Exam 1 Flashcards
Define: Chargaf’s Rule
DNA of all organisms should have a 1:1 ratio of purine and pyrimidine bases. Specifically, A/T and G/C should both be 1.
Does the Watson-Crick structure agree with Chargaf’s rule?
Yes
What makes stacking possible?
- Van der Waals Interactions
- Hydrophobic effects
What does the Meselson-Stahl experiment show about replication?
-Replication is semiconservation
Method:
- Increased density of parent DNA with N15
- Put it in an environment of N14 and allowed to divide.
- Put forth question: What is the distribution of N14 and N15 in DNA molecules after successive rounds of replication?
- Test question via density-gradient sedimentation
Result:
-after 1st generation, there’s a single band detected by absorption of UV light–density of band of DNA is halfway in between density of N14 and N15 –> shows that parent DNA didn’t stay intact and absence of N14 shows that daughter DNA got some of their atoms from parent (hybrid daughter DNA)
-after 2nd generation, there’s 2 bands of DNA; 1 was hybrid and the other N14 DNA
How would you view circular and supercoiled DNA?
Electron Microscopy
What is the structural shape of circular/relaxed DNA?
Has no helical turns
What is the structural shape of supercoiled DNA? What’re the advantages (2)?
Shape: Extreme helix
Advantages:
- more compact
- may hinder/favor the capacity of double helix to unwind which in turn affects the interactions b/w DNA and other molecules
How can 2 strands of a double helix be separated (in a lab and in an organism) and what’s it called?
Methods:
- In Lab: a) heating b) addition of acid/alkali to ionize base
- In organism: Helicase
Name: Melting
Why: because the separation of the 2 strands occurs abruptly at a specific temperature
What types of intramolecular base pairings occur in single-stranded nucleic acids?
- Stem-loop structure: when 2 complementary sequences within a single strand come together to form a double-helical structure
- Non-Watson-Crick base pairing: complementary bases match up but do not pair up with the one naturally parallel to it; results in bulges coming out of helix and a decrease in structure stability
- Trinucleotide complexes: Complexes of 3 bases joined together; gives rigidity to structure and helps to stabilize non-watson-crick base pairing.
What are the key components in DNA replication?
- DNA polymerase
- Primer strand
- Activated pre-cursors
Define: DNA polymerase
2 Functions:
- Enzyme that catalyzes phosphodiester bonds (in order to add nucleotide corresponding to one on DNA template strand) by adding onto the 3’ end of the primer strand
- Corrects mistakes in DNA by removing mismatched nucleotides
Define: Primer Strand
-A short fragment of RNA that’s created and paired with a part of the DNA strand which the DNA polymerase can build off of
How does DNA polymerase use primer strand for elongation/to form a phosphodiester bridge?
- 3’ -OH group on the primer attacks the innermost phosphate group on the incoming nucleotide triphosphate
- Results in formation of a phosphodiester-bridge and the release of pyrophosphate (PPi) from the incoming nucleotide triphosphate
- PPi gets hydrolyzed and results in 2 ions of orthophosphate (Pi)
- Pi helps to drive polymerization forward
Define: Activated Pre-Cursors (of DNA)
dATP, dCTP, dGTP, dTTP
What are the 2 ways that viruses that store their genetic info in single-stranded RNA replicate?
- RNA-directed polymerase
2. RNA-directed reverse transcriptase
Define: RNA-directed polymerase
RNA is replicated based off of a template
RNA is less stable than DNA but this instability proves advantageous to viruses. How so?
- Allows for a higher chance of mutation
- Means that they’re constantly changing which decreases chance of detection and getting caught
Define: RNA-directed reverse transcriptase
- Done by Retroviruses
- Overall transforms viral RNA into viral DNA
Steps of RNA-directed reverse transcriptase
- Reverse transcriptase catalyzes addition of a complementary strand of DNA to the viral single stranded RNA–> produces a DNA-RNA hybrid
- DNA-RNA hybrid can now be incorporated into chromosomal DNA
- From this, reverse transcriptase is used again to separate viral DNA from viral RNA strand
- Reverse transcriptase on the viral DNA strand results in a double-helical viral DNA
- This can no be inserted into the host and be replicated alongside with host DNA
What are the 3 major RNAs involved in gene expression (transcription and translation) and what’s the function of each.
