Chapter 6 Flashcards
Nucleoside
Five-carbon sugar (pentose) and nitrogenous base
Nucleotide
Nucleoside plus 1-3 phosphate groups
Nucleotides linked by phosphodiester bonds
Watson-Crick Model
Base-Pairing RUles:
DNA: A pairs with T (2 H bonds)
RNA: A pairs with U (2 H bonds)
C pairs with G (3 H bonds)
Structural Differences DNA vs RNA
DNA:
* contains deoxyribose
* contains thymine
* usually double stranded
RNA:
* contains ribose
* contains uracil (excluded from DNA because results from cytosine degradation)
* single stranded
Both proceed in 5’ to 3’ direction
Aromaticity in Nucleic Acids
Ex: purines and pyrimidines
Make compounds very stable and unreactive
Stability: important for storing genetic information and avoiding spontaneous mutations
Chargaff’s Rules
With RNA, complementarity seen in DNA doesn’t exist
%C doesn’t equal %G, %A doesn’t equal %U
5 Histone Proteins in Eukaryotic Cells
- H1 (only one not in histone core where DNA wraps to form chromatin)
- H2A
- H2B
- H3
- H4
Heterochromatin
- Dense chromatin packing
- Dark appearance under light microscopy
- Silent transcriptional activity
Euchromatin
- Uncondensed chromatin packing
- Light appearance under light microscopy
- Active transcriptional activity
Telomeres and Centromeres
Stay tightly raveled even when rest of DNA is uncondensed due to high GC-content increaing H bonding
Helicase
Unwinds DNA double helix
Found in prokaryotes and eukaryotes
Single-stranded DNA-binding Protein
Prevents reannealing of DNA double helix during replication
Found in prokaryotes and eukaryotes
Primase
Places ~10-nucleotide RNA primer to begin DNA replication
Found in prokaryotes and eukaryotes
DNA Polymerase III
Adds nucleotides to growing daughter strand
Found in prokaryotes
DNA Polymerase a
a as in alpha
Adds nucleotides to growing daughter strand
Found in eukaryotes
DNA Polymerase I
Fills in gaps left behind after RNA primer excision
Found in prokaryotes
RNase H
Excises RNA primer
Found in eukaryotes
DNA ligase
Joins DNA strands (especially between Okazaki fragments)
Found in prokaryotes and eukaryotes
DNA topoisomerases
Reduces torsional strain from positive supercoils by introducing nicks in DNA strand
Found in prokaryotes and eukaryotes
Lagging Strand
More prone to mutations because must constantly start and stop process of DNA replication
Contains many more RNA primers that must be removed and filled in with DNA
Telomere
Ends of eukaryotic chromosomes
* Contain repetitive sequences of noncoding DNA
* Protect chromosome from losing important genes from incomplete replication of 5’ end of DNA strand
Oncogenes (AKA proto-oncogenes)
Code for cell cycle-promoting proteins
When mutated, proto-oncogene -> oncogene promoting rapid cell cycling
Like stepping on gas pedal
Tumor Suppressor Genes
Code for repair/cell cycle-inhibiting proteins
* When mutated, cell cycle allowed to proceed unchecked
Like cutting brakes
* Most likely to result in cancer from inactivation/loss of function mutations
DNA Polymerase Distinguishment
Parent strand: more heavily methylated
Daughter strand: barely methylated
Can distinguish based off of this during proofreading
DNA Polymerase
Proofreading
Cell Cycle Phase: S
Key enzymes/genes: DNA polymerase
Mismatch Repair
Cell Cycle Phase: G2
Key enzymes/genes: MSH2, MLH1 (MutS and MutL in prokaryotes)
Nucleotide Excision Repair
Corrects lesions that are large enough to distort double helix
Cell Cycle Phase: G1, G2
Key enzymes/genes: Excision endonuclease
Base Excision Repair
Corrects lesions small enough not to distort double helix
Cell Cycle Phase: G1, G2
Key enzymes/genes: Glycosylase, AP endonuclease
Genomic Libraries
Include all DNA in organism’s genome including noncoding regions
* Useful for studying DNA in introns, centromeres, or telomeres
cDNA Libraries
Only include expressed genes from given tissue
* Can be used to express recombinant proteins or to perform gene therapy
cDNA formed from processed mRNA strand by reverse transcription
PCR
Increases the number of copies of a given DNA sequence
Can be used for a sample containing very few copies of DNA sequence
Southern blotting
Useful when searching for particular DNA sequence because seperates DNA fragments by length and then probes for sequence of interest
Dideoxyribonucleotides
- Lack 3’ -OH group required for DNA strand elongation
- Once added to growing DNA molecule no more nucleotides can be added because can’t form a bond
Transgenic Mouse
Gene introduced into germ line/embryonic stem cells to look at effect of that gene
* Best suited for studying effects of dominant alleles
Knockout Mouse
Gene of interest has been removed instead of added
Melting Temperature DNA
Temperature where DNA double helix seperates into two single strands (AKA denatures)
* H bond linking base pairs broken
* Higher GC-content higher melting point vs AT
Aromatic Rings
- Contain conjugated pi electrons (alternating single and multiple bonds or lone pairs)
- Won’t exist in carbohydrate ring structures (only single bonds present)
- Nucleic acids are aromatic heterocycles
- Proteins have at least one aromatic amino acid usually (ex: tryptophan, phenylalanine, tyrosine)
Aromatic
- Cyclic, planar, and conjugated (every atom has at least one unhybridized p-orbital)
- Contain 4n + 2 pi electrons
- Most have alternating single and double bonds
- Can be aromatic with triple bonds (would permit at least one unhybridized p-orbital)
Polymerase Chain Reaction
Used to clone sequence of DNA using DNA sample (complementary sequence to part of DNA of interest), primer, free nucleotides, and enzymes
* Polymerase from thermus aquaticus used because reaction regulated by thermal cycling (would denature human enzymes)
* Repeated heating/cooling allow enzymes to act specifically and replaces helicase
* Each cycle doubles amount of DNA of interest
Restriction Endonucleases
Used in gene therapy, southern blotting, and DNA repair
Prokaryotic DNA
- Lacks nucleosomes (circular and lacks histone proteins)
- Replicated by different DNA polymerase (occurs in both but vary in identities)
- Circular chromsomes
Eukaryotic DNA
- Has telomeres
- DNA organized into chromatin that can condense to form linear chromsomes
Gene Sequencing
Issues of consent and privacy
* Genetic screening provides information on direct relatives (invasion of privacy in communicating information to family members at risk)
* Fairly accurate
* No significant physical risks
* Not invasive
