Unit 1 Flashcards
Name kinetic energy in living systems (4)
Radiant Energy Thermal Energy Mechanical Energy Electrical Energy
Name potential energy in living systems (4)
(1) Chemical Bonds
(2) Concentration Gradients
(3) Electrical Fields
(4) Redox Pairs
First law of Thermodynamics
Energy is neither created, nor destroyed. It can be converted but always conserved.
Second law of Thermodynamics
The entropy of the universe is always increasing
Gibb’s free energy equation (chemical)
ΔG = ΔH - TΔS
Gibb’s free energy equation (redox reaction)
ΔG = -nFΔE
Gibb’s free energy under non-standard conditions
ΔG = ΔG°’ + RT lnQ
Transcription
DNA -> RNA
Translation
RNA -> Protein
Building blocks of nucleic acids
Ribonucleotide 2’ deoxy-nucleotide
Universal energy currency of the cell
ATP
Nucleotide
Sugar-Base-Phosphate
Nucleoside
Sugar-Base
Relative Solubility of nucleotide components
Nucleotide > Nucleoside > Pyrimidine > Purine
Nucleotide linkages
Phosphodiester bonds 5’ - 3’
Reverse Transcriptase inhibitors
(1) ddI (dideoxyinosine)
(2) AZT (azideothymidine)
Chargaff’s Rule
%G = %C
%A = %T
B form DNA characteristics (6)
(1) Two strands in right-handed helix
(2) Anti-parallel arrangement
(3) Sugar-phosphate backbone is on outside of helix
(4) Bases are paired on the inside
(5) Geometry favors A-T and G-C pairs only
(6) Complementary of base pairing suggests a molecular mechanism for replication
Stabilization of DNA (Increased Tm) (3)
(1) Increased salt concentration
(2) Increased chain length
(3) Increased GC content
Major causes of Base-Change mutation (5)
(1) Deamination (A, C, G)
(2) Depurination/ Depyrimidination
(3) Oxidative damage (8-oxo-dG)
(4) UV induced covalent linkage (Thymidine dimers)
(5) Alkylating agents (O6-meG)
What recognizes the replication origin?
Origin binding proteins (Origin recognition complex)
What melts/unwinds DNA?
DNA helicase
What relaxes the torsional stress ahead of the replication fork?
Topoisomerase/gyrase
What protects unwound single-stranded DNA?
Single stranded binding proteins Replication Protein A
What synthesizes RNA primer?
Primase
What elongates DNA from the RNA primer?
DNA Pol III
DNA Pol δ & DNA Pol ε
What removes RNA primer and replaces with DNA?
DNA Pol I
DNA Pol α
What ligates DNA fragments?
DNA Ligase
What do origin binding proteins (origin recognition complexes) do?
Recognize origin of replication
What does DNA helicase do?
Unwinds DNA
What does topoisomerase/ gyrase do?
Relaxes torsional stress ahead of replication fork
What do single stranded binding proteins (replication protein A) do?
Protect unwound single-stranded DNA
What does primase do?
synthesizes RNA primers
What does DNA Pol III (DNA Pol δ & DNA Pol ε) do?
Elongates DNA from RNA primer
What does DNA Pol I (DNA Pol α) do?
Removes RNA primer and replaces with DNA
What does DNA ligase do?
Ligates DNA fragments
Characteristics of replication origins (3)
(1) Unique DNA segments with multiple short repeats
(2) Recognized by multimeric origin-binding proteins
(3) Rich in A-T base pairs
What contributes to the high processivity of DNA Pol III (DNA Pol δ)
β-subunit Proliferating Cell Nuclear Antigen
What do the β-subunit (Proliferating Cell Nuclear Antigen) do?
Contribute to the processivity of DNA Pol III (DNA Pol δ)
What elongates Telomeres (as a reverse transcriptase)?
Telomerase
What does Telomerase do?
Elongates telomeres using a reverse transcriptase function
Major causes of Structure-Change mutation (6)
(1) Insertion/Deletion of nucleotides
(2) Bulky chemical adducts
(3) Replication errors
(4) Intra/inter-strand crosslinks
(5) DNA Strand breaks
(6) Stalled DNA replication forks
Types of DNA Repair (4)
(1) Direct Reversal
(2) Excision
(3) Tolerance/Bypass
(4) Strand Break repair
Types of Direct Reversal (3)
(1) Single-stranded DNA Break by DNA LIGASE
(2) UV-caused base damage by PHOTOLYASE
(3) Base alkylation by O6-meG METHYLTRANSFERASE
Types of Excision Repair (3)
(1) Damage that doesn’t distort DNA - BASE EXCISION REPAIR
(2) Damage that distorts DNA - NUCLEOTIDE EXCISION REPAIR
(3) Misincorporated nucleotides during DNA Replication - MISMATCH REPAIR
Types of Strand Break Repair (2)
(1) Single-strand break repair (SSBR)
(2) Double-strand break repair (DSBR)
Types of Double-Strand Break Repair (2)
(1) Homologous Recombination (HR)
(2) Nonhomologous End Joining (NHEJ)
Types of Excision Repair (3)
(1) Base Excision Repair
(2) Nucleotide Excision Repair
(3) Mismatch Repair
Base Excision Repair
Repairs base damages that do not distort DNA. Uses base specific glycosylases to remove damaged base
Nucleotide Excision Repair
Repairs base damages that distort DNA Removes oligonucleotide that contains damaged base
Mismatch Repair
Removes misincorporated nucleotides during DNA replication Distinguishes between template strand and new strand
Common Steps to Excision Repair Mechanisms
(1) Recognition of damaged/mismatched nucleotide
(2) Cutting of phosphodiester backbone (endonuclease)
(3) Removal of DNA fragment (nuclease)
(4) Synthesis of missing nucleotides (DNA polymerase)
(5) Sealing of nick in phosphodeister backbone (DNA ligase)
What does Endonuclease do?
