Strategies in Organic and Biological Chemistry

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What is the routine for designing a synthesis?

Analysis

  • Recognise functional groups in target molecule

  • Disconnect with known reliable reactions in mind

  • Repeat as necessary to find avaliable starting materials


Synthesis

  • Write out plan adding reagents and conditions

  • Modify plan according to unexpected failures or successes in lab


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<p>How is this molecule synthesised?</p>

How is this molecule synthesised?

Friedel-Crafts acylation

<p>Friedel-Crafts acylation</p>
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<p>How is this molecule synthesised? (2 ways)</p>

How is this molecule synthesised? (2 ways)

Friedel-Crafts alkylation

<p>Friedel-Crafts alkylation</p>
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What is a nucleobase?

Molecule that contains N heterocycle with a purine or pyrimidine structure, which is a component of nucleotides in nucleic acids.

<p>Molecule that contains N heterocycle with a purine or pyrimidine structure, which is a component of nucleotides in nucleic acids. </p>
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What is a nucleoside?

A nucleoside is formed when a nucleobase is attached to a sugar molecule, specifically ribose or deoxyribose, without any phosphate groups.

<p>A nucleoside is formed when a nucleobase is attached to a sugar molecule, specifically ribose or deoxyribose, without any phosphate groups. </p>
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What is a nucleotide?

A nucleotide is a building block of nucleic acids, consisting of a nucleobase, a sugar (ribose or deoxyribose), and one or more phosphate groups.

<p>A nucleotide is a building block of nucleic acids, consisting of a nucleobase, a sugar (ribose or deoxyribose), and one or more phosphate groups. </p>
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What is a polymer of nucleotides called?

Oligonucleotides, nucleic acids, RNA & DNA

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What are the structure and properties of nucleobases?

  • Derivates of pyrimidine or purine

  • Nitrogen-containing heteroaromatic molecules

  • Planar or almost planar structures

  • Absorb UV light around 250-270 nm


<ul><li><p>Derivates of pyrimidine or purine</p></li><li><p>Nitrogen-containing heteroaromatic molecules</p></li><li><p>Planar or almost planar structures</p></li><li><p>Absorb UV light around 250-270 nm</p></li></ul><p></p>
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<p>Why is the UV absorption range for nucleobases 250—270 nm?</p>

Why is the UV absorption range for nucleobases 250—270 nm?

Due to π → π* electronic transitions


Excited states of common nucleobases decay rapdily via radtionless transitions

  • Effcective photoprotection of genetic material

  • No fluorescence of nucleic acids


<p>Due to π → π* electronic transitions</p><p></p><p>Excited states of common nucleobases decay rapdily via radtionless transitions</p><ul><li><p>Effcective photoprotection of genetic material</p></li><li><p>No fluorescence of nucleic acids</p></li></ul><p></p>
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<p>What is a H-bond donor and H-bond acceptor?</p>

What is a H-bond donor and H-bond acceptor?

H-bond donor: Hydrogen attached to highly electronegative atom

H-bond donor: Strongly electronegative atom O,N,F

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How do you work out acid dissociation constant and pKa?

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What is the Hasselbalch equation?

The Henderson–Hasselbalch Equation - Chemistry Steps


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Why are purine and pyrimidine bases good H-bond donors (d) and acceptors (a)?

N atoms are able to donate lone pairs

  • Neutral molecules at pH 7


<p>N atoms are able to donate lone pairs </p><ul><li><p>Neutral molecules at pH 7</p></li></ul><p></p>
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<p>What are prototropic tautomers?</p>

What are prototropic tautomers?

Structural isomers that differ in location of protons

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<p>What is keto-enol tautomerism? </p>

What is keto-enol tautomerism?

Tautomerism that is common in ketones

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<p>What is lactam-lactim tautomerism?</p>

What is lactam-lactim tautomerism?

Occurs in some heterocycles

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<p>With these isomers, which tautomers is the most predominant in neutral pH?</p>

With these isomers, which tautomers is the most predominant in neutral pH?

Lactam tautomer

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Show the Fischer projection of ribofuranose (aldehyde and beta-furanose)

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Show the Haworth projection of ribofuranose (aldehyde and beta-furanose)

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What is the RNA name of ribofuranose?

