Quiz 6

Functions of Nucleic Acids

Storage of genetic info (DNA)
Transmission of genetic info (mRNA)
Protein synthesis (tRNA and rRNA)
Processing of pre-mRNA (small nuclear RNA)

Functions of Nucleotides

Energy for metabolism (ATP)
Enzyme cofactors (NAD+)
Signal transduction (cAMP)

syn conformation

Which conformation is this nucleoside?

anti conformation

Which conformation is this nucleoside? Hint: It's favored in normal DNA.

3’,5’-phosphodiester bonds

The Nucleic Acid Backbone (same strand) is held together by what bond?

3'

The new nucleotide always gets added to what end (on existing strand)?

Structure of RNA

Always composed of a single-strand
Primary structure is 5' --> 3' sequence
Can adopt 2 prime and 3 prime structures

2

How many H-bonds are between A-U?

3

How many H-bonds are between G-C?

lacks OH group (RNA can undergo rapid hydrolysis)

Why is DNA double helix more stable than RNA in alkaline conditions?

Structure of DNA

Two polynucleotide strands wind together to form a long, helical molecule.
Strands run antiparallel.
Negatively charged phosphate groups are all situated on the exterior surface.
Base pairs (planar) stack together on the interior through hydrophobic interactions and van der Waals forces (called base stacking). Allows them to more easily H-bond.
Hydrogen bonds formed between A=T and CΞG bases.
Strands run in opposite directions (antiparallel).
Double-helix = 2o structure
Strands are held together through interchain hydrogen bonds with complementary bases (base pairing).

2

How many H-bonds between A-T?

3

How many H-bonds between C-G?

Rosalinda Franklin

Who used X-ray diffraction methods to discover that there are two forms of DNA, A and B (more common)

Watson and Crick

Who used model-building to solve the DNA structure problem?

DNA is helical

In this picture, what does the cross mean?

The phosphate-sugar backbone is on the outside

In this picture, what do the diamonds mean?

The sugar-phosphate backbones of the helix are not equally spaced along the helix axis

Why does DNA have major and minor grooves?

Major groove

What groove is large enough to accommodate an alpha helix from a protein?

They influence DNA binding by regulatory proteins

Why are local variations in DNA conformation (chromatin) important in the regulation of gene expression?

conformational variations of the sugar residues and the relative orientations of the planes of the bases between the two strands

Additional forms of the double helix exist as a result of:

B

What is the major conformation of DNA?

Disruption of hydrogen bonds (temperature, pH, ionic strength)

Nucleic Acids can be denatured and renatured through:

Higher

Does a higher G-C content result in a higher or lower melting temp?

Hyperchromic effect

decrease in A280 from free nucleotides to single strands to double strands

its UV absorbance increases by 30-40% (hyperchromic shift). (stacked base pairs in native DNA absorb less light)

When DNA is heated to >80oC (unwinding of the DNA double helix)...

base composition, DNA length (longer DNA, higher Tm), pH and ionic strength (high salt increases Tm)

The midpoint of melting (Tm) depends on:

Replication by DNA polymerase

Analogs of glutamine

Chemotherapeutic/Antiviral Drug used to synthesize nitrogenous bases. Competitively inhibits enzyme in purine synthesis.

Truvada (emtricitabine/tenofovir)

Chemotherapeutic/Antiviral Drug that inhibits reverse transcriptase. Affects ability to add new nucleotides during genome replication.

Lipids

Class of biomolecules defined by low solubility in water and high solubility in nonpolar solvents (largely hydrocarbon in nature).

storage, membrane, specific biological activities

Classes of lipids:

Fatty acids

The simplest lipids, which are also constituents of many more complex lipids.
Their basic structure exemplifies the amphipathic lipid model:
a long hydrocarbon chain (“tail”) and a terminal carboxyl group (“head”)
Almost all have an even # Cs
Most are unbranched
Occur in large amounts in cells but are rarely in a free, uncomplexed state

Saturated fatty acid

no double bonds between carbons in the chain

Monounsaturated

one double bond between carbons in the chain (prevents close packing and increases flexibility)

Polyunsaturated

more than one double bond in the alkyl chain (prevents close packing and increases flexibility)

Partial hydrogenation

What is the process done to cooking oils that produces trans fatty acids to improve their shelf life?

triacylglycerols (TAGs) or triglycerides (fats)

Energy storage lipid
Fatty acid esters of glycerol
Three fatty acids each in ester linkage to 1 glycerol
Stores chemical potential energy in nonpolar covalent bonds (C-C and C-H)

Waxes

Used as storage and water repellent
Esters of long-chain (C14 to C36) saturated and unsaturated fatty acids with long-chain alcohols (C16 to C30)

lipid bilayers.

In cells, lipids do not pack well into micelles but rather tend to form...which are amphipathic and consist of two leaflets of lipid monolayers.

Phospholipids

hydrophobic region attached to polar group by phosphate

Glycolipids

hydrophobic region attached to polar group (sugar)

Sterols

rigid system of four fused hydrocarbon rings

Glycerol backbone

glycerophospholipid
2 fatty acids at C1 & C2 (usually one saturated & one unsaturated)
C3 carbon has a highly polar or charged group attached through a phosphodiester bond

Sphingosine backbone

phosphosphingolipid
one fatty acid at C2
C1 carbon attachment to head group