- rRNA: major component of ribosomes and catalyst for protein synthesis
- tRNA: acts as an adapter molecule that recognizes 3 base “codons” and carry aminoacyl groups to ribosome for peptide-bond formation (acts as a translator)
- mRNA: template for protein synthesis (messenger)
What does RNA polymerase-catalyzed transcription of DNA need?
- Template: either a single or double stranded DNA
- Activated precursors (ATP, GTP, UTP, CTP)
- A divalent metal ion (Mg2+ or Mn2+)
What is different about RNA polymerase-catalyzed transcription and DNA polymerase-catalyzed transcription.
-RNA does not need a PRIMER STRAND
How is RNA polymerase-catalyzed transcription similar to DNA polymerase-catalyzed transcription.
- Synthesis goes in the direction of 5’–>3’
- Mechanism of elongation
- Synthesis is driven by the hydrolysis of pyrophospate (Pi)
Define: Promoter Sites
Regions on DNA template where DNA polymerase can bind to
-They determine where transcription begins
What is the name of the promoter site in eukaryotic organisms?
TATA box or Hogness box
Define: Enhancer Sequences
Sequences further down from the promoter site that further stimulate transcription of genes
Define: Terminator Sequence * not sure
A sequence found on the DNA template which when RNA polymerase comes across it, the
newly synthesized RNA spontaneously dissociates from RNA polymerase
2 Types:
- Base-pair hairpin structure found in newly synthesized RNA sequence, which disrupts RNA polymerase
- Rho factor (an RNA helicase protein complex) that disrupts mRNA-DNA-RNA polymerase ternary complex
Can transcription self-terminate?
Yes
What happens during modification of RNA in eukaryotes and when does it occur?
When: After transcription
What happens:
1. A “cap” structure is added to 5’ end
2. A Poly(A) tail is added to the 3’ end
(coding region is in between these 2 modifications)
Parts of Structure of tRNA
- Amino Acid Attachment SIte
- carboxyl group of amino acid gets esterified to the 3’ hydroxyl group of ribose unit at the 3’ end of tRNA chain
- Template Recognition Site
- made up of a sequence of 3 bases known as an ANTICODON–anticodon will recognize a complementary sequence of 3 bases on mRNA known as CODON
What enzyme is used to catalyze the joining of an amino acid to a tRNA molecule?
Enzyme: Aminoacyl-tRNA synthetase
Complex: Aminoacyl-tRNA
What are 3 characteristics of the genetic code?
- Degenerate (some codes code for the same amino acid but none code for nothing)
- Non-overlapping (letters only occur once ex. ABC, DEF, GHI etc NOT ABC, BCD, CDE)
- Punctuationless (just read sequentially from a fixed starting point)
Define: Stop Codons
3 codons that designate the termination of translation
- They are UAA, UAG, UGA
- THey are read by release factors
Define: Synonyms
Codons that code for the same amino acid
-usually only differ from each other by the last letter
Define: Reading Frame
-Groups of 3 nonoverlapping nucleotides which get defined starting with initiator AUG codon once AUG has been located by fMet (in prokaryotes) or H2N-Met (in eukaryotes)
What are the components of the start signal in mRNA for protein synthesis?
- Shine-Dalgarno Sequence: a purine rich sequence that base-pairs with complementary ribosomal RNA
- AUG
Define: Release factor
Specific proteins that, when bound to stop codons in ribosome, releases the newly synthesized protein
Define: Introns (intervening sequences)
Sections of the primary transcript that get removed from RNA strand
-Always start with a GU and end with an AG preceded by a pyrimidine-rich tract
Define: Exons (expressed sequences)
Sections of the primary transcript that are retained in RNA strand
