The nucleus and cytoplasm of all plant and animal cells
How are nucleotides linked together in DNA and RNA backbones?
What are the components of a nucleotide?
-Pentose sugar (ribose or deoxyribose)
-At least one phosphate moiety
Which is more unstable: DNA or RNA?
What can be a target of hydrolysis on RNA?
Hydroxide on the ribose
What is a nucleoside?
A pentose sugar and a nitrogenous base
What are the types of nitrogenous bases?
Purines and pyrimidines
How are the sugars and bases linked in a nucleoside?
-Above the plane of sugar
How is a triphosphate group labeled?
In what direction is DNA polarized?
5' to 3'
What are some properties of bases?
-Planar in structure
-Absorb UV light
What bases are purines?
Adenosine and guanine
What bases are pyrimidines?
Thymine, Cytosine, and Uracil
What is Chargaff's rule?
Ratio of A:T and C:G is very close to one in DNA from all species
What are the main features of the Watson-Crick model proposed in 1953?
-Two helical polynucleotide chains which are in anti-parallel orientation
-Bases are in the interior of the helix
-Plane of the bases is perpendicular to the helix axis
-Diameter of helix is 20 A, helical structure repeats every 34 A (10 bases)
-Chains of double helix are held together by H-bonding of bases (A-T and C-G)
-Sequence of bases is not restricted
-Order of bases carries the genetic information
How many H-bonds form between C-G? A-T?
C-G = 3 H-bonds
A-T = 2 H-bonds
Do proteins recognize the major or minor grooves of DNA?
How is the DNA double helix stabilized?
By H-bonds and hydrophobic interactions
How does the stacking of base pairs inside the helix contribute to the stability of the double helix?
1. Hydrophobic bases cluster in the interior of the helix and hydrophobic effect stacks the bases one atop of the other
2. Stacked base pairs attract each other through van der Waals forces
What strand is the template strand?
Antisense (3' to 5')
What is the coding strand?
Sense (5' to 3')
What is meant by semiconservative replication?
Each strand of the DNA molecule serves as a template for the synthesis of a new molecule
How was semiconservative replication first detected?
-Parent strand with isotope nitrogen
-Nitrogen (14) used as source thereafter
-Followed the presence of each isotope
How can the two strands of DNA be separated?
By heating or alkali (breaks H-bonds)
How is strand separation monitored?
The hyperchromic effect
How does the hyperchromic effect work?
Heat and supercool DNA so strands remain separate
-ssDNA shows increased absorbance at 260 nm
What is Tm?
The temperature at which half of the helical structure is lost
What factors lead to an increase in Tm?
-DNA with high G-C composition
What factors lead to a decrease in Tm?
-Increasing hydrophobicity of the solution
What is annealing?
Two complementary DNA strands come together
-Occurs 10-20 degrees below Tm
What is the replication of DNA catalyzed by?
What do DNA polymerases do?
Catalyze the addition of deoxyribonucleotides to 3' end of an elongating DNA chain (one at a time)
What are some requirements for DNA polymerization?
1. All four deoxyribonucleotides and Mg
2. Template DNA strand
3. Primer DNA strand (with free 3' OH group for addition of dNTP's
Describe the mechanism of DNA polymerization.
Involves nucleophilic attack of 3' OH group of the primer on alpha-phosphate of the incoming nucleotide (triphosphate)
In what direction does DNA polymerization proceed?
5' to 3'
What are the exceptions to the general rule that genetic information is carried in DNA?
1. RNA virus (RNA to RNA replicase to protein)
Describe the process of viral RNA being incorporated into host cell's DNA.
Viral RNA --reverse transcriptase-synthesis of complementary DNA to RNA --> DNA-RNA hybrid --Reverse transcriptase, digestion of RNA --> DNA transcript of viral RNA --reverse transcriptase, synthesis of 2nd DNA strand --> double helical viral DNA --> integrated into host cell's chromosomal DNA
What is transcription?
Transformation of DNA information into functional molecules (RNA)
What carries information for protein synthesis?
What is RNA synthesized from?
What are the three different major forms of RNA that exist in all cells?
What are some of the other RNA's that are found in cells?
micro RNA (inhibits protein synthesis)
small interfering RNA (degrade mRNA)
small nuclear RNA (splicing)
What is RNA polymerase?
An enzyme that catalyzes the formation of an RNA strand complementary to a DNA template
Does RNA polymerase have a repair function?
Is a primer required for RNA transcription?
What is the RNA sequence transcribed the same as?
Sense DNA strand
What direction does RNA transcription take place?
5' to 3'
What are promotor sequences?
Sequences specific for the start of transcription
What is the sigma subunit?
What is meant by sigma subunit specific initiation?
-Decreases affinity of the enzyme for DNA in non-promoter sites
-Reads DNA sequence-find specific promoter sequences
Describe the DNA template for prokaryotic promoter sites.
-35 region (TTGACA)
-10 Pribnow box (TATAAT) **promoter site
+1 Start of RNA
Describe the DNA template for eukaryotic promoter sites.
-75 CAAT box (GGNCAATCT)
-25 TATA box-Hogness box (TATAAA)
+1 Start of RNA
When is mRNA modified in eukaryotes?
Modified right after transcription
-Addition of cap structure and poly-A tail
What is a cap structure
Methylguanylate attached to 5' end
-Important for protein synthesis
What is a poly A tail?
A sequence of adenylates added to the 3' end
-May help stabilize RNA
Why are most eukaryotic mRNAs spliced?
To remove introns
Most eukaryotic genes are mosaics of what?
Introns and exons
What are coding sequences?
What are coding sequences interrupted by?
What types of RNA are involved in protein translation?
mRNA (genetic information)
What is the anticodon on tRNA used for?
Used to recognize sequence on mRNA
Describe the translation start sites in prokaryotes.
fMet start of protein
Describe the translation start site in eukaryotes.
5' end-cap mRNA
H2N-Met start signal
What is protein translation?
The process of decoding the nucleotide sequence of mRNA into amino acid sequence of proteins
How many nucleotides are in a codon?
What are some of the features of the genetic code?
-Three nucleotides encode an amino acid
-The code is non-overlapping
-The code no punctuations
-The code is degenerate
-The genetic code is nearly universal
What is meant by a degenerate genetic code?
Most amino acids are encoded by more than one codon (first two nucleotides are usually the same)
How many stop codons are there?
How many start codons are there?
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