Chapter 4 [Pg. 109­134]

What are the different kinds of rnas?

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

Why supercoiling is important?

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

Who is arthur kornberg?

If you want to learn more check out The best way to reach innovators is through what?

 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