BIO1: DNA REPLICATION&REPAIR/EUKARYOTIC CHROMOSOMES Flashcards
Define nucleic acid
Macromolecule composed of nucleotide monomers
Define nucleotide
Nitrogenous base + sugar + 1-3 phosphates
Define nucleoside
Nitrogeneous base + sugar
Nucleotides are joined by what type of bonds?
Phosphodiester bonds
What does the nucleic acid “backbone” refer to?
Sugar and phosphate groups of each nucleotide linked by phosphodiester bonds
What type of bond links nitrogenous bases on double stranded DNA?
Hydrogen bonds
What type of bonds are used within nucleosides?
Glycosidic bonds between sugar and nitrogenous base
How do DNA and RNA differ in nucleotide structure?
DNA (deoxyribose) has an H on the 2’ carbon while RNA (ribose) has an OH on the 2’ carbon
Where does the nitrogenous base link on sugar?
1’ carbon
Where does the phosphate group(s) link on the sugar?
5’ carbon
Identify the purine bases
Adenine and Guanine
Define the structure of purines
Double ring structure
Identify the pyrimidines
Cytosine, Uracil (RNA), and Thymine (DNA) “pyramids CUT”
Define the structure of pyrimidines
Single ring structure
How do the nitrogenous bases of DNA and RNA differ?
DNA uses thymine and RNA uses uracil
What is the difference in structure between DNA and RNA nitrogenous bases?
Thymine has a methyl group and Uracil just has a H
What nitrogenous base is Adenine paired with?
Thymine /Uracil (RNA)
What nitrogenous base is Guanine paired with?
Cytosine
Which nitrogenous base pair is stronger?
Cytosine/Guanine because it has 3 H-bonds and is a stronger base pair
What does the double helix refer to?
DNA structure of linking of 2 nucleic acid strands by H-bonds between the nitrogenous bases in a right-handed helix
How are nucleic acid strands arranged?
Anti-parallel
What group is linked to the 5’ end of the nucleic acid strand?
Phosphate group
What group is linked to the 3’ end of the nucleic acid?
OH group
How are DNA sequences read/written?
5’ -> 3’ for both strands
How is the polynucleotide built?
5’ end of the nucleotide (phosphate containing) is added to the 3’ OH of existing strand using pyrophosphate to drive reaction
Define pyrophosphate
Two phosphates
When does DNA replication occur during the cell cycle?
S phase (synthesis phase)
What is the outcome of DNA replication?
One DNA molecule is replicated into two identical copies
What cellular process is DNA replication a part of?
Cell division
Define the general process for DNA replication
Parent DNA strand serves as a template and replication is iniatiated by an RNA primer and free floating nucleotides are added to the new daughter strand
What is the function of DNA helicase?
Unwinds the parent DNA strand
How does DNA helicase function?
Breaks H-bonds between nitrogenous bases
What is the function of topoisomerase
Relaxes DNA supercoils that accumulate due to the unwinding of DNA
Define DNA gyrase
A type of topoisomerase (relaxes DNA supercoils that accumulate due to the unwinding of DNA)
What is the function of SSB proteins?
Single strand binding proteins stabilize the single parent strands of DNA once unwound
What is the function of primase?
A type of RNA polymerase that lays down the RNA primer to initiate transcription
What is the function of DNA polymerase?
- Builds the daughter strand of DNA
- Proofreads and corrects errors
- Replaces the RNA primer
What is the function of ligase?
Links the Okazaki fragments of DNA daughter strand
Define the step-by-step process for DNA replication
- Helicase binds to the ORI and begins to unwind forming a replication bubble
- Topoisomerase relaxes the supercoils upstream of the replication bubble
- SSBPs stabilize the newly separated parent strands
- Primase lays down the primer (later removed by DNA polymerase)
- DNA polymerase adds nucleotides one by one using parent strand as template
Define annealing
Recombination of DNA when double-stranded DNA are separated
What is the structure of free floating nucleotides?
Nucleoside triphosphates (dNTPs) containing 3 phosphates; pyrophosphate is eventually released to provide energy for nucleotide linkages
How are new nucleotides added to the new daughter strand?
3’ OH on the last nucleotide of the daughter strand nucleophilically attacks the 5’ end of the phosphate of the incoming nucleotide
What is the nucleophile in the DNA replication process?
The 3’ OH on the daughter strand is the nucleophile (e- rich species) that nucleophilically attacks the electrophile which is the 5’ phosphate group (e- deficient)
Define the leading strand
The leading strand is synthesized in the same direction as the extending replication fork and is a single continuous strand
Define the lagging strand
The lagging strand is not continuous and made up of multiple Okazaki fragments that are joined together by DNA ligase
Define the bidirectional synthesis of DNA
Because double stranded DNA is unwound and creates a replication bubble, the leading strand (3’ -> 5’) is replicated continuously (5’ -> 3’) whereas the lagging strand (5’ -> 3’) is replicated backwards as the DNA is unwound/DNA polymerase is laid reverse of how DNA is usually read/written (5’ -> 3’)
Describe the differences between DNA replication in eukaryotes and prokaryotes
- Location
- # of ORIs
- DNA polymerases
- Only eukaryotes have telomeres
Describe DNA replication in eukaryotes
DNA replication in eukaryotes occurs in the nucleus and has many ORIs/DNA molecule which enables fast replication. Eukaryotes have 5 DNA polymerases and telomeres
Describe DNA replication in prokaryotes
DNA replication in prokaryotes occurs in the cytosol and only has 1 ORI/DNA and has 3 DNA polymerases
List the 2 main DNA polymerases used in prokaryotic DNA replication
DNA Pol III and DNA Pol I
Describe the function of DNA Pol III
Main DNA pol that extends the daughter strand
Describe the function of DNA Pol I
Slower than Pol III
Exonuclease activity enables it to remove RNA primer and replace with DNA
DNA error repair
Define theta replication
In prokaryotic DNA replication due to the circular DNA of prokaryotes and singularity of ORI, the DNA creates 2 replication forks similar to the theta
Define telomeres
Non-coding repeats added to the ends of the lagging strand of DNA that protect DNA and shorten with each round of replication
Define senscence
Biological aging due to telomere shortening; if telomere is too short, the cell will stop dividing and fnctioning properly
What is the function of telomerase?
