DNA Replication

Remember: DNA -(__)--> RNA -(__)--> protein

                     I– (__) -> DNA

transcription, translation

replication

DNA makes __ makes __

RNA : protein

RNA->DNA? __

Rare (viruses)

Protein->RNA: __

no

Associated with cell division, either __ (production of two daughter cells) or __ (produces gametes like sperm and egg cells)

mitosis : meiosis

Bases are ALWAYS added to the _’-end of the DNA strand

3

Remember: DNA is a __ strand

double

__: The synthesis of RNA molecules using DNA as a template. The three main types of RNA in the cell are:

Transcription

The three main types of RNA in the cell are:

• I. __ RNA (__): Used as template for translation

• II. __ RNA: (__): Component of the ribosome. Protein/RNA complex responsible for translating nRNA to proteins

• III. __ RNA (__): bind activated amino acids and bring them to the ribosome to make proteins

• Messenger : mRNA

• Ribosomal : rRNA

• Transfer : tRNA

__: Synthesis of polypeptides (proteins) from mRNA templates (strands)

Translation

Proteins: Key functional units that carry out the vast majority of cellular functions, __ transcription and translation

including

Proteins are composed of __

amino acids (AA)

Each DNA strand of a double helix is an exact __ to the other (recall 5’ to 3’ anti-parallel structure)

complement

During replication each strand can therefore acts as a __

template

DNA replication is __, which means each ‘daughter’ molecule contained one of the parent strands

semi-conservative

DNA double helices are stable and difficult to break apart without extremely hot temperatures (near __)

boiling

How are they split apart during cell replication at ‘normal’ cell temperature (e.g. 37C)?!

-Answer: with specialized __, and with the fact that the hydrogen bonds between each base pair are relatively weak by themselves

enzymes

The sum of many __ gives the overall stability to double-stranded DNA

hydrogen bonds

The positions where DNA is first opened are called __

• These origins are approximately __ bp long

replication origins

• 100

Replication origins are typically enriched with A-T base pairs. Why A-T?

-Answer: A-T pairs share only __ hydrogen bonds, where G-C pairs share three hydrogen bonds; the A-T pairs are therefore easier to split apart

-two : three

Bacteria usually have a __ origin of replication (ORI)

single

The human genome has ~ __ ORIs

10,000

DNA molecules in the process of replication from Y-shaped junctions called __

replication forks

Two forks are formed at each origin that unzip the DNA in opposite directions, which is referred to as __

bidirectional replication

The forks move at a speed of __bp/sec in bacteria and __bp/sec in humans and other eukaryotes

1000 : 100

___ catalyzes synthesis of ne DNA strand

-It moves in the __ direction of the __, adding only to the 3’ end of the growing strand

-Nucleotides are added as nucleoside triphosphates, and release __(PPi) during the addition

DNA polymerase

-5’ to 3 : NEW STRAND

-pyrophosphate

Nobody is perfect: DNA polymerases make about 1 mistake per __ bases incorporated

10^9

__: 3’-5’ exonuclease activity of the polymerase = If the base was a mismatch, polymerase chops it off

Proofreading

The Replication is __

Asymmetrical

DNA polymerase can easily extend one of the new strands (__) into the replication fork, but not the other

leading strand

The ___ needs to be ‘back-stitched’ by growing discontinuously. The discontinuous pieces are called ___ fragments

lagging strand. Okazaki

Lags Behind: Top red

Mechanism of Lagging Strand Synthesis

1. ___: __DNA to start replication

2. The —— need to be replaced by DNA

3. RNA primers are __ away and the gaps they leave behind are filled by a polymerase

4. The nickels are sealed by a ___

1. RNA Primer

3. digested

4. ligase

__ + __: Open the double strand

Helicase + Topoisomerase

__: Adds RNA primer for polymerase

Primase

__: Extends DNA and proofreads the new strand

Polymerase

__: Allows Polymerase to slide down the DNA

Sliding Clamp

__: Joins the Okazaki fragments together

Ligase

__: Nucleases removes RNA primer and a repair polymerase fills in the gaps

Helpers

DNA helicase:

-An enzyme that spends energy (__) to unwind the double-strands

-Helicase facilitates the unwinding of the DNA, (___ handles the torsion from the unwinding). Helps __ the DNA

-ATP

-topoisomerase : unwinding

Single-Strand DNA binding proteins:

-Work with helicase from the origin of replication (ORC)

-Both strands are kept separated by single-strand binding proteins

-Target single-stranded DNA and prevent the formation of the . Keeps the DNA

double helix : single-stranded

The polymerases that are used for replicating chromosomal DNA have two main functions:

-__ new strand

-__ the product

-Synthesizes

-Proofreads

DNA polymerase cannot initiate a new strand of DNA- it needs a starter template, otherwise known as a __

primer

An enzyme called __ is able to create a short primer (made from RNA) based on the DNA template

primase

RNA is very similar to DNA expected the sugar is __ instead of deoxyribose

-Also, RNA does not contain thymine (T), instead it uses __(U)

-The __ bond behaves the same way as the __ bond

ribose

-uracil

- A-U : A-T

___ is primed once, __ is primed for each Okazaki fragments

-Primes DNA for __ by attaching small RNA “primers”

Leading strand : lagging strand

-Polymerase

The lagging strand made from discontinuous Okazaki fragments requires __ additional enzymes to form a continuous stretch of DNA

1. __- separates the DNA from RNA

2. __ - replaces RNA with DNA

3. __- joins the DNA fragments together

three

1. nuclease

2. Repair polymerase

3. DNA ligase

DNA polymerase makes about 1 error every __ nucleotides 

-Eros are corrected as they occur in a process known as __

-The removal of erroneous nucleotides is performed by __ domain of the polymerase, which works in the 3’-5’ direction

10^7

-proofreading

-nuclease