Ch 8 Nucleic Acids

What are the 4 major roles nucleotides play in celullar metabolism?

• Energy currency in metabolic transactions

• Essential chemical links in the response of cells to hormones and other extracellular stimuli

• Structural components of an array of enzyme cofactors and metabolic intermediates

• Constituents of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acids (RNA)

Do nucleic acids act as a repository or a functional expression of biological information? Or both?

Both

The transmission of biological information relies on what?

Molecular complementarity

What are the largest molecule in any cell?

Chormosomes

What are chromosomes?

Polymers composed of a small set of common nucleotides, with information embedded in the nucleotide sequence

Is potential for variable sequence and complementarity, and thus information storage and transmission a property of any other class of biological molecule?

No

Is DNA damage a constant? If so, what is the result of it?

Yes which results in occasional mutation

Biological information is subject to what 2 principle factors?

Natural damage and change

What are the 3 principle ways we can use biological information in the laboratory?

• Access it

• Interpret it

• Alter it

What is the ultimate product of catabolic pathways?

ATP (Adenosine tri phosphate)

Nucleoside triphosphates occupy what type of role in cellular metabolism? How do they serve this function?

NTPs occupy a central role in cellular metabolism serving as an energy currency and as important regulatory signals.

What role does ATP serve in anabolic pathways?

Fuel

What is an example of a nucleic acid that stores genetic info?

DNA

What is an example of a nucleic acid that aids in transmission of genetic information?

mRNA

What is an example of a nucleic acid that is used for processing of genetic information?

Ribozymes

What is an example of 2 nucleic acids that are used for protein synthesis?

tRNA and rRNA

Nucleotides are also used in monomer form for cellular functions primarily what 3?

Enzyme for metabolism (ATP)

Enzyme cofactors (NAD+)

Signal transductions (cAMP)

How is rRNA primarily used?

Component of ribosomes

How mRNA primarily used?

Intermediates in protein synthesis

What is tRNAs primary function?

Adapter molecules that translate the information in mRNA into a specific amino acid sequence

Do noncoding RNAs serve a specific function or a wide variety of function?

A wide variety

What is a nucleotide made up of?

• Nitrogenous base (purine or pyrimidine)

• Pentose

• Phosphate

What is a nucleoside made up of?

• Nitrogenous base (Purine or pyrimidine)

• Pentose

What is the major difference between a nucleotide and a nucleoside?

A nucleoside lacks the phosphate group which a nucleotide has.

In a cyclic nitrogenous base are only carbons numbered or carbon and nitrogen atoms?

Both carbon and nitrogen atoms are numbered

What charge does the phosphate group have at a neutral pH?

Negative

At what carbon on a nitrogenous base is the phosphate group typically attached to?

C5

Nucleic acids are built using what version of the nucleotide?

5’-triphosphates (ATP, GTP, TTP, CTP)

Completed nucleic acids contain how many phosphate moiety per nucleotide?

One

In special function cases of nucleotides the phosphate group may or may not be attached to other positions?

It may differ in position

The pentose form used may or may not differ in some nucleic acids and nucleotides?

It may differ in a variety of puckered conformations

What specific form of pentose is used in RNA

Beta-d-ribofuranose

What specific form of pentose is used in DNA?

Beta-2’-deoxy-d-ribofuranose

What type of molecule are nitrogenous bases?

Nitrogen-containing heteroaromatic molecules

Are nitrogenous bases planar or non-planar?

Planar

In what spectrum and at what wave length do nitrogenous bases absorb light?

UV light around 250-70nm

What three nitrogenous bases are found in both DNA and RNA?

• Cytosine

• Adenine

• Guanine

What nitrogenous base is only found in DNA?

Thymine

What nitrogenous base is only found in RNA?

Uracil

Are nitrogenous bases good H-bond donors and acceptors?

Yes

At pH 7 what charge do nitrogenous bases have?

Neutral

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Deoxyadenylate (deoxyadenosine 5’-monophosphate)

Nucleoside: Deoxyadenosine

Symbols: A, dA, dAMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Deoxyguanylate (deoxyguanosine 5’-monophosphate)

Nucleoside: Deoxyguanosine

Symbols: G, dG, dGMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Deoxythymidine (deoxythymidine 5’-monophosphate)

Nucleoside: Deoxythymidine

Symbols: T, dT, dTMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Deoxycytidylate (deoxycytidine 5’-monophosphate)

Nucleoside: Deoxycytidine

Symbols: C, dC, dCMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Adenylate (adenosine 5’-monophosphate)

Nucleoside: Adenosine

Symbols: A, AMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Guanylate (guanosine 5’-monophosphate)

Nucleoside: Guanosine

Symbols: G, GMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Uridylate (uridine 5’-monophosphate)

Nucleoside: Uridine

Symbols: U, UMP

What molecule is this? Give the nucleotide and nucleoside names as well as the 3 symbols that represent it

Nucleotide: Cytidylate (cytidine 5’-monophosphate)

Nucleoside: Cytidine

Symbols: C, CMP

In nucleotides the pentose ring is attached to the nitrogenous base via what type of bond?

