DNA Structure/Function/Replication

Look over DNA replication animations

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The DNA polymerase moves from 3' to 5' end while the daughter strand is formed from 5' to 3' since the DNA coils have opposite ends.

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What are the three parts of a nucleotide?

Deoxyribose, sugar, and one of the four nitrogenous bases

T/F: DNA can replicate without attaching to RNA

FALSE

T/F: DNA polymerase can accomodate replication in multiple directions.

FALSE; it can only go one direction. However, DNA replication overall happens in both directions (antiparallel) with more than one polymerases. That's why there is a leading strand and a lagging strand.

What kind of bonds connect the nitrogenous bases?

Hydrogen bonds

What characteristic of DNA makes DNA replication accurate?

Specificity of hydrogen bonding between base pairs

T/F: DNA polymerase can only add nucleotides to a pre-existing chain of nucleotides

TRUE

T/F: DNA replication results in two identical daughter molecules each consisting of one old (original) strand and one newly-synthesized strand.

TRUE

T/F: Sugar-phosphate backbones are the "uprights" of the DNA ladder

TRUE

T/F: You can only add nucleotides to the growing 3' end.

TRUE

T/F: For a given species, there are always equal amounts of adenine and thymine and equal amounts of guanine and cytosine.

TRUE; This is known as Chargaff's Rule

Brief replication process

The original helix unwinds, two new strands are made, and two helices are produced.

Replication Fork

The point where separation of the DNA occurs is called the replication fork.

DNA repair enzymes function

They proofread daughter DNA strands because it's possible for polymerase to make a mistake in replication.

Leading strand vs. Lagging strand

They replicate in OPPOSITE directions. Leading strands are continuous while the lagging strand is discontinuous

DNA polymerase I (Exonuclease)

This DNA will take out the RNA primer that was laid down because you don't want RNA to be in the DNA and replaces it with DNA nucleotides (This comes at the end). There are still gaps.

What would result from the actions of DNA polymerase during DNA replication?

Two DNA polymerase molecules act to synthesize daughter DNA strands, one via a long, continuous strand and a second via short segments of DNA that must be joined by ligase.

Who is credited with inventing the structure of DNA?

Watson and Crick

Point mutation

a mutation in which a single base pair in DNA has been changed.

insertion mutation

a mutation in which one or more pairs of nucleotides are inserted into a gene.

deletion mutation

a mutation in which one or more pairs of nucleotides are removed from a gene.

Inversion

a mutation that occurs when a piece of DNA is cut out of a chromosome, turned around and reinserted into the gap.

Translocation

a mutation that occurs when a piece of DNA is removed from one chromosome and attached to another chromosome

DNA polymerase III

adds nucleotides on the lagging strand

Primase

aka RNA is laid down first. DNA attaches to RNA or primase. It's like a "primer". It consists of a short sequence of RNA nucleotides, that are complementary to the section of DNA strand that's replicating.

DNA strands run in opposite direction..AKA

antiparallel

DNA replication begins __

at the origin of replication

The correct nucleotides to be added to the new DNA strand are determined by

base pairing between the free nucleotides and bases on the template strand

DNA replicates in ___ direction(s).

both

ligase

Inserts phosphate groups into the gaps after RNA is replaced with DNA nucleotides

DNA polymerase -____

can add nucleotides only to the free sugar end of a DNA molecule (3' end)

What is numbered 1'-5'

carbon atoms in the sugar

Replication bubbles -___

consist of two replication forks moving in opposite directions

The sugars and phosphates in the "backbone" of a DNA strand are held together by

covalent bonds

SSB (single stranded binding protein)

keep the strands separated because the natural force is for them to come together.

What is DNA repeating subunit?

nucleotide

What are the fragments in the lagging strand called?

okazaki fragments

What is the approximate error rate for DNA polymerase?

one error for every 10,000 bases added

What is the approximate error rate for all of DNA replication?

one error for every billion nucleotides

How can enzymes repair the DNA?

recognize the mismatch, cut out the incorrect nucleotide and replace it with a nucleotide containing the complementary base. Sometimes the enzymes replace the parental nucleotide instead of the mismatched one. The resulting base pair is complementary but WRONG.

Topoisomerase/gyrase

releases the tension in the DNA coil. Straight out.

Helicase

splits the DNA molecules apart, breaks the hydrogen bonds, starting at DNA replication origins

What part of the nucleotide accounts for the naming of the DNA?

sugar

Leading strand always goes towards ______

the fork (where the DNA opens up)

The purpose of DNA replication is to produce

two identical DNA double helices

Hydrogen bonds b/t complementary base pairs are (weak/strong)?

weak

British scientists ____ ____ and ____ ____ used x-ray diffraction to study the DNA molecule.

Maurice Wilkins and Rosalind Franklin

What are mutations?

Occasional changes in nucleotides. They are often harmful. But some mutations are beneficial

In DNA, there are multiple origins of replication. Why?

Our DNA is SUPER long. It would take forever to replicate by starting from only one origin.

What are the complementary bases?

A-T, C-G

What are the 4 nitrogenous bases?

Adanine,Thymine, Guanine, cytosine

Relationship between A, G, T, C

Adenine and guanine are larger than thymine and cytosine. A and G have two fused rings while T and C only have one ring. Since it's A-T and C-G, the rungs of the ladder have a constant diameter.

Single DNA strand

All nucleotides in a single DNA strand are oriented the same direction. So the two ends of a DNA strand differ: one has a "free" or unbonded sugar, and the other end has a "free" or unbonded phosphate.

Sequence of Replication

1) Helicase attaches and unwinds Dna 2) SSB attaches to keep the DNA apart 3) Primase (RNA PRIMER) assembles at the replication origin site 4) DNA polymerase adds new nucleotides to the single parent strand 5) Then, the DNA polyermase I removes the primase and replaces it with DNA. 6) The leading strand is replicated continuously in one direction while the lagging strand is replicated in short segments (okizaki) in the other direction. 7) Meanwhile, the primases on the lagging strand are replaced by DNA polymerase I with DNA nucleotides 8) Finally, ligase fills in the leftover gaps

New nucleotides are always added to the ___ end of the daughter strand

3'

What's attached to the 3' end? 5' end?

3': OH group 5': phosphate group

Imagine that you are studying a newly discovered bacterium from a hot springs in Yellowstone National Park. When you examine the nucleotide composition of this organism, you find that 10% of the nucleotides in its DNA are adenine (A). What percentage of nucleotides are guanine? Explain.

40%, because A pairs with T (accounting for 20% of the bases), leaving 80% of the nucleotides as G-C base pairs; half of 80% is 40%. Because of DNA's double-helix structure and base-pairing rules, if you know the percentage of one nucleotide in a DNA sample, you can figure out the percentage of all of the others.

The structure of DNA explained Chargaff's observations because

A-T, C-G

Why do we start with breaking A-T pairs rather than G-C pairs?

Because A-T pairs only have two hydrogen bonds while there's 3 connecting G-C. So it's less energy to break apart A-T

How is the DNA shaped?

Coiled, double helix