Lecture 2 - Basic molecular mechanisms and nuclei acids

Question 1

4 molecular genetic processes

Answer 1

1. Transcription 2. RNA processing 3. Translation 4. Replication

Question 2

Where 4 molecular genetic processes occur

Answer 2

Transcription + RNA processing + Replication = In nucleus. Translation = In cytosol

Question 3

4 cell cycle phases

Answer 3

M, G1, S, G2 , M, …

Question 4

M cell cycle phase (2 things)

Answer 4

Mitosis (nuclear division) and Cytokinesis (cytoplasmic division)

Question 5

G1 phase (key event)

Answer 5

Growth + Transcription initiation

Question 6

S

Answer 6

DNA replication

Question 7

G2 (nothing in particular)

Answer 7

?

Question 8

DNA : what it contains and where info is stored

Answer 8

1. Contains all info required to build CELLS and TISSUES of an organism
2. Info stored in UNITS called GENES

Question 9

Transcription definition

Answer 9

Information stored in DNA is copied into RNA for eventual use

Question 10

Translation definition

Answer 10

Process where info is used to create a protein of specific amino acid sequence

Question 11

DNA/RNA basic definition (biochem)

Answer 11

Linear polymers of monomers called nucleotides

Question 12

Nucleotides (what is it)

Answer 12

pentose phosphate (which backbones deoxyribose in DNA/ribose in RNA) + purin (A G) or pyrimidin base (T C U)

Question 13

Why DNA more stable (2 reasons) than RNA

Answer 13

1. Double stranded. H bonds 2. No hydroxyl on carbon 2’. Hydroxyde catalizes slow hydrolisis of phosphodiester bonds between nucleotides at neutral PH

Question 14

Effect of base pair composition

Answer 14

DNA more stable if higher % of G-C base pairs because G-C = 3 H bonds and A-T = 2 H bonds so breaking it down is more energy requiring

Question 15

What would be optimal for high transcription

Answer 15

A-T rich DNA (less energy requiring)

Question 16

Directionality explanation

Answer 16

Free 5’ phosphate at one end. Free 3’ hydroxyl at other hand. 2 Antiparallel strands

Question 17

Phosphodiester bond (what is it)

Answer 17

Link between 3’ hydroxyl group of one base to 5’ phosphate group of adjacent base

Question 18

Natural pair bonding (RNA and DNA) and why + name

Answer 18

A-T (DNA) and A-U (RNA) (cause 2 H bonds) and G-C(cause 3 H bonds) (Watson-Crick base pairing)

Question 19

Exceptions to natural pair bonding (2)

Answer 19

1. G-T and C-T possible (fits within double helix) and possible in artificial DNA in lab
2. G-U exists in double-helical regions of RNA (can exist if this form of RNA occurs)

Question 20

Groove definition

Answer 20

Space between two intertwined strands

Question 21

Particularities of A DNA if compared to B DNA (3)

Answer 21

1. Obtained when most of water is removed from DNA (under lab condition)
2. Wider + deeper major groove, More narrow and shallow minor groove
3. RNA:DNA or RNA:RNA exists in A DNA form in cells and in vitro

Question 22

Why DNA flexible

Answer 22

No H bonds parallel to its long axis

Question 23

What can bend DNA

Answer 23

DNA binding proteins

Question 24

DNA bending advantage

Answer 24

Necessary for it to be packed in chromatin

Question 25

TBP ? what does it do

Answer 25

TATA box-binding protein. Must attach to promoters to most of the eukaryotic genes in order to transcript them. (Bends and untwists DNA)

Question 26

how transcription initiated

Answer 26

promoters in genes

Question 27

who absorbs more UV light ssDNA or dsDNA

Answer 27

ssDNA

Question 28

what stabilizes dsDNA and allows it to exist at higher Temp.

Answer 28

G-C base pairs

Question 29

How to denature dsDNA. what phenomenon do theses conditions influence ?

Answer 29

1. Raise Temp. 2. Extremes of pH. 3. Reducing ionic concentration 4. Agents that destabilize hydrogen bonds (formamide or urea). Nucleic acid hybridization depends upon these properties.

Question 30

how to renature ssDNA (+ one condition)

Answer 30

Reverse conditions (low temp, normal pH, high ionic conentration). + Renaturation depends upon base-pairing so a complementary strand/sequence must exist.

Question 31

Name of process by which ssDNA (or RNA) anneals to complementary DNA or RNA

Answer 31

Nucleic acid hybridization

Question 32

What form of DNA appears in prokaryotes and viruses. Two forms and enzyme that changes them.

Answer 32

Circular. Supercoiled to relaxed circle (Topoisomerase 1)

Question 33

How replication initiated

Answer 33

Complexes attract enzymes. Chromatory modelling complexes recruited to replication site and make DNA accessible.

Question 34

Why DNA flexible

Answer 34

No H bonds along its axis

Question 35

Difference between RNA and DNA 3D structure formation

Answer 35

DNA : By interacting with proteins | RNA : Reacts with itself

Question 36

Specific structures of RNA (3) and how they form

Answer 36

Some regions base-pair to form 1. Hairpin 2. Stem-loop (with double-helical stem region) and 3. Pseudoknot (2 stems and 2 loops)