Lecture 7 - Nucleotides and Nucleic Acids

8/18/2019 Lecture 7 - Nucleotides and Nucleic Acids

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The Structure of Nucleotides and Nucleic Acids

Morning on the other side of planet Earth

Zhongshan, Guangdong Province, China


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There are two basic kinds of nucleic acids

• Deoxyribonucleic acid, DNA

storage of genetic information, genes and regulatory sequences that controlexpression of genes.

• Ribonucleic Acid, RNAinvolved in the expression of genetic information in the processes of

transcription (mRNA) and translation (tRNA, rRNA).A variety of small RNA molecules also play gene expression regulatoryroles in the cell.

• All cellular life forms on earth use DNA to store genetic information.

• Many viruses use RNA instead of DNA to store genetic information.


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What’s in a Name

• The terms nitrogenous base, nucleoside, and nucleotide have precise meanings

• in common speech, we frequently use theterm adenine when referring to thenucleotide version as well.

Nitrogenous base

Adenine

Nucleoside Nucleotide

Adenosine Adenosine

monophosphate, AMP

Adenosine diphosphate, ADP

Adenosine triphosphate, ATP

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Nitrogenous bases

• the bases in nucleotides or nucleic acids are derivatives of either purine orpyrimidine.

•

the rings in in both base types are referred to as ‘Heterocyclic’ meaning theycontain elements other than carbon (e.g. nitrogen).• the ring structure of purines are a fusion between a 6C pyrimidine ring and

a 5C imidazole ring• atoms making up molecules are numbered as indicated

What is the

difference

between

uracil and thymine?

Have you encountered

an imidazole ring

elsewhere?


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Two purines participate in the formation of nucleic acids but many other purinesexist in nature

http://localhost/var/www/apps/conversion/tmp/scratch_1//upload.wikimedia.org/wikipedia/commons/1/1f/Purines.svg


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Chemistry of Nitrogenous Bases

• the bases are aromatic (have resonance structures) and are relatively hydrophobic.

• the bases are planar, can engage in stacking interactions with each other andwith other aromatic groups like the side chains on certain amino acids.

• because of their aromaticity, the nitrogenous bases absorb UV radiation at260 nm very strongly. This is why we measure DNA concentrations in solution

at 260 nm.


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Nitrogenous base groups that can participate in Hydrogen bonding


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Nucleosides

• nucleosides are compounds formed when a base is covalently linked to a5C sugar called ribose.

it is the absence of an oxygen atomon the 2’ (pronounced “two prime”) carbon atom that results in namedeoxyribonucleic acid.


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The nucleosides used in ribonucleic acid (RNA)

Nelson p812

• nitrogenous bases and certain nucleotides are used extensively in cellsfor purposes other than nucleic acid synthesis but the nucleosides not so much.

• Adenosine is an interesting exception… it acts as a sort of hormone.


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in mammals adenosine has a variety of hormonal functions in the body

• blood vessel dilation• smooth muscle contraction• neurotransmitter release• metabolism of fat

for example, after extensive exercise adenosine levels rise in muscle tissuecausing blood vessel dilation and increased blood flow to muscle cells.

Adenosine also regulates sleep:upon prolonged wakefulness, adenosine levels rise and promotesleepiness by interacting with neuron receptors

Caffeine, which is a structural mimic of adenosine, blocks adenosine functionby binding to the same neuronal receptors.

adenosine

http://localhost/var/www/apps/conversion/tmp/scratch_1//upload.wikimedia.org/wikipedia/commons/1/1f/Purines.svghttp://localhost/var/www/apps/conversion/tmp/scratch_1//upload.wikimedia.org/wikipedia/commons/e/e8/Adenosin.svghttp://localhost/var/www/apps/conversion/tmp/scratch_1//upload.wikimedia.org/wikipedia/commons/e/e8/Adenosin.svghttp://localhost/var/www/apps/conversion/tmp/scratch_1//upload.wikimedia.org/wikipedia/commons/1/1f/Purines.svg


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Nucleotides

• A nucleotide results when phosphoric acid is linked to the sugar of a nucleosideby an ester linkage.

• the ester linkage occurs on the 5’ carbon of the sugar

Nelson p813


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Formation of di- and tri-phosphate nucleotides

• phosphate groups linked by phosphoanhydride linkages• ATP is an energy carrier in cell and contributes needed energy to many reactions

because of the energy carried in the anhydride bonds.• in the cell, the tri-phosphate forms are used to build nucleic acids (ATP or dATP)

Nelson p814


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Nucleic acids are polymers of nucleoside monophosphates

•

nucleic acids have directionality called5’ to 3’, this is the order in which DNA

is read.

