
Enzymes that unwind the double helix at the replication forks
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Why does helicase unwind DNA?
In order to make it accessible for primate and polymerase to synthesize the new DNA strands
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Single Strand Binding Proteins (SSB)
Bind to and stabilize the single stranded DNA left behind from the action of helicase
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Topoisomerase
Corrects "overwinding" ahead of replication forks caused from unwinding at the replication forks
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why does overwinding need to be resolved?
In order to relieve the strain on the DNA strands
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How does topoisomerase correct overwinding?
By making cuts, twisting, and then rejoining the DNA strands
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Primase
An enzyme that lays down a primer on the parental DNA strand
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Primer
5 to 10 nucleotides of RNA segments; acts as an attachment point for the enzyme DNA polymerase
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What happens when polymerase binds to a primer?
It causes the polymerase to scan the entire length of DNA by moving in a 5' to 3' direction
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DNA Polymerase
Catalyzes DNA synthesis and requires a template along with all 4 deoxyribonucleoside triphosphates
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DNA Polymerase III
Catalyze the elongation of new DNA by adding nucleotides to the free 3' of the daughter strand
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In which direction does chain elongation occurs in?
5' to 3' direction
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What is required when making a new daughter strand?
A primer and a template strand
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DNA Polymerase I
An enzyme which removes the primers from the DNA stand and then it replaces the gaps with DNA
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Why are the primers removed?
Because RNA doesn't belong with DNA
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DNA Ligase
An enzyme that replaces the gaps left behind from the removal of primers with new DNA
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DNA polymerases can only add nucleotides in the ______ ______ end of a growing chain
free 3'
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A new strand can only be synthesized in the ______ to ______ direction
5'; 3'
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DNA polymerase III can create only 1 of the 2 strands in a continuous manner called the...
leading strand
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The other strand DNA polymerase III creates has to be done so by in small fragments called ______ ______ by using primers going in the 5' to 3' direction
Okazaki fragments
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1st key issue resolved during replication:
Unwinding of the helix
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2nd key issue resolved during replication:
Relieving the strain at one end generated during unwinding at the other end
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3rd key issue resolved during replication:
Discontinuous synthesis of the lagging strand
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4th key issue resolved during replication:
Removal of the RNA primers
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5th key issue resolved during replication:
Joining the gaps in lagging strand of DNA, left by removal of primers
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6th key issue resolved during replication:
Proofreading for errors and fixing if any found
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What enzymes are involved in DNA replication?
Helicase, DNA polymerase I, DNA polymerase III, Ligase, Topoisomerase, Primase
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Any incorrect ______ found are replaced with correct ones
nucleotides
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What enzymes are involved in DNA repair?
DNA polymerases, Glycosylases, Endonucleases, Ligases
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DNA can be damaged by:
Radioactive emissions, UV light, free radicals and chemicals
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Mismatch Repair
Enzymes correct errors in base pairings; The cellular process that uses specific enzymes to remove and replace incorrectly base pairings.
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How does mismatch repair work?
One enzyme detects the mismatch and the other gets endonuclease to cleave the new DNA at the point where the mismatch occurred
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Base Excision Repair
Repairs damage to a single nitrogenous base
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How does base excision repair work?
Glycosylases removes a single nitrogenous base to create an apurinic or aplyrimidinic site (AP site) then AP endonuclease nick the damaged DNA backbone at the AP site then DNA polymerase removed the damaged region using its 5' to 3' exonuclease activity and correctly synthesis the new strand
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Nucleotide Excision Repair
Needed when a few DNA nucleotides are damaged
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How does nucleotide excision repair work?
Either endonuclease or exonuclease cuts out the damaged nucleotides then DNA polymerase I lays down new DNA in the space that is available then ligase joins the newly laid DNA to the existing DNA strand
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Transcription and translation are also called...
gene expression
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Transcription
The synthesis of RNA by using the information stored in DNA
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Where does transcription take place?
Inside the nucleus
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Translation
The synthesis of proteins by using the information stored in RNA
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Where does translation take place?
Cytoplasm
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What are the types of RNA?
mRNA, rRNA, tRNA, miRNA, snRNA
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mRNA
Messenger RNA; the one that makes proteins; DNA transcription
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rRNA
Ribosomal RNA; the one that makes ribosomes; nucleolus
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tRNA
Transfer RNA; the one that makes the transfer molecule; transfer amino acids
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miRNA
Micro RNA; one that play a role in RNA silencing
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snRNA
Small nuclear RNA, plays a role in RNA silencing
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Which RNA's are the building proteins?
mRNA, rRNA, tRNA
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Which RNA's are the destroying proteins?
miRNA, snRNA
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In Prokaryotes mRNA ______ undergo additional processing from transcription
doesn't
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Prokaryotes is translated into proteins ______
immediately
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In Eukaryotes mRNA ______ undergo additional processing from transcription
does
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Eukaryotes yields a ______ mRNA which is translated into proteins
modified
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RNA polymerase reads ______ and makes ______
3' to 5'; 5' to 3'
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Stages of transcription:
Initiation, elongation, termination
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Transcription - initiation in prokaryotes
Starts at the promoter region; RNA polymerase binds to the promoter region to read and transcribe DNA into RNA
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What binds to the promoter region?
RNA polymerase
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What is inside the promoter region?
Pribnow Box
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Pribnow box
TATAAT
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Transcription - elongation in prokaryotes
RNA polymerase adds nucleotides to the growing strand
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Transcription - termination in prokaryotes
Ends at the terminator region on the template strand
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Terminator Region
a certain sequence on the transcription unit that signals the RNA polymerase to end transcription
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Transcription - Initiation in eukaryotes
Begins with the uncoiling of the chromatin; inside the promoter region there is a TATA box; RNA polymerase rely on transcription factors to bind to DNA along a promoter and needs enhancers and silencers to control transcription regulation
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TATA Box
TATATA
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Transcription - elongation in eukaryotes
RNA polymerase adds nucleotides to the growing strand; RNA polymerase adds 40 nucleotides per second
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Transcription - termination in eukaryotes
RNA polymerase reads DNA until the gene length is exhausted and falls off; RNA polymerase continues even when pre-mRNA is sliced out of the growing RNA chain
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RNA processing and editing modify the mRNA ______ after transcription
immediately
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RNA Processing
Ends of the pre-mRNA (5' and 3') are altered; The removal of introns and the combining of exons
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What is the alteration of the pre-mRNA on the 5' end?
A nucleotide cap
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What is the alteration of the pre-mRNA on the 3' end?
A poly-A tail
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How do the alteration of the pre-mRNA affect it?
It helps facilitate the export of mRNA outside of the nucleus and into the cytoplasm; It helps protect the degradation of mRNA from hydrolytic enzymes; It helps the mRNA slide into the ribosome
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Introns
Non-coding sequences
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Exons
Coding sequences
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RNA splicing
The removal of introns and the joining of exons
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RNA splicing is carried out by the enzyme ______
Spliceosome
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RNA Editing
a process by which some cells can make distinct changes to specific nucleotide sequences within an RNA transcript
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RNA editing is ______ ______ as RNA processing
not common
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How many types of RNA editing are there?
2
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Substitution editing
Individual nucleotide bases are altered
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Insertion/Deletion Editing
Nucleotides are added/deleted from the total number of bases
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What is required for translation?
mRNA, tRNA, ribosomes, amino acids
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mRNA function in translation
The ribosome reads mRNA in codons to make proteins
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How many codons are there?
64
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How many codons code for amino acids?
61
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What are the 3 codons that don't code for amino acids called?
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