BIOC 3021, Ch.12 Nucleosides Nucleotides DNA RNA

6 Nucleic Acids Functions

• Store of genetic information as DNA

• Carries and translates genetic information

• Carries out enzymatic reactions

• Energy storage molecules

• Signaling molecules (cAMP)

• Redox coenzymes (NADH, NADPH)

the 4 major biopolymers

Proteins, carbohydrates, lipids, and nucleic acids

the 3 monomer units of nucleic acids

nitrogenous base, sugar, and phosphate

location where nucleic acids are concentrated

the nuclei

At a pH of 7, the phosphate group of nucleic acids are ______________________.

basic and negatively charged

SO, DNA/RNA are anionic negatively charged compounds.

2 types of Nitrogenous bases

Pyrimidines and Purines

Pyrimidines physical features

One 6” heterocyclic ring

Smaller compound

Purines physical features

One 6” ring fused to a 5” ring

Larger compound

Once pyrimidines is combined to a sugar, the suffix ________ is used

-idine

Once purines is combined with a sugar, the suffix ________ is used

-osine

3 types of pyrimidines

Cytosine

Thymine (only found in DNA)

Uracil (only found in RNA)

2 types of purines

Adenine

Guanine

T/F, Purines can ONLY bond with Pyrimidines

TRUE

pyrimidines bonding with other pyrimidines is energetically ______________, because ___________________.

unfavorable // they are too far apart

purines bonding with other purines is energetically ______________, because ___________________.

unfavorable // they are too close together

In A/T bonding, the distance between the  1’ carbon of the deoxyribose in a DNA chain is ___ nm apart.

1.1 nm

In G/C bonding, the distance between the  1’ carbon of the deoxyribose in a DNA chain is ___ nm apart.

1.08 nm

cytosine base structure

Amino group @ 4’

carbonyl oxygen @ 2’

thymine base structure

carbonyl oxygen @ 2’ AND 4’

methyl group @ 5’

uracil base structure

carbonyl oxygen @ 2’ AND 4’

adenine base structure

amino group @ 6’ on 6” ring

guanine base structure

amino group @ 2’ on 6” ring

carbonyl oxygen @ 6’ on 6” ring

bases have conjugated double bond systems which allows them to _______.

absorb UV light

the ability of nitrogenous bases to absorb UV light is measured by ___________ using a ____________.

Lambert-Beer Law // spectrophotometer

Lambert-Beer Law

• A = εbc // where…

  • A = absorbance of solution

  • ε = molar coefficient (M^-1cm^-1)

  • b = pathlength of light (cm)

  • c = concentration of solution (M)

A spectrophotometer is composed of..

• UV light source

• A slit

• Silica cuvette

• A detector

A nitrogenous base is combined with ribose or deoxyribose on a specific H+. Name the ring

pyrimidines = on the 6” ring

purines = on the 5” ring

2 types of sugar components in nucleic acids

β-D-Ribofuranose

2-Deoxy-β-D-Ribofuranose

β-D-Ribofuranose is different from 2-Deoxy-β-D-Ribofuranose because _______________.

• β-D-Ribofuranose (RNA)

  • hydroxyl group @ 2’ on furanose ring.

• 2-Deoxy-β-D-Ribofuranose (DNA)

  • H atom @ 2’ on furanose ring.

When a base combines with a sugar, _______ is released and a __________ is produced.

water // nucleoside

a nucleoside is composed of

a base and a sugar

a nucleotide is composed

base, sugar, AND at least 1 phosphate group

In nucleotides, the phosphate group can be esterified to any hydroxyl group of the sugar residue. Name is sites of each of the sugars where this happens.

For ribose, this can happen on the 3’ or 5’ OHs

For deoxyribose, this can happen on the 2’, 3’ or 5’ OHs

what bond holds sugars together

3’-5’ phosphodiester linkage/bond

what holds the base and sugar together

β-N-glycosidic linkage (glycosidic bond)

rotation is restricted about the N glycosidic bond of a sugar and base, which gives 2 possible orientations 

• Anti, base and sugar are rotated away from each other

  • Favored in most circumstances

• Syn, base and sugar are rotated parallel to each other

Adenosine 5’- triphosphate is abbreviated to ___.

 5’-ATP or just ATP

ATP is composed of

3 phosphate groups linked via 2 phosphoanhydride bonds, a ribose furanose, and a adenosine base.

phosphoanhydride bonds function as a ___________.

reservoir of chemical energy that's released by hydrolysis.

In ATP, a phosphate group is linked to a ribose furanose via a ____________________.

phosphodiester bond

When ATP reacts with H₂O, what is produced

ADP and an inorganic phosphate

When ATP + H₂O → ADP + inorganic phosphate, how much energy is released?

7.3 kcal/mol of energy (30.5 kJ/mol)

ATP functions to _______.

Promotes the synthesis of biopolymers for muscle contraction

Energies transport of ions and metabolites across biological membranes

deoxyadenylyl-(3’,5’)-deoxyguanosine is abbreviated as ____________.

• dApdG

• (d)ApG

• (d)AG

Naming a molecule starts at the___’ end in DNA or RNA

5’

what is supercoiling

DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than one turn per 10 base pairs) from its normal relaxed state.

DNA double helix characteristics

• anti parallel strands (one runs 3’-5’ the other runs 5’-3’)

• Opposing strands are complementary in nitrogenous bases

• Negatively charged phosphate groups are on the outside of the helix

• nitrogenous bases are on the inside of the helix

• 10 base pairs per helix turn

• Contains major and minor grooves

• is stabilized by aromatic stacking of bases

how many hydrogen bonds are between A and T

2

how many hydrogen bonds are between G and C

3

Watson and Crick, 1950s published a paper proposing the _______________.

features of a DNA double helix and a mechanism for DNA replication dubbed the “semi-conservative replication”

What did the Meselson Stahl Experiment prove?

DNA replicated semi-conservatively, meaning that each strand in a DNA molecule serves as a template for synthesis of a new, complementary strand.

How did the

used bacteria grown in a medium containing heavy nitrogen (N15) to label their DNA, then transferred them to a medium with normal nitrogen (N14) to replicate, allowing them to isolate and analyze the DNA's density using density gradient centrifugation, which revealed that the newly replicated DNA had an intermediate density, supporting the semi-conservative model of DNA replication where one strand of the parent DNA is conserved in each new DNA molecule; this meant that each new DNA molecule contained one strand from the original parent molecule and one newly synthesized strand.