Biochemistry Lecture 1

Front 1

Nucleoside

Back 1

base + sugar

Front 2

Nucleotide

Back 2

Nucleoside (base+sugar) + phosphate group

Front 3

Nucleoside and Nucleotide

Back 3

Front 4

Nucleotide Structure

Back 4

Front 5

Phospho diester bond requires energy, derived from cleaving other two phosphate groups off

New nucleotides always added at 3' end!

Back 5

Front 6

Base stacking

Back 6

Hydrophobic interactions between adjacent bases in a single nucleic acid strand - hydrophilic pushed to outside and hydrophobic stays on inside

Front 7

DNA structure - Complementarity

Back 7

2 strands that run anti-parallel to each other, held together by hydrogen bonds between bases on opposite chains - creates a minor and major groove in the structure. Major groove is where most interactions take place

Front 8

Structurally relevant forms of DNA

Back 8

A and B turn to the right – B happens in Nature
Z turns to the left and only occurs in lab

Front 9

Organizational structure of DNA

Back 9

DNA strands wrap around histones => histones bind closely together => make up chromosome

Front 10

Cell Cycle G1 Phase

Back 10

Biosynthetic activities are at a high rate

Synthesis of millions of proteins required in S-Phase for DNA replication

Front 11

Cell Cycle S Phase

Back 11

DNA replication phase, ends when DNA has "effectively doubled"
Fastest phase of the cell cycle

Front 12

Cell Cycle G2 Phase

Back 12

Synthesis of millions of proteins required in mitosis

Creation of microtubules and centrosomes necessary for mitosis

Front 13

Cell Cycle Mitosis phase

Back 13

cell separates chromosomes in its cell nucleus into two identical sets in two nuclei - the daughter cells

Front 14

Cell cycle regulation - Cyclins

Back 14

Cyclins - proteins that control cycle by activating cyclin-dependent kinase (Cdk) enzymes (Cdk stay at constant level)

Cyclins build up to certain points before moving cell cycle to next phase

Front 15

Cell cycle regulation - Cyclin dependent kinases

Back 15

Enzymes that are normally off unless activated by cyclins, they activate other proteins via phosphorylation - continue in cell cycle regulation

Front 16

Maturation promoting factor
S-phase promoting factor

Back 16

Must be bound by cyclins and complex subsequently can activate the machinery to keep the process going

Front 17

Helicase

Back 17

Hydrolyzes (breaks down with water) H bonds and unwinds DNA - works best in major groove

Front 18

Topoisomerase

Back 18

Relieves supercoiling/stress ahead of the helicase molecule, cuts through phosphodiester bond

Front 19

Single Strand Binding Protein (SSBP)

Back 19

- Binds to single strands and protects them from destruction by cell
- Prevents strands from re-annealing
- Tells replicating factors where to bind

Front 20

Origin of replication complex

Back 20

multi sub-unit complex that binds chromatin to DNA strand, at origin of replication - necessary for DNA replication to occur

Front 21

Primase (aka RNA polymerase)

Back 21

adds a 10-15 nucleotide primer to unwound DNA strand, this triggers DNA polymerase to attach and begin DNA synthesis

Front 22

DNA polymerase alpha (α)

Back 22

Begins synthesizing new DNA
- has low processivity (does not stay bound to DNA well)
- needs RNA primer to begin
- can only build in the 5'-->3' direction

Front 23

DNA polymerase Delta (δ) and Epsilon (ε)

Back 23

Take over replication after DNA polymerase alpha
- have better processivity due to Proliferating Cell Nuclear Agent (PCNA)

Front 24

Proliferating Cell Nuclear Agent (PCNA)

Back 24

Protein that acts to increase processivity for polymerase delta and epsilon

Front 25

Geminin

Back 25

Stops newly synthesized DNA from re-replicating into new strands

Front 26

Flap endonuclease 1 and RNAase H

Back 26

removes RNA primers

Front 27

DNA polymerase Delta (δ)

Back 27

Adds in new DNA bases to missing gaps on lagging strand

Front 28

DNA Ligase

Back 28

Comes in after DNA polymerase Delta (δ) and seals the new bases in place

Front 29

Semi-conservative replication

Back 29

During DNA replication each new daughter strand will have an original parent strand and a newly created daughter strand

Front 30

Process of DNA replication (quick)

Back 30

helicase unwinds -> ssbp binds -> topisomerase releases tension -> origin of replication complex binds -> RNA primase forms primer -> DNA poly alpha starts replication -> DNA poly delta/epsilon take over -> geminin binds -> RNA primers removed -> gaps filled in/sealed -> histones bind and wrap

Front 31

Okazaki fragment

Back 31

Short, newly synthesized DNA fragments that are formed on the lagging template strand

Front 32

Fidelity

Back 32

How accurate DNA polymerases can copy the DNA - held high due to exonuclease proofreading

Front 33

3'-5' Exonuclease proofreading

Back 33

Enzymatic activity that goes back and essentially removes and replaces mismatched nucleotides

Front 34

S Phase promoting factor (SPF)

Back 34

S-CDK-protein that initiates the start of the S-phase

Front 35

Mitosis promoting factor (MPF)

Back 35

M-CDK-protein that initiates the start of the mitosis-phase