Description
Chapter 4 [Pg. 109134]
DNA, RNA, and the Flow of Genetic Information
DNA Transcription RNA Translation Protein
DNA RNA mRNA = (Transcription)
Gene expression Codon introns and exons = (Translation)
A Nucleic Acid Consists of 4 Kinds of bases linked to a sugar phosphate backbone
DNA & RNA are linear polymers
DNA & RNA Differs in the Sugar Component and One of the Bases
DNA – Deoxyribose ( 2’ Carbon of the sugar lacks oxygen atom) RNA – Ribose ( 2’ Carbon of the sugar has oxygen atom) Backbone of DNA and RNA 3’-5’ phosphodiester linkages Purines: Adenine, Guanine
Pyrimidines: Cytosine, Uracil, Thymine
DNA has U instead of T
Nucleotides are the monomeric Units of Nucleic Acids
N-9 of purine, N-1 of pyrimidinse is attached to C-1’ of sugar by N-Glycosidic linkage
Beta-Glycosidic linkage (base lies above the plane of sugar) 5’- ATP
3’- dGMP- differs from ATP; contains guanine rather than adenine, contains deoxyribose rather than ribose; one phosphate group at the 3’
DNA base sequence is 5’-3’ direction
A pair of Nucleic Acid Chains with Complementary Sequences can form a Double-Helical Structure If you want to learn more check out In what year did toyotomi hideyoshi died and made his followers promise to keep the power available for his infant son?
X-ray diffraction shows DNA, which the stack of nucleotide bases are 3.4 Å apart
The Double Helix is Stabilized by Hydrogen Bonds and Van Der Waals Interactions
Maurice Wilkins and Rosalind Franklin x-ray diffraction of DNA fibers
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Watson & Crick- Structural model for DNA
Features:
1) 2 helical polynucleotide chains are coiled around a common axis with a right-handed screw sense. The chains are
antiparallel- opposite polarity
2) Sugar-phosphate backbones are on the outside and the purine and pyrimidine bases lie on the inside If you want to learn more check out What is the difference between shia and sunni?
3) Bases are nearly perpendicular to the helix axis; adjacent bases are separated by 3.4 Å. The helical structure repeats every 34 Å, 10 bases. Each base rotated 36 degree form one below (360 degree/ full turn/ 10 bases per turn) We also discuss several other topics like Starting from a pure exchange equilibrium, an increase in the demand for a commodity will result in?
4) Diameter of the helix is 20 Å
G-C [3 H-Bonds] / A-T [2 H-Bonds]
- Stabilize by hydrogen bonds
- Van der Waals stacking force
Most DNA is in the B-form. Right handed, C-3’ endo- lies out of plane
A-form DNA wider and shorter than B-form, base pairs is tilted rather than perpendicular. Also right handed, C-2’ endo-lie in approx. plane
Z-from- left handed double helix in which backbone phosphate zigzag
Alexander Rich
Structure of CGCGCG- Anti-parallel strands held together by W-C base-pairing We also discuss several other topics like Find (f+g)(3) when f(x)=x2+1 and g(x)=2x+1
- Left- handed and has zigzagged backbone (Z-DNA) Different forms show DNA is flexible
Some DNA Molecules are Circular and Supercoils
Human DNA is linear
Bacteria and archae are circular
- Can be supercoiled into super helix
- Relaxed molecule- not super coiled
Supercoiling is important:
- Supercoiling DNA is more compact than its relaxed counterpart
- Supercoiling may hinder or favor the capacity of the double helix to unwind and affect the interaction btw. DNA and other molecules
Single-Stranded Nucleic Acids Can Adopt Elaborate Structures
Stem-loop- from single strand DNA/RNA
RNA can have more complex structure that can be stabilized by metal ions such as (Mg2+)
The Double Helix Facilitates the Accurate Transmission of Hereditary Info.
The sequence of bases of one strand of the double helix precisely determines the sequence of the other strand Don't forget about the age old question of What is proposition 209 all about?
