Biology (DNA and RNA) Flashcards
Viruses and how they reproduce
- Protein coat= capsid protein
- Single or double stranded DNA or RNA
Reproduce:
- attach and inject viral genome into cell.
- Degradation of host genome.
- replication of viral genome and synthesis of viral proteins.
- assembly and release
- new virus
Lytic cycle
- virus enters cell.
- virus replicates.
- host cell lyses (destructs)
- releases viruses
- new viruses infect other cells.
Lysogenic Cycle
- Viral nucleic acid incorporated into host cell chromosome.
- viral nucleic acid replicated along with DNA.
- there is no lysis. Host cell survives.
- if DNA exists, enters the lyric pathway and infects.
Retrovirus
Single stranded RNA uses reverse transcriptase to make DNA
DNA vs RNA containing virus
DNA virus
- replicating in host cell nucleus use host cells DNA polymerase.
- replicating in host cell cytoplasm need own DNA and RNA polymerase.
RNA virus:
Replicate in host cell’s cytoplasm
Nucleobases
Pyrimidines: CUT the pie (CT)
Purines: pure As Gold (AG)
G-C bond and forms 3 hydrogen bonds between them.
A-T bond as firms 2 hydrogen bonds between them.
DNA
Nucleotide: sugar phosphate and base
Nucleoside: sugar and base only
Sugar <-> Base ( N- glycosidic bond)
3’ bonded to Phosphate bonded to 5’ (phosphodiester linkage).
DNA replication
- DNA is semi conservative
- Two strands in one running it anti-parallel.
- Has half of the original parent strand and adds a new daughter strand.
- leading strand: DNA polymerase adds nucleotides in 5’ to 3’.
- lagging strand: nucleotides added in 3’ to 5’ direction
- semi-discontinuous: leading and lagging strand
Enzymes in DNA Replication
- Helicase: separates two DNA strands by cutting H bonds between nucleotides.
- Single Stranded Binding Proteins: Protect the two strands from cleavage and stabilize two strands preventing them from snapping back together.
- Primase: Replication to start needs RNA primer which is a sequence of RNA Nucleotides.
- DNA Polymerase III: Once it recognizes the RNA primer it begins to synthesize new strand in 5’ to 3’ direction
a. Continuous in leading strand.
b. Discontinuous in lagging strand.
c. Has exonuclease activity in 3’ to 5’ direction. (proofreading). - DNA Polymerase I: In lagging strand removes RNA primer and replaces it with DNA
a. Spaces left called Okazaki fragments
b. Has exonuclease activity in 3’ to 5’ direction. (proofreading).
c. Has exonuclease activity in 5’ to 3’ direction. (DNA repair).
DNA ligase: seals the nick after the primer is replaced with DNA.
Transcription
Occurs in three stages: Initiation, Elongation, and Termination.
Initiation:
- RNA polymerase binds to promoter region(short sequence of DNA). In eukaryotes the sequence is TATAAA (TATA BOX)
- DNA sequence is located 25 nucleotides upstream where transcription begins.
Elongation:
- RNA polymerase it causes two DNA strands to separate.
- Begins adding nucleotides to the growing mRNA strand in 5’ to 3’
- RNA Polymerase however, reads DNA strand in 5’ to 3’
- Template strand (antisense) is used to create new mRNA and non-template strand (sense) DNA sequence matches mRNA strand.
Termination:
- RNA polymerase and mRNA strand separate from DNA template strand.
- Poly A polymerase enzyme caps 3’ end of mRNA strand. Called poly A tail
- At start of transcription 5’ end also capped
- Reason for capping is to protect mRNA from degradation by certain enzymes.
Post-transcriptional modifications
hRNA (pre-mRNA)—> mRNA
Occurs in 4 stages
1) Capping: pull phosphate off 5’ end and insert methyl G.
2) Polyadenylation: 3’ tail (add adenosines).
3) Editing: bases changed or deleted.
4) RNA Splicing: Intron (long sequences of nucleotides) removal and exons (shorter sequences of nucleotides) synthesize proteins. Final mRNA from exons.
Translation
- mRNA associates with a free ribosome or ribosome on rough ER.
- set of 3 nucleotides represent codon
- mRNA codons march with tRNA codons (anticodons)
- codon corresponds with specific amino acid.
- it’s how info in mRNA strand can be used to construct specific proteins.
Initiation:
- Ribosome composed of small and large subunit and ribosome had 3 active sites: P, A and E.
- AUG start codon and corresponds to anti-codon UAC, which is methionine.
- tRNA molecules enters the ribosome at P(peptidyl site) where peptide bonds formed.
Elongation:
- Another tRNA enters A site
- covalent bond will form between two amino acids in A and P site.
- tRNA molecule leaves through the E site and as this process repeats growing polypeptide chain on P site.
- This creates a protein.
Termination:
- Last step of termination begins when a stop codon is read.
Types of mutation
Point mutation: One amino acid switched for another.
Silent mutation: Amino acid doesn’t change after
Frame-shift mutation: nucleotide added/deleted causing reading frame to shift.
Non-sense mutation: Codon changed to Premature stop codon.
Missense mutation: Code for a new amino acid.
Enzyme features
Increase rate of reaction by lowering activation energy.
Do not change:
- Equilibrium constant.
- Free energy Δ G (overall energy released during reaction).
Classifying enzymes
Oxidoreductases: redox, transfer electrons
Transferases: transfer of functional group, include kinases.
Hydrolases: uses water to break bonds
Lyases: breaks bonds without water. Often results in new, double bonds.
Isomerases: convert isomer into another
Ligases: joining of two large molecules