DNA Structure and Replication (Ch. 12-1, 12-2)

DNA DNA is one of the 4 types of macromolecules known as a nucleic acid. DNA is one of the 4 types of macromolecules known as a nucleic acid. DNA stands for deoxyribonucleic acid. DNA stands for deoxyribonucleic acid.

Components and Structure of DNA DNA must be able to: DNA must be able to: carry genetic information from one generation to the next (genes are made of DNA) carry genetic information from one generation to the next (genes are made of DNA) be easily and accurately copied before cell division. be easily and accurately copied before cell division.

Nucleotides The monomer repeating subunits that make up nucleic acids like DNA are called nucleotides. The monomer repeating subunits that make up nucleic acids like DNA are called nucleotides.

3 parts of a Nucleotide 1. one 5-carbon sugar called deoxyribose one phosphate group one phosphate group one nitrogenous (nitrogen- containing) base one nitrogenous (nitrogen- containing) base

2 types of Nucleotides 1) purines (two rings) adenine (A) adenine (A) guanine (G) guanine (G)

2) pyrimidines (one ring) cytosine (C)cytosine (C) thymine (T)thymine (T)

Lets review how to draw a nucleotide… Lets review how to draw a nucleotide…

When nucleotides bind together, they form a chain, which is the polymer DNA. When nucleotides bind together, they form a chain, which is the polymer DNA. the sugar and phosphate groups form the backbone of the chain (sides of a ladder) the sugar and phosphate groups form the backbone of the chain (sides of a ladder) the nitrogenous bases stick out sideways from the chain (rungs of the ladder) the nitrogenous bases stick out sideways from the chain (rungs of the ladder)

The chain has a direction determined by whether the ribose is right side up, or upside down. The “top” of the molecule will have a phosphate sticking out, and the sugar will be pointing up. It is known as the 5’ end (5 prime).

If the sugar is pointing down and there is no phosphate sticking out, it is the 3’ end (3 prime). If the sugar is pointing down and there is no phosphate sticking out, it is the 3’ end (3 prime).

It looks like a twisted ladder. The strands run in opposite directions; called antiparallel (like opposite flows of traffic )

Constructing the DNA Polymer 5’3’ 5’3’ 3’5’ 3’5’

Erwin Chargaff ( ) discovered that in any DNA sample Erwin Chargaff ( ) discovered that in any DNA sample 1. the amount of guanine is always equal to the amount of cytosine, 2. the amount of adenine was always equal to the amount of thymine. Chargaff’s Rules:

This eventually led to our base pairing rules. This eventually led to our base pairing rules. 1. Adenine from one strand and thymine from the other always pair together with two hydrogen bonds,

2. guanine on one strand and cytosine on the other strand always bond together with three hydrogen bonds.

If there was a DNA strand with the following bases, what would the opposite, or complementary, strand have? A T T A G C A G G A A T A C G If there was a DNA strand with the following bases, what would the opposite, or complementary, strand have? A T T A G C A G G A A T A C G T A A T C G T C C T T A T G C T A A T C G T C C T T A T G C

X-ray evidence (1952): Rosalind Franklin studied the DNA molecule using x-ray diffraction (bending of waves around an edge or barrier) to see the structure of DNA. Rosalind Franklin studied the DNA molecule using x-ray diffraction (bending of waves around an edge or barrier) to see the structure of DNA. From her work she was able to see that the DNA strands were twisted around each other forming a helix. From her work she was able to see that the DNA strands were twisted around each other forming a helix.

The Double Helix Model (1953): Francis Crick and James Watson were trying to figure out the structure of DNA by building models with cardboard and wire. When they saw Franklin’s pictures they soon were able piece all the information together to come up with the 3-dimensional structure of DNA: a double helix with two strands winding around each other. Francis Crick and James Watson were trying to figure out the structure of DNA by building models with cardboard and wire. When they saw Franklin’s pictures they soon were able piece all the information together to come up with the 3-dimensional structure of DNA: a double helix with two strands winding around each other.

DNA and chromosomes DNA molecules are extremely long. In order to fit into cells, they must fold up as much as possible. DNA molecules are extremely long. In order to fit into cells, they must fold up as much as possible. DNA double helix Chromosomes Histone proteins

In humans, the amount of DNA in the nucleus is more than 1 meter long. In humans, the amount of DNA in the nucleus is more than 1 meter long. Remember, in eukaryotic cells the DNA is bound to proteins forming chromatin. Remember, in eukaryotic cells the DNA is bound to proteins forming chromatin. To fit the DNA into the nucleus, the DNA and histone proteins are packed tightly a process called supercoiling. To fit the DNA into the nucleus, the DNA and histone proteins are packed tightly a process called supercoiling.