Semiconservative replication
Differences in DNA Density Established the Validity of the Semiconservative – Replication Hypothesis
Matthew Meselson and Franklin Stahl Semiconservation replication test
15N and 14N labeled DNA revealed by density- gradient equilibrium sedimentation
-Absence of 15N DNA indicated that parental DNA was not preserved as an intact unit after replication. Absence of 14N DNA indicated that all the dDNA derived some of their form from the parent DNA
-RESULT: contains 14N DNA
The Double Helix Can be Reversibly Melted
DNA comes apart when H-bonds are disrupted
Tm (melting temp.)- Temp at which half of the helical structure is lost
(In cell)- Proteins “helicases” use chemical energy from ATP to disrupt the helix
Hypochromism-stacked base in nucleic acids absorb less ultraviolet light than do un-stacked bases
-Melting of nucleic acid can be monitored by measuring their absorption of light at 260nm
Annealing- renature process of complementary strands (reannel hybridize)
DNA is Replicated by Polymerases that Take Instructions from Templates
Arthur Kornberg isolated DNA polymerase from E.Coli DNA polymerase catalyzes phosphodiester- bridge formation:
-DNA polymerase catalyzes step-by-step addition of
deoxyribonucleotide units to a DNA chain
(DNA)n + dNTP <-> (DNA)n+1 + PPi
DNA synthesis characteristics:
1) Requires 4 activated precursors: the deoxynucleoside 5’- triphosphates dATP, dGTP, dCTP, TTP, and Mg2+ ion
2) The new DNA chain is assembled directly on a preexisting DNA template
-DNA polymerase is a template-directed enzyme
-Chai-Elongation Reaction- DNA polymerase catalyze the formation of a phosphodiester bridge
3) DNA polymerase require a primer to begin synthesis - A primer strand having free 3’-OH group must be already bound to the template
- Chain-elongation reaction- a nucleophilic attack by the 3’-OH terminus of the growing chain on the innermost phosphorus atom of the deoxynucleoside triphosphate
- A phosphodiester bridge is formed and pyrophosphate is released
- 5’-3’ direction
4) DNA polymerases are able to correct mistakes in DNA by removing mismatched nucleotides
DNA Polymerases are Able to Correct Mistakes in DNA by Removing Mismatched Nucleotides
RNA template: RNA-directed RNA polymerase
Retroviruses- genetic info flow from RNA DNA
- On entering cell, RNA is copied into DNA through reverse transcriptase: Synthesis of the RNA, digestion of RNA, subsequent synthesis of DNA strand
Gene expression is the transformation of DNA info into functional molecules
Different kinds of RNAs:
1) mRNA- the template for protein synthesis, or translation 2) tRNA (Transfer)- Carries amino acids in an activated form to the ribosome for peptide-bond formation
3) rRNA- Major component of ribosomes- catalyst for protein synthesis- most abundant
4) SnRNA- participate in splicing of exons
5) Small RNA- essential component of the signal- recognition particle; helps guide newly synthesized proteins to intracellular or extracellular destinations
6) miRNA (micro)- a class of small noncoding RNAs that bind to complementary mRNA and inhibit their translation
7) SiRNA (Small interfering)- a class of small RNA molecules that bind to mRNA and facilitates its degradation
8) RNA is a component of telomerase maintains the telomeres ends of chromosomes during DNA replication
All Cellular RNA is Synthesized by RNA Polymerase (RNA)n+ ribonucleoside triphosphate <-> (RNA)n+1 + ppi
RNA polymerase requires:
1) Template: Double-stranded or single-stranded DNA 2) Activated precursors- ATP, GTP, UTP, CTP
3) A divalent metal ion, Mg2+ or Mn2+
- Similar to DNA synthesis except RNA polymerase don’t need a primer and the ability to correct mistakes is not as extensive
RNA Polymerases take instructions from DNA Templates Complementarity btw. mRNA and DNA
Transcription Begins Near Promoter Sites and Ends at Terminator Sites
DNA templates contain regions: promoter sites that bind RNA polymerase and determine the starting site
Eukaryotic have promoter sites with TATAAA -> TATA box or ”Hogness box”
Some have CAAT box- GGNCAATCT
Pribnow box- TATAAT
RNA synthesis can be terminated by rho
Start and stop signals for transcription are encoded in DNA template
In Eukaryotes: modification of mRNA 5’Cap --- Coding region--- Poly A tail 3’
Transfer RNAs are the Adaptor Molecules in Protein Synthesis
tRNA contains an amino acid attachment site and a template recognition site
the amino acid is esterified to the 3’-hydroxyl group of the terminal adenylate of tRNA
Anticodon is the template recognition site
Clover leaf structure
Anticodon recognizes condon on mRNA
Amino Acids are Encoded by Groups of 3 Bases Starting From a Fixed Point
Genetic code:
1) 3 nucleotides encode an amino acid (codon)
2) The code is nonoverlapping
3) The code has no punctuation; the sequence of bases is read sequentially from a fixed starting point
4) Genetic code is degenerate
Major Features of the Genetic Code