N-glycosidic bond

In nucleotides the anomeric carbon of the sugar is in what configuration?

Beta

The N glycosidic bond in pyrimidines is formed at what position?

N1

The N glycosidic bond in purines is formed at what position?

N9

The N-glycosidic bond is quite stable toward what lysis process? Particularly so in pyrimidines or purines?

Quite stable toward hydrolysis, especially in pyrimidines

Bond cleavage of the N-glycosidic bond can achieved through what reaction process?

Acid catalysis

Describe the solubility of nucleotides in pH 7.0 water and what interactions may occur

• Hydrophobic

• Relatively insoluble

• Leads to stacking interactions (van der Waals and dipole-dipole)

Describe the solubility of nucleotides at acidic or alkaline pH values

• More soluble than at pH 7.0

• Charged

In free nucleotides what type of rotation can occur about the

N-glycosidic bond?

Free rotation

An angle near 0 degrees corresponds to what type of nucleotide conformation?

Synconformation

An angle near 180 degrees corresponds to what type of nucleotide conformation?

Anti conformation

Identify which adenosine is in the synconformation and which is in the anti conformation

Synconformation adenosine is on the left

Anti conformation adenosine is on the right

What nucleotide conformation is found in normal B-DNA?

Anti conformation

What are prototropic tautomers?

Structural isomers that differ in the location of protons

What type of tautomerism is common in ketones?

Keto-enol tautomerism

What type of tautomerism is occurs in some heterocycles?

Lactam-lactim

Do nitrogenous bases have tautomers?

Yes

What type of tautomerism occurs in Uracil?

Lactam-lactim

In lactam-lactim tautomerism both tautomers exist in solution but at a neutral pH (7.0) which forms are predominant?

Lactam forms are predominant at neutral pH.

What RANGE of UV light wavelengths can Nucleobases absorb?

250-270nm

When measuring light absorption for mixtures of nucleotides what specific wavelength is used?

260nm

What can UV light absorption measurements be used to tell us about the nucleic acids in a solution?

Can be utilized to quantify the concentration of nucleic acids in a solution

What spectrum range do nucleobases absorb light from?

The UV range

Are there minor nucleosides in DNA and RNA?

Yes

When does modifications of nucleosides occur?

After DNA synthesis

What modified nucleoside is common in eukaryotes and also found in bacteria?

5-Methylcytosine

What modified nucleoside is common in bacteria but not found in eukaryotes?

N6-Methyladenosine

What is another term for the modifications of DNA?

Epigenetic markers

How do prokaryotes utilize epigenetic markers?

Use them as a way to mark own DNA so that cells can degrade foreign DNA

How do eukaryotes utilize epigenetic markers?

Use them as a way to mark which genes should be active

Could the environment turn genes on and off in an inheritable manner?

Yes

What is inosine? How is it made? What is its use?

A modified nucleoside in RNA sometime found in the “wobble position” of the anticodon in tRNA. Made by de-aminating adenosine. It provides a richer genetic code.

What is unique about Pseudouridine as a modified nucleoside?

It’s modification occurs after RNA synthesis

What is Pseudouridine? Where is it found? How is it made? What are its uses?

Pseudouridine is a modified nucleoside in RNA. It is found widely in tRNA and rRNA. ~every 10-20 nucleosides. More commonly found in eukaryotes but also found in eubacteria. Made from uridine by enzymatic isomerization after RNA synthesis. It may help stabilize the tRNA structure and may help in folding of rRNA

Are modified nucleotides functionally relevant?

Yes

How do you synthesize DNA or RNA from individual nucleotides?

Phosphoryl group transfer reaction

The phosphorous atom in phosphate groups is an “easy target” for what type of attack?

Nucleophilic

Hydrolysis of a phosphodiester bond in nucleoside triphosphates can be coupled commonly to what type of reaction?

Creation of a phosphodiester bond between two nucleotides

What is DNA synthesized 5’ → 3’ only?

Because the 3’ OH is the only free reactive hydroxyl group where new nucleotides can be added

What type of bond and linkage are required to form polynucleotides?

Covalent bonds which are formed via phosphodiester linkages

What charge does the backbone of polynucleotides possess?

Negative

Which backbone is more stable DNA or RNA?

DNA

In water how long can RNA last?

A few years

In cells how long can mRNA last?

It is degraded in a few hours

What enzyme is responsible for accelerated hydrolysis of DNA?

DNAse

Is the structure of polynucleotides linear, branched, or linear with cross-links

Linear

How are polynucleotides read?

From 5’ → 3’

Two bases can form what to make a base pair?

Hydrogen bond(s)

Monomers or polynucleotides which has more base pair possibilities?

Monomers

A pairs with what?

T