Cell Lectures 7, 8, 9

Front 1

Allopurinol

Back 1

* is a purine analog used to treat Gout (excess uric acid)
* All purines are catabolized to uric acid, which has low water solubility
* Allopurinol is oxidized to alloxanthine (AKA oxypurinol) by xanthine oxidase
* Alloxanthine binds to xanthine oxidase and acts as a competitive inhibitor bound to the active site
* As a result, the patient excretes a mix of uric acid, xanthine and hypoxanthine that is more soluble than uric acid alone

Front 2

Tautomers

Back 2

* structural isomers that differ in the location of protons.
* Keto, enol / amino, imino
* pH dependent.
* Spontaneous tautomeric shifts of DNA bases can cause point mutations

Front 3

In nucleotides, the pentose ring is attached to the base via what kind of bond?

Back 3

N-glycosidic bond

Front 4

DNA polymerase

Back 4

* main enzyme in DNA replication. It catalyzes the joining of deoxyribonucleoside 5′- triphosphates (dNTPs).
* DNA polymerase is a name for a whole sweep of enzymes that “grow” DNA
* Synthesize DNA only in the 5′ to 3′ direction.
* Add new dNTPs only to a primer strand that is hydrogen-bonded to the template; they can’t initiate DNA synthesis from free dNTPs.

Front 5

Primase

Back 5

enzyme that synthesizes short fragments of RNA that act as primers for the lagging strand

Front 6

leading strand

Back 6

only one strand of DNA is synthesized in a continuous manner in the 5′ to 3′ direction

Front 7

lagging strand

Back 7

* formed from short (1–3 kb), discontinuous pieces of DNA that are synthesized backward
* these small pieces are called Okazaki fragments

Front 8

ligase

Back 8

Okazaki fragments joined by this enzyme

Front 9

RNase H

Back 9

* In eukaryotic cells, RNA primers are removed by RNase H, which degrades the RNA strand of RNA-DNA hybrids, and 5′ to 3′ exonucleases.
* The resulting gaps are then filled by Polymerase δ and the fragments joined by DNA ligase

Front 10

polymerase accessory proteins

Back 10

* Clamp loading protein (replication protein C) [RPC]
* sliding clamp protein (proliferating cellular nuclear antigen) [PCNA]
* RPC loads PCNA onto the DNA and then dissasociates
* PCNA loads polymerase onto the primer and maintain its stable association with the template

Front 11

Helicases

Back 11

* catalyze the unwinding of parental DNA ahead of the replication fork
* mutations in Helicases have been implicated in cancer predisposition and aging

Front 12

Single-stranded DNA-binding proteins

Back 12

then stabilize the unwound template DNA so that it can be copied by the polymerase.

Front 13

Topoisomerases

Back 13

* as the DNA unwinds, the DNA ahead of the replication fork is forced to rotate, which would cause circular DNA molecules to twist.
* Topoisomerases catalyze reversible breaking and rejoining of DNA strands. * the transient breaks serve as swivels that allow the two strands to rotate freely around each other.

Front 14

Bacterial type II topoisomerase inhibitors

Back 14

* DNA replication is an attractive target for antimicrobial agents (this is one such agent)
* ex. Ciprofloxacin, nalidixic acid

Front 15

Human type II topoisomerase inhibitors

Back 15

* DNA replication is an attractive target for chemotheraputic agents (this is one such agent)
* ex. Etoposide, doxorubicin

Front 16

autonomously replicating sequences (ARSs)

Back 16

* Eukaryotic origins of replication were first studied in the yeast S. cerevisiae.
* They were identified as sequences that can support replication of plasmids in transformed cells.
* include an 11-base-pair core sequence common to many different ARSs.
* The core sequence is the binding site of a protein complex (origin recognition complex, or ORC) that is required for initiation of DNA replication.

Front 17

gene

Back 17

is a contiguous segment of DNA, which contains a minimum of :
* A start and stop location and encodes for a specific RNA
- This RNA may be translated into a polypeptide, but may also code for structural or regulatory RNAs
* A binding site for the RNA polymerase (promoter)
* Associated with chromosomal regions which assist in regulation of expression, e.g.: Operator, Enhancer

Front 18

alternate splicing

Back 18

Introns also allow exons of a gene to be joined in different combinations, resulting in different proteins from the same gene