Only Try and Met are encoded by just one triplet each (special) - Leu, Arg, Ser 6 condons each
Number of Codons correlates with its frequency of occurrence in proteins
Synonyms- condons that specify the same amino acid Degeneracy minimizes the deleterious effects of mutations
mRNA Contains Start and Stop Signals for Protein Synthesis
mRNA is translated into protein on ribosomes
(Bacteria)- start with a modified amino-acid fMet recognizes AUG or GUG
-Initiate codon is preceded away by a purine-rich sequence Shine Dalgarno Sequence
- UAA, UAG, UGA Chain termination, read by release factors (NOT tRNA)
The Genetic Code is Nearly Universal (to against mutation)
Mitochondria encodes a distinct set of tRNA
- AGA and AGG Stop
Most Eukaryotic Genes are Mosaic of Introns and Exons
RNA processing generates mature RNA
Coding sequences are linked by a splicing enzyme to form the mature mRNA
-Removed (introns)
-Retained (exons)
Spliceosomes- Splice introns out
- Intron begins with GU and end with an AG that is preceded by a pyrimidine-rich tract
- 5’—GU—Pyrimidine tract—AG—3’
Many Exons Encode Protein Domains
Introns were present in ancestral genes and were lost in the evolution of organisms that have become optimized for very rapid growth, such as prokaryotes,
Advantages of split genes:
- Many exons encode discreet structural and functional units of proteins
- New proteins arose in evolution by the rearrangement of exons encoding discrete structural elements, binding sites, and catalytic sites= (exon shuffling)- no deleterious effect on encoded proteins
- Potential for generating a series of related proteins by splicing a nascent RNA transcript in different ways (alternative splicing)
Chapter 6 [Pg. 173191]
Exploring Evolution and Bioinformatics
Orthologs homologs that are present within different species and have very similar or identical functions
Homologs two molecules from common ancestor
Paralogs homologous molecules that are found in one species and have acquired different functions through time
Sequence alignment two sequences (hemoglobin and myoglobin) are aligned to each other to identify regions of significant overlap
Sequence identities slide one sequence past the other, one amino acid at a time, and count the number of matched residues
Alignment with gap insertion compensate for the insertion or deletion of nucleotide
Statistical significance of alignments can be estimated by shuffling Conservative substitution replaces one amino acid with another that’s similar in size and chemical properties – only has minor effects on protein structure and often can be tolerated
Neoconservative substitution amino acid is replaced by one that’s structurally dissimilar
Substitution matrix a scoring system for the replacement of any amino acid with each of the other 19 amino acids (+ score to a substitution that occurs frequently/ score to a substitution that occurs rarely)
commonly used substitution: Matrix Blosum 62 each column represents one of the 20 amino acids
Blosum62 indicates: Conservative substitution (Lysine for Arginine) + score. Noncompetitive substitution (Lysine for Tryptophan) score
Lack of a statistically significant degree of sequence similarity does not rule out homology
BLAST (Basic Local Alignment Search Tool)
Examination of 3D structure to Understand Function of Biomolecule
Tertiary structure is more conserved than primary structure
Ex:
Hemoglobin, myoglobin, leghemoglobin Heme group contains Fe atom Actin and Hsp70 have similar structure but different functions and sequence identity
3D structures can aid in evaluation of sequence alignments Generates: Sequence template a map of conserved residues that are structurally and functionally important and are characteristic of particular families of proteins
Repeated motifs can be detected by aligning sequences with themselves sequence alignment of internal repeats
Converged Evolution
Process which different evolutionary pathways lead the same solution Ex:
Serine proteases in both chymotrypsin and subtilisin’s active site
Comparison of RNA sequences can be a Source of Insight into RNA secondary Structure
Reveals clues to the 3D structure
Ribosomal RNA from E.Coli and human: position 9 & 22 retains WatsonCrick pairs
Evolutionary Trees can be constructed on the Basis of Sequence Information
Similar sequences had less evolutionary time to diverge than sequences that are less similar
Reveal the relative divergence time
Modern Techniques to Directly Examine the Course of Evolution
PCR Direct examination of DNA sequences
Combinatorial chemistry to examine molecular evolution by producing large populations of molecules en masse and selecting for a biochemical property
Molecular Evolution Examination Processes:
1. Generation of a diverse population
2. Selection of members based on some criterion of fitness
3. Reproduction to enrich the population in these morefit members through in vitro