ch 4 - nucleic acids + RNA

nucleotides

The *monomers of nucleic acids*; consist of a 5-carbon sugar (pentose), phosphate group, and nitrogenous base

Two types:

- Deoxyribonucleotides in DNA

- Ribonucleotides in RNA

Question: What type of nucleotide is represented in the picture? How do you know? (hint: look at sugar)

DNA

Nucleic acid made of deoxyribonucleotides (*deoxyribose* sugars and adenine, *thymine*, cytosine, guanine bases)

- Made of *two strands* that form a *double helix*

- Both strands have a hydrophilic sugar-phosphate backbone

- Stores information for its own *semi-conservative* replication and for the creation of proteins and RNA molecules

RNA

Nucleic acid made of *ribonucleotides* (*ribose* sugars and adenine, *uracil*, cytosine, guanine bases)

- *Single stranded!*

- Has wider variety in function; involved with catalysis (rRNA, snRNA, ribozymes), protein creation (mRNA, tRNA, rRNA, miRNA, snRNA), and more

deoxyribose

The 5-carbon sugar inside deoxyribonucleotides (that form DNA)

Compared to ribose, deoxyribose lacks the additional hydroxyl group on the 2' carbon

ribose

The 5-carbon sugar inside ribonucleotides (that form RNA)

Compared to deoxyribose, ribose has an additional hydroxyl group on its 2' carbon that makes RNA more reactive

pyrimidines

*Single-ringed* nitrogenous bases; refer to cytosine, uracil (in RNA), and thymine (in DNA)

Helpful memorization tool: CUT (cytosine, uracil, thymine) the Pyramid

purines

*Double-ringed* nitrogenous bases; refer to adenine and guanine

Helpful memorization tool: Pure As (adenine) Gold (guanine)

Phosphodiester bond

Bonds formed between the 3' *hydroxyl group* of a nucleotide and the 5' *phosphate group* of another nucleotide through dehydration synthesis

Nucleotides are linked together by phosphodiester bonds to create nucleic acids.

Nucleic acid polymerization

An input of energy is required to polymerize nucleic acids; this energy is obtained from the hydrolysis of phosphate groups from activated nucleotides (triphosphates)

Nucleic acid directionality

Nucleic acids are read, replicated, and created in a *5' → 3' direction*

In reference to sugar-phosphate backbone: 5' free phosphate group → 3' free hydroxyl group ... new nucleotides can only be added to a 3' free hydroxyl group

complementary base pairing

In a *double-stranded DNA molecule*, the amount of adenine = the amount of thymine (A = T) and the amount of cytosine = the amount of guanine (C = G)

These nitrogenous bases are linked together by hydrogen bonds across strands

DNA and RNA primary structure

The same for both DNA (uses thymine) and RNA (uses uracil); refers to the *5' → 3' order of nucleotide bases*

DNA secondary structure

An *antiparallel double helix*, stabilized by complementary base pairing (hydrogen bonding) and base stacking (hydrophobic and van der Waals interactions)

DNA tertiary structure

*Supercoiling and clumping* around positively charged histone proteins (nucleosomes)

RNA secondary structure

*Stem-and-loop configuration* stabilized by hydrogen bonding on the *same single strand* of RNA

RNA tertiary structure

*Pseudoknot* stabilized by hydrogen bonding between *distant* nitrogenous bases on the *same single strand* of RNA

DNA and RNA quaternary structure

Do DNA and/or RNA have a quaternary structure? That is up to you to decide...BUT we recommend recalling proteins' quaternary structure (the aggregation of multiple polypeptide subunits). Are there examples where multiple DNA and/or RNA subunits aggregate to form a new functional unit?

Gel electrophoresis

Experimental technique used to separate molecules based on size and charge

Usable with both DNA (- charge) and proteins (- charge given through SDS denaturant); both will therefore migrate toward the positive electrode

Smaller molecules will travel farther distances on the gel

Darker bands = more DNA / protein is present in that sample