Chapter 12

DNA & RNA

12 – 1 DNA

Deoxyribonucleic acid

Nucleotides• Units that make up DNA

molecule

• Made of three parts

1. 5 carbon sugar (deoxyribose)

2. Phosphate group

3. Nitrogen bases

4 kinds of nitrogen bases1. Adenine (A)

2. Guanine (G)

3. Cytosine (C)

4. Thymine (T)

Chargaff’s Rule• A=T and G=C

X-Ray Evidence• Rosalind Franklin• British Scientist• Used a technique

called X-Ray diffraction

• Provided important clues about the structure of DNA

X-Ray Evidence• There were 2

strands• Strands were

twisted around each other (helix)

• The nitrogen bases are in the middle

Watson & Crick

The Double Helix• Francis Crick & James Watson• Trying to understand the structure of DNA by

building models• Unsuccessful until early 1953, Watson was

shown a copy of Franklin’s X-ray pattern• “The instant I saw the picture my mouth fell open

and my pulse began to race.”– James Watson

• Within weeks Watson and Crick had figured out the structure of DNA

• Published their results in a historic one page paper in April of 1953

• Watson and Crick later discovered what held the two strands together

• Hydrogen bonds could form between certain nitrogen bases and provide enough force to hold the two strands together

• Hydrogen bonds could only form between certain base pairs adenine and thymine and guanine and cytosine

• This principal is called Base pairing

• This explains Chargaff’s Rule

Chromosomes and DNA Replication

• To extract DNA for analysis, you need to know where to find it and how its organized

• DNA is located in the nucleus

• DNA is organized into chromosomes

Prokaryotic Cells• Prokaryotic cells have a single

circular DNA molecule that contains nearly all of its genetic information

• Located in the cytoplasm

Eukaryotic Cells• Much more complex

• 1000 times the amount of DNA as prokaryotes

• DNA is located in the nucleus in the form of chromosomes

Chromosome Structure• Q: If eukaryotic DNA can contain

a meter or more of DNA, how does it get packed in so tight into chromosomes?

• A: Eukaryotic chromosomes contain both DNA and protein that form a substance called chromatin

Histones• Proteins that coil up DNA

• DNA + histone molecules form a bead-like structure called a nucleosome

• Nucleosomes pack together to form thick fibers that loop and coil together to form chromosomes

DNA coils around histones to form nucleosomes, which coil to form chromatin fibers. The chromatin fibers super coil to form chromosomes that are visible in the metaphase stage of mitosis.

DNA Replication• When Watson and Crick discