Nucleic Acids - Exam 2

DNA

Stores genetic information in cells and many viruses

RNA

Transfers and interprets genetic information

Nucleotides contain…

a pentose sugar, and a phosphate group

Nucleosides contain…

a pentose sugar and a phosphate group

Ribose

A pentose in RNA containing 2’-OH

Deoxyribose

A pentose in RNA containing 2’-H

Purines

2 fused rings → Cytosine, Thymine, Uracil

Pyrimidine

1 ring → Adenine & Guanine

Nucleic acids absorb UV light near…

260 nm

T or F: In a nucleotide, the base is attached to C1’ of the sugar and the phosphate is attached to C5’

T

T or F: In a nucleic acid chain, a phosphodiester bond links the 3’ bond links the 3’-hydroxyl of one nucleotide to the 5’-phosphate of the next

T

T or F: Nucleic acid sequences are written in the 3’→5’ direction

F

T or F: The DNA double helix is left-handed

F

T or F: The minor groove displays more sequence-specific patterns of hydrogen-bond donors and acceptors than the major groove

F

RNA is chemically less stable than DNA because…

the 2’-hydroxyl of ribose can attack the adjacent phosphodiester bond

T or F: Depurination removes a purine base from DNA, creating an abasic site

T

T or F: Hairpin structures can form in RNA but never in DNA

F

Sugar-phosphate backbone is…

Negatively charged

T or F: Hoogsteen base pairing uses a different edge of the base than Watson-Crick pairing and can allow a third DNA strand to bind in the major groove, forming a triple helix

T

G-quadruplexes form when 4 __ pair with one another through Hoogsteen-type H bonds

G

T or F: Intramolecular base pairing allows a single RNA strand to form double-helical stems

T

T or F: The cloverleaf secondary structure of tRNA folds further into an L-shaped tertiary structure

T

What are the 2 major interactions that stabilize the double helical structure of DNA?

Base pairing H bonds & base-stacking interactions

How many H bonds does G-C contain?

3

How many H bonds does A-T contain?

2

Base stacking involves…

π interactions, van der Waals contacts, and hydrophobic effects

Adjacent bases stack about…

3.4 Å apart

What can denature DNA strands?

Heat or extreme pH

Mirror repeats

DNA repeat that have symmetry within the individual strands

Palindromes

DNA repeat that have symmetry across the 2 strands

Hoogsteen pairing

Uses an alternative base edge; can make a third strand, can support DNA triple helices

Deamination

Removes an amino group from base; C becomes U

tRNA (transfer RNA)

Positions AAs and anticodons during translation

T or F: tRNA functions as an extended single strand without stable secondary or tertiary structure

F

T or F: RNA has a flexible backbone with multiple rotatable dihedral angles, which helps it fold into diverse tertiary structures

T

T or F: Divalent cations such as Mg²⁺ destabilize RNA tertiary structure by increasing repulsion between phosphate groups

F

Riboswitches

Bind metabolites and regulate gene expression

Ribozymes

Catalyze biochemical reactions

Ribosome

Uses rRNA as its catalytic core

T or F: Riboswitches are RNA elements, often in the 5’ UTR of bacterial mRNAs, that bind small molecules such as metabolites

T

T or F: Ligand binding to a riboswitch changes the RNA structure, which can altar transcription or translation of a downstream gene

T

T or F: Ribozymes are protein-based enzymes that digest RNA

F

2 major types of reactions for ribozyme catalysis

RNA processing reactions and peptide-bond formation

RNA processing reactions

Breaking and joining RNA phosphodiester bonds

Peptide-bond formation

Linking AAs during protein synthesis

Catalysis depends on…

rRNA