Telomerase is an RNA-dependent DNA polymerase that catalyzes the lengthening of telomeres to reverse telomere shortening; a DNA polymerase then backfills the nucleotides on the lagging strand
Where is telomerase found?
Germ line, stem cells, and cancerous cells
Define RNA-dependent DNA polymerase
An enzyme that can make DNA using RNA as a template
Define the types of DNA mutations
- Point mutations
2. Insertions and deletions
Define point mutations and the types
Point mutations are substitution errors and described by their effect
- Silent mutations
- Missense mutations
- Nonsense mutations
Define silent mutations
Silent mutations occur when a different base pair is added but the same amino acid is translated
Define missense mutations
Missense mutations occur when a differen base pair is added resulting in a different amino acid that is translated; missense mutations are conservative when the new AA has similar biochemical properties to the old one
Define nonsense mutations
Nonsense mutations occur when a base pair change causes the DNA and transcribed mRNA to encode a stop signal so that transcription and translation terminate prematurely
Define insertion and deletion mutations
Insertions occur when one or more additional base pairs are inserted and deletions occur when one or more base pairs are deleted; may result in a frameshift
Define frameshift
When insertion/deletion does not occur in a multiple of 3 base pairs so that the reading frame of the gene is changed so that all of the downstream regions of the gene will also be affected
Define transposon
Transposon/transposable elements are regions of DNA that can move around in the genome and often cause structural changes/mutations in the DNA
Where are transposons found?
Transposons are found in both prokaryotes and eukaryotes
Define transposase
Parts of the transposon that encodes for enzymes that copy/cut and paste DNA segment into a different place in the genome
List the mechnisms of DNA repair
- DNA polymerase
- DNA MMR
- Nucleotide and Base Excision Repair
- Homologous End Joining
- Non-Homologous End Joining
- Homologous End Joining
What happens if the mutation cannot be fixed?
The cell undergoes apoptosis
What activity acts as a backspace button for incorrect base pairs?
Nuclease activity
Define the DNA MMR pathway
The mismatch repair pathway occurs when a base mismatch (A/C, G/T) is identified on the daughter strand, removed, and replaced
Define the Nucleotide and Base Excision Repair
Removes a section of DNA surrounding errors caused by mutagens; DNA polymerase replaces the region, DNA ligase joins the fragments
Describe Homologous Recombination and Non-Homologous End Joining
Fixes double strand breaks and removals of DNA regions; HR must be done after DNA replication and creates an exact copy; NHEJ occurs when homologous DNA is not available where cleaved ends are ligated together (mutagenic)
How are sister chromatids linked?
Centromere
Define sister chromatids
Sister chromatids are identical copies of dsDNA
Describe how human chromosomes are ordered
There are 46 total chromosomes that represent 23 pairs (22 autosomal and 1 sex) chromosomes that are each composed of one maternal chromosome and one paternal chromosome
Define p and q arms of the chromosome
When the centromere is off-center, it creates a shorter arm (p arm) and longer arm (q arm)
Define nucleosome
Regions of DNA wrapped around a histone octamer (8 histone proteins)
What charge do histones have and why?
Histones are positively charged to attract negatively charged DNA
Define chromatin
Chromatin are combination of DNA and histone proteins (beads on a string) which bundles and condenses
What are centromeres composed of?
Binding proteins and specific DNA sequences to link DNA molecules on the sister chromatids
What are the types of chromatin?
- Heterochromatin
2. Euchromatin
Define heterochromatin
Densely packed chromatin that tis not accessible to enzymes of transcription (transcriptionaly “silent”)
Define euchromatin
Loosely packed chromatin that is accessible to transcriptional enzymes (transcriptionally active)
Describe aneuploidy
Aneuploidy occurs when an organism has an abnormal number of chromosomes (+/- 46)
Describe polysomy
Polysomy occurs when an organism has one or more additional copies of a chromosome (e.g. trisomy 21/down syndrome, triple X, kleifelter’s syndrome, turner syndrome)
Describe post-translational protein modification
When proteins require support to fold into their native conformation after translation
List the types of post-translational protein modification
- Chaperone protein helps fold into native conformation
- Cleavage of a region of the polypeptide (zymogen)
- Glycosylation
- Lipidation
- Acetylation and methylation
- Formation of disulfide bonds
Define zymogens
An inactive precursor of an enzyme that requires a biochemical change to activate it (e.g. conformational change)
Describe glycosylation
The addition of sugars to help a protein fold and stabilize
Describe lipidation
The addition of lipids that regulates protein function
Describe acetylation
An organic esterification reaction with acetic acid by introducing an acetyl functional group into a chemical compound
Describe DNA methylation
Adding methyl groups to regulate gene expression