• fragments also begin with 5’ phosphate

and end with 3’ OH group.

• nucleic acids have a net negative charge.

• the ribose of each nucleotide is joined by

a phosphodiester bond.

moran p580

If the molecule to the right was RNA

instead of DNA, what would it look like?


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H+ +pKa = 2

2

1

3

[acid]=[conjugate base]

pH

4

5

Why are nucleic acids called acids?

at physiological pH

this form exists

-O-OHO

-OOH


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Complementary strands of DNA form Double-stranded DNA

• note the antiparallel directions of opposing strands• note the base pairing rules and the H bonding patterns• identify the components of each participating nucleotide

moran p581


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5’-ATCGTAGCCGATGCCGCTACGTGCGTAGCTAGCGATGCTAGTA-3’

3’-TAGCATCGGCTACGGCGATGCACGCATCGATCGCTACGATCAT-5’

A short segment of DNA

Notice:

• 5’ to 3’ directionality of top strand of DNA

• the complementarity of the nucleotides in each strand(A always basepairs with T)(G always basepairs with C)

• the anti-parallel directionality of bottom strand (3’ to 5’)

How many nucleotides make up your DNA?


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Double-stranded DNA forms a helical structure

• the helix is the result of several intra-molecular interactions and formsspontaneously in water


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Stabilizing Features of double-stranded helical DNA

ds DNA is stabilized by 3 major interactions types

• Hydrogen bonding between bases on opposite strandsthese are widely thought to be the major stabilizing force in DNAstructure. But they provide only small contribution to stability.

• The Hydrophobic effectthe nitrogenous bases are hydrophobic. It is entropically favorableto shield these from contact with water molecules.

•

Stacking interactions between bases on same strandmainly van der Waals forces between adjacent planar basesthese are the main contributors to DNA helix stability.


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Hydrogen bonding occurs between base pairs on opposite strands

what are the donors and acceptors in these bonds?

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predominant format pH 7

predominant formabove pH 9.7

•

hence, pH can influence the stability of double-stranded nucleic acids.


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The Hydrophobic Effect

Double stranded DNA adopts a compact structure where the hydrophobic bases

are largely shielded from contact with water molecules.

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3. Induced dipole-induced dipole. Randomfluctuations in electron distribution in onemolecule sets up temporary dipole. This inducesdipole in adjacent molecule, resulting ininteraction. Weak but very important to thecohesiveness of everything.

Also known as London Dispersion Forces.

Adjacent base pairs stack together along the helix

• each adjacent pair is separated by a distance that is ideal for the formation ofvan der Waals interactions

• these are the interactions in ds DNA thatcontribute the most stability to thehelix, not H bonding as is commonlythought.


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Alternative views of the stacking arrangementof bases in DNA

note the substantially hydrophobic

core to the helix



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The Overall Topology of Double-stranded DNA (B-form)

moran pg 583

right-handed helix

width 2.4 nmrise 0.33 nm

pitch 3.4 nm

there are 10-11 nucleotidesper complete turn of DNA

about 4,000 DNA strands laid side by side

would equal the width of a human hair


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The geometry of the base pairs explain the origin ofmajor and minor grooves

Nelson p840


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Many Proteins bind DNA in a base sequence-dependent fashion

• e.g. proteins involved in DNA replication and gene expression regulating proteins

•

these proteins usually make contact with the major groove where functional groupson the bases are exposed. This is how a specific nucleotide sequence isrecognized by a protein. Consequently nucleotide recognition sites are often

about 10-11 nucleotides apart.



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lambda bacteriophage cII DNA binding protein (λcII)

Relevant Dimensions

Major groove 10 ÅMinor groove 5 Å

α-helix 5 Å

5’-AAACGTTGCGTTTGTTTGCCACGAACCATA-3’

3’-TTTGC AACGCAAACA AACGGTGCTTGGTAT-5’

recognition/binding site (red) in DNA for lambda cII protein


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molecular interaction

pattern matching

BIOL3073

Biochemistry of Gene Expression


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Major and minor groove groups available for molecular interaction


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So, the major groove is the primary site of specificinteraction by DNA binding proteins because:

-dimension of major groove vs minor groove fits a protein α-helix

-more information exposed (i.e. more molecular interaction sites)

-more diversity in pattern of molecular interaction sites


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In this discussion of nucleotide and nucleic acid structure,

notice how you needed knowledge of:

-molecular interactions-acid base concepts

Lecture 7 - Nucleotides and Nucleic Acids

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