Nucleotides +. Nucleic Acids

Question 1

What is the difference between nucleosides and nucleotides?

Answer 1

Nucleosides: Pentose + purine or pyrimidine base

Nucleotides: Pentose + Purine or pyrimidine base + Esterified phosphates.

Question 2

What are the pKas of phosphate oxygens on a nucelotide?

Answer 2

1-6, ionized at pH 7

Question 3

What are the 2 purine bases?

Answer 3

Adenine and guanine

Question 4

What are the two Pyrimidine bases?

Answer 4

Cytosine, Thymine, Uracil

Question 5

How are bases coupled to pyrimidines and purines?

Answer 5

C1 of the sugar is coupled via B linkage with N9 of a purine, or N1 oof a pyrimidine.

Question 6

Where are phosphates bound in nucleotides?

Answer 6

Usually C4, but may be C2, C3 or C2 AND 3 (cyclic)

Question 7

How are nucleotides used as energy currency?

Answer 7

5’-OH group of nucleosides may be esterified to pyrophosphate (PPi) to diphophate or triphosphate.

Question 8

How are nucleotide units held together?

Answer 8

Held together via phosphodiester bonds. 3’ OH binds to phosphate of 5’ end.

Question 9

What was found in Watson and Crick’s Xray diffraction data?

Answer 9

1. 2 DNA strands coil to form a right handed double helix where DNA strands run antiparallel
2. Sugarphosphates are exposed to water and hydrophobic base pairs form a hydrophobic interior.
3. Bases interact via van der waals, dipole dipole, and H bonding.

Question 10

How many bonds does A-T form, and how many bonds does C-G form?

Answer 10

A-T: 2 hydrogen bonds

C-G: 3 hydrogen bonds

Question 11

Why are nucleic acids more flexible than proteins?

Answer 11

Nucleic acids have 7 bonds that are able to rotate to adopt torsion angles, while proteins only have 2.

Question 12

How does DNA melt?

Answer 12

DNA exhibits random dynamic localized separation of bases and reforming of base pairs/stacking. Increased T causes increased motion, shifting equilibrium to separation.

Question 13

How does UV light cause melting?

Answer 13

Melting causes increased absorption of UV light since base pairs are no longer interacting (which prevents UV absorption in single nucleotides).

Question 14

What is tM?

Answer 14

melting temperature where half of the base pairs in DNA are denatured (single stranded) and half are still double stranded

Question 15

what does it mean when DNA has a higher Tm

Answer 15

DNA has a higher Gc percentage as GC base pairs have 3 hydrogen bonds, which promote stronger stacking than AT.

Question 16

What are DNA polymerases?

Answer 16

Enzymes that replicate the genome via strand separation and synthesis of a daughter strand. Often assisted by additional proteins to avoid mutations.

Question 17

Why is RNA chemically less stable than DNA?

Answer 17

RNA has a functional OH group at C2’ which under alkaline conditions (OH-) can bind the phosphate’s O’s to C2 and C3 to create a cyclic nucleotide.

Question 18

What is the hairpin double helix?

Answer 18

Structure of single stranded RNA where its own bases pair with themselves. C doesn’t necessarily equal G, and A doesnt equal T. Example of secondary structure.

Question 19

What are examples of tertiary structure?

Answer 19

transfer RNA and hammerhead ribozymes.

Question 20

What are the 4 major types of RNA found in cells?

Answer 20

1. mRNA
2. tRNA
3. rRNA
4. miRNA

Question 21

What is mRNA?

Answer 21

Conveys information from a particular gene to the protein synthesizing machinery during translation. Base sequence = coding strand on DNA.

Question 22

How are mRNA capped?

Answer 22

5’ terminus is capped by 7-methylguanosine triphosphate linked to ribonucleoside at 5’OH. Helps ribosome recongnize mRNA and protect it from degradation.

Question 23

How is mRNA tailed?

Answer 23

3’ end have a sequence of 20-250 adenine nucleotides involved in stabilizing mRNA against degradation and helping ribosome recognize mRNA.

Question 24

What are tRNA’s?

Answer 24

Cloverleaf adaptors and carriers of amino acids used for translation of mRNA info into protein. 20+ types, each with an AA bound at 3’ end and anticodon on middle leaf.

Question 25

What is rRNA?

Answer 25

RNA complexed with proteins that works as a machine to synthesize proteins based on mRNA info interpreted by tRNA.

Question 26

What are the 2 major ribosomal subunits in eukaryotes?

Answer 26

60S subunit (large): 5S, 28S, 5.8S

40S subunit (small): 18S + 30 polypeptides

Question 27

What is miRNA?

Answer 27

Very small RNA cut from long precursors by ribonucleases. Complimentary base pair with particular mRNA’s to prevent them from being used by ribosomes to syntehsize protein which prevents overproduction of particular proteins during biological development.

Question 28

What is deamination?

Answer 28

Mutation where cytosines are replaced by uracil.

Question 29

What is depurinaytion?

Answer 29

Removal of a purine base from phosphodiester backbone.

Question 30

How does UV light create mutations in thymine?

Answer 30

induces formation of cyclobutane dimer (C5 and C6 of each thymine) and 6-4 photoproduct

Question 31

What are mutagenic agents?

Answer 31

chemicals that cause mutations in DNA and are often carcinogens that affect normal cell growth patterns. (e.g. radiation, ooxidative damage via H2O2, chemicals)