DNA Replication: How is DNA copied? The process of copying DNA is called DNA replication. The process of copying DNA is called DNA replication. Because DNA is double stranded, each strand can be used as a template to make the other strand through the process of base pairing. Because DNA is double stranded, each strand can be used as a template to make the other strand through the process of base pairing. Because of this, the two strands are called complementary (think about angles in Geometry). Because of this, the two strands are called complementary (think about angles in Geometry).

During DNA replication: the DNA is unwound and unzipped by the enzyme Helicase. the DNA is unwound and unzipped by the enzyme Helicase. The strands are held apart by single-stranded binding protiens (also known as ssbps) The strands are held apart by single-stranded binding protiens (also known as ssbps) each original DNA strand is used as a template (or model) to make a new DNA strand with base pairing each original DNA strand is used as a template (or model) to make a new DNA strand with base pairing

ENZYMES USED IN DNA REPLICATION New DNA strand

The enzyme Primase lays down an RNA Primer a few base pairs long to which the new DNA can be added. The enzyme Primase lays down an RNA Primer a few base pairs long to which the new DNA can be added. Another enzyme, called DNA Polymerase, adds new bases to the RNA Primer. It always reads 3’ to 5’ and synthesizes the new strand from 5’ to 3’. This occurs in the direction following Helicase opening up the “replication fork”. For this reason, theis new strand is called the leading strand. Another enzyme, called DNA Polymerase, adds new bases to the RNA Primer. It always reads 3’ to 5’ and synthesizes the new strand from 5’ to 3’. This occurs in the direction following Helicase opening up the “replication fork”. For this reason, theis new strand is called the leading strand. ENZYMES USED IN DNA REPLICATION

Another DNA Polymerase also “proofreads” the new DNA to check for errors. Another DNA Polymerase also “proofreads” the new DNA to check for errors. Meanwhile, on the other strand, known as the lagging strand, Primase and DNA Polymerase synthesize DNA from 5’ to 3’ away from the replication fork. These small spurts of replication form what are known as Okazaki fragments. Meanwhile, on the other strand, known as the lagging strand, Primase and DNA Polymerase synthesize DNA from 5’ to 3’ away from the replication fork. These small spurts of replication form what are known as Okazaki fragments. The Okazaki fragments are joined together by the enzyme Ligase. The Okazaki fragments are joined together by the enzyme Ligase. On both strands, the RNA Primer is replaced with DNA nucleotides by the enzyme DNA Polymerase. On both strands, the RNA Primer is replaced with DNA nucleotides by the enzyme DNA Polymerase. ENZYMES USED IN DNA REPLICATION

When replication is complete, each DNA molecule is made of one old strand and one new strand. This is described as the semi-conservative model of replication. The new DNA molecules are rewound by the enzyme Gyrase. When replication is complete, each DNA molecule is made of one old strand and one new strand. This is described as the semi-conservative model of replication. The new DNA molecules are rewound by the enzyme Gyrase. Original DNA New DNA (one old strand, one new strand)

Chromosome Arrangement Prokarytoic cells (bacteria) Prokarytoic cells (bacteria) Prokaryotic cells have one circular chromosome that is free-floating in the cytoplasm. Remember, prokaryotic cells do not have a nucleus. Prokaryotic cells have one circular chromosome that is free-floating in the cytoplasm. Remember, prokaryotic cells do not have a nucleus. When prokaryotic cells copy their DNA, the process begins at one point in the chromosome and moves around the circle in both directions until complete. When prokaryotic cells copy their DNA, the process begins at one point in the chromosome and moves around the circle in both directions until complete.

Eukaryotic cells Eukaryotic cells have more chromosomes than prokaryotic cells, and DNA replication begins at hundreds of places and continues in both directions until each chromosome is completely copied. Eukaryotic cells have more chromosomes than prokaryotic cells, and DNA replication begins at hundreds of places and continues in both directions until each chromosome is completely copied.

DNA Polymerase only works in one direction. One strand is read and synthesized continuously while the other is synthesized in fragments. DNA Polymerase only works in one direction. One strand is read and synthesized continuously while the other is synthesized in fragments. Growth Replication fork DNA polymerase New strand Original strand DNA polymerase Nitrogenous bases Replication fork Original strand New strand