Beta-D-ribofuranose

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What is the DNA name for ribofuranose?

beta-d’-deoxy-D-ribofuranose

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<p>In nucleotides, how is the pentose ring attached to the nucleobase?</p>

In nucleotides, how is the pentose ring attached to the nucleobase?

N-glycosidic bond

  • Bond formed to anomeric carbon of sugar in beta configuration

  • Bond formed to N1 in pyrimidines

  • Bond formed to N9 in purines


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<p>Is N-glycosidic bond stable towards hydrolysis?</p>

Is N-glycosidic bond stable towards hydrolysis?

Yes especially in pyrimidines

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<p>How is N-glycosidic bond cleaved and catalysed</p>

How is N-glycosidic bond cleaved and catalysed

Catalysed by acid

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<p>Is there relatively free rotation around N-glycosidic bond in free nucleotides?</p>

Is there relatively free rotation around N-glycosidic bond in free nucleotides?

Yes

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<p>What conformation are the free nucleotides if there is an angle rotation of near 0 degrees?</p>

What conformation are the free nucleotides if there is an angle rotation of near 0 degrees?

Syn conformation

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<p>What conformation are the free nucleotides if there is an angle rotation of near 180 degrees?</p>

What conformation are the free nucleotides if there is an angle rotation of near 180 degrees?

Anti conformation (in B-DNA)

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<p>What charge are the phosphate groups attached to 5’ at neutral pH? </p>

What charge are the phosphate groups attached to 5’ at neutral pH?

Negatively charged → Prevents tangling of electron-electron repulsion (soluble)

  • Nucleic acids built using 5’-triphosphates ATP,GTP,TTP,CTP


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<p>What charge are the phosphate groups attached to 5’ at neutral pH? </p>

What charge are the phosphate groups attached to 5’ at neutral pH?

Negatively charged

  • Nucleic acids contain one phosphate moiety per nucleotide


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: A, dA, dAMP

  • Nucleoside: Deoxyadenosine


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: G, dG, dGMP

  • Nucleoside: Deoxyguanosine


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: T, dT, dTMP

  • Nucleoside: Deoxythymidine


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: C, dC, dCMP

  • Nucleoside: Deoxycytidine


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<p>What is the symbol name and nucleoside name for this nucleotide?</p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: A, AMP

  • Nucleoside: Adenosine


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: G, GMP

  • Nucleoside: Guanosine


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: U, UMP

  • Nucleoside: Uridine


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<p>What is the symbol name and nucleoside name for this nucleotide? </p>

What is the symbol name and nucleoside name for this nucleotide?

  • Symbols: C, CMP

  • Nucleoside: Cytidine


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<p>What are the differences between DNA and RNA? </p>

What are the differences between DNA and RNA?

  • Difference in monosaccharide

  • Difference in nucleobase


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<p>How are covalent bonds formed in this nucleic acid?</p>

How are covalent bonds formed in this nucleic acid?

  • Covalent bonds formed via phosphodiester linkages → Phosphate groups more stable when its part of polymer chain

  • Negatively charged backbone → Makes polymers more soluble


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<p>Is this nucleic acid structure linear?</p>

Is this nucleic acid structure linear?

YES

→ No branching or cross links

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<p>What is the directionality for this nucleic acid structure?</p>

What is the directionality for this nucleic acid structure?

  • 5’ end is different from 3’ end

  • Read sequence from 5’ to 3’


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What is the DNA backbone like?

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Fairly stable

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What is the RNA like?

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Chemically unstable

→ In water, RNA lasts for few years

→ In cells, mRNA is degraded in few hours

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Why is RNA instable? (Show dimer of 2 nucleobases)

  • Basically RNA is unstable of OH- group → Deprotonation and O- interacts with phosphate backbone

  • Hydrolysis also catalysed by enzymes (RNase)

  • RNase abundant throughout nature


<ul><li><p>Basically RNA is unstable of OH- group → Deprotonation and O- interacts with phosphate backbone</p></li><li><p>Hydrolysis also catalysed by enzymes (RNase)</p></li><li><p>RNase abundant throughout nature</p></li></ul><p></p>
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<p>What is Watson-Crick-Franklin base pairs?</p>

What is Watson-Crick-Franklin base pairs?

When two bases can hydrogen bond to form base pair (not covalent bond)


<p>When two bases can hydrogen bond to form base pair (<strong>not covalent bond</strong>)</p><p></p>
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<p>How big are the possibilities of base pairs being found in monomers? </p>

How big are the possibilities of base pairs being found in monomers?

Large number

<p>Large number </p>
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How big are the possibilities of base pairs being found in polynucleotides?

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Only a few possibilites exist

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Do Watson-Crick-Franklin (WCF) base pairs predominate more in double-stranded DNA or RNA?

Predominates in double-stranded DNA

→ Purine pairs with pyrimidine

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<p>What are the Watson-Crick-Franklin base pairings in this image?</p>

What are the Watson-Crick-Franklin base pairings in this image?

A=T (2 Hydrogen bonds are formed)

C=G (3 Hydrogen bonds are formed)

→ The two strands are complimentary

<p>A=T (2 Hydrogen bonds are formed)</p><p>C=G (3 Hydrogen bonds are formed)</p><p>→ The two strands are complimentary</p>
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<p>What is the process of DNA/RNA denaturation? </p>

What is the process of DNA/RNA denaturation?

  • Covalent bonds remain intact → Genetic code remains intact (Hydrogen bonding breaks instead)

  • Hydrogen bonds are broken → Two strands separate

  • Base stacking is lost → UV absorbance increases and becomes more free in solution and Bases are more flexible


<ul><li><p>Covalent bonds remain intact → Genetic code remains intact (Hydrogen bonding breaks instead)</p></li><li><p>Hydrogen bonds are broken → Two strands separate</p></li><li><p>Base stacking is lost → UV absorbance increases and becomes more free in solution and Bases are more flexible</p></li></ul><p></p>
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<p>How is denaturation of DNA/RNA induced?</p>

How is denaturation of DNA/RNA induced?

High change in pH

<p>High change in pH</p>
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<p>How is denaturation in DNA/RNA reversible?</p>

How is denaturation in DNA/RNA reversible?

Annealing

<p>Annealing</p>
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<p>What are the several factors that affect the midpoint of transition (T<sub>m</sub> = Melt temperature) → <strong>Called melt transition</strong></p>

What are the several factors that affect the midpoint of transition (Tm = Melt temperature) → Called melt transition

Tm increases with:

  • Higher GC content

  • Higher concentration

  • Longer oligomer length

  • pH values nearer to neutral

  • Higher salt concentration


RNA duplex is 20 degrees more stable than DNA


<p><u>T<sub>m</sub> increases with:</u></p><ul><li><p>Higher GC content</p></li><li><p>Higher concentration</p></li><li><p>Longer oligomer length</p></li><li><p>pH values nearer to neutral</p></li><li><p>Higher salt concentration</p></li></ul><p></p><p><strong>RNA duplex is 20 degrees more stable than DNA</strong></p><p></p>
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<p>What is required to replicate DNA?</p>

What is required to replicate DNA?

Template

→ Each new duplex comprimises a template and daughter strand


<p>Template</p><p>→ Each new duplex comprimises a template and daughter strand </p><p></p>
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What is a template?

original double-stranded DNA molecule, where each separated single strand acts as a template to guide the synthesis of a new complementary strand

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What are the three steps to biosynthesis of biopolymers?

  1. Initiation

  2. Elongation

  3. Termination


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What is the initation step for the biosynthesis of biopolymers?

  • Double helix opened with aid of initiatior proteins and unwound with helicases


  • Replication bubble required so bubble can grow at both ends


<ul><li><p>Double helix opened with aid of initiatior proteins and unwound with helicases</p></li></ul><p></p><ul><li><p>Replication bubble required so bubble can grow at both ends</p></li></ul><p></p>
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<p>What is the elongation step for the biosynthesis of biopolymers?</p>

What is the elongation step for the biosynthesis of biopolymers?

  • Incoming nucleoside triphosphate (binds of anhydride groups) pairs with base in template strand

  • DNA polymerase catalyzes covalent linkage of nucleoside triphosphate into growing new strand


<ul><li><p>Incoming nucleoside triphosphate (binds of anhydride groups) pairs with base in template strand</p></li><li><p>DNA polymerase catalyzes covalent linkage of nucleoside triphosphate into growing new strand</p></li></ul><p></p>
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What is a primer?

Short oligonucleotide sequence created by primase enzyme

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What is DNA polymerase?

Enzyme that can build complementary DNA strand starting from an existing primer