Cuts phosphodiester backbone
What does Nuclease do?
Removes damaged DNA fragments
What does DNA polymerase do?
synthesizes nucleotides
What does DNA ligase do?
Ligates phosphodiester backbone nicks
Steps in Base Excision Repair
(1) Modified base recognized by specific DNA GLYCOSYLASE
(2) AP site-specific endonuclease (APE1) cleaves sugar-phosphate backbone
(3) Gap filled in by DNA Pol
(4) Nick sealed by DNA ligase
Steps in Nucleotide Excision Repair
(1) Recognition and binding of damaged site by multi-protein complex
(2) Local unwinding of DNA duplex by helicases (TFIIH) to form ~25base bubble
(3) Incision of damaged strand by two endonucleases ~30base
(4) Gap filled by DNA Pol 5. Nick sealed by DNA ligase
Two ways NER machinery recognizes damage
(1) Global Genome NER - recognizes damage anywhere in genome
(2) Transcription-Coupled NER - recognizes damage within transcribed region
How does MMR recognize which strand to repair?
Lagging strand marked by transient 5’ DNA ends of Okazaki fragments Leading strand marked by transient ribonucleotides processed into nicks?
When is DNA damage tolerance/ bypass employed?
When there is too much damage for normal repair machineries to handle
What do bypass DNA pol lack?
3’-5’ exonuclease activity
Characteristics of Non-homologous end-joining
No homology needed Inaccurate, resulting in deletion/insertion
Characteristics of Homologous end-joining
Extended sequence homology needed Accurate
Three main classes of RNA
(1) Structural (rRNA, tRNA, snRNA, snoRNA)
(2) Regulatory (miRNA, siRNA)
(3) Information Containing (mRNA)
Why is RNA more easily hydrolized than DNA?
Due to nucleophilic attack by 2’ OH on phosphodiester bond.
What is Puromycin?
A nucleotide analogue that mimics tRNA which terminates translation
What is the segment of DNA which gets transcribed into RNA?
Transcription Unit
What are two features of Transcription
(1) Unidirectional
(2) Completely processive
What is the product of transcription called?
Primary Transcript
What is a Transcription Unit?
The segment of DNA which gets transcribed into RNA
What is a Primary Transcript?
The product of transcription
Which strand complements the RNA transcript?
DNA Template Strand
Which strand codes the RNA transcript?
DNA Non-Template Strand (Coding Strand)
What are the three steps of Transcription Initiation?
(1) Polymerase binds to promotor sequence in duplex DNA
(2) Polymerase melts duplex DNA near transcription start site forming transcription bubble
(3) Polymerase catalyzes phosphodiester linkage of two initial rNTPs.
What happens in RNA Transcription Elongation?
RNA Pol advances 3’ - 5’ down template strand, melting duplex DNA and adding rNTPs.
What happens at RNA Transcriptino Termination?
At transcription stop site, polymerase releases completed RNA and dissociates from DNA.
What are the functions of C-terminal domains in RNA Pol II?
Binding of proteins that regulate elongation and processing of RNA transcript.
What directs RNA Pol to the start of genes?
Promoters
What helps direct assembly of pre-initiation complexes at the promoter?
TATA-Box Binding Proteins
What does TFIIH do?
Functions in Transcription and DNA Repair
What are the three steps in RNA modification?
(1) Capping
(2) Splicing
(3) Polyadenylation
What caps RNA?
RNA Pol II
What are the steps for the 5’ capping?
(1) Triphosphatase
(2) Guanylyltransferase
(3) Guanine 7 methyl transferase
How are introns recognized by spliceosomes
(1) 5’: GU
(2) 3’: AG
(3) Branchpoint: A
How does splicing proceed?
(1) Attack by the 2’ OH of branch point A - Forms lariate intermediate
(2) Attack by the 3’ OH of exon 1
How can different proteins be encoded for by a single gene?
Alternative splicing
What are the steps in 3’ polyadenylation?
(1) Cleavage
(2) Polyadenylation (poly-A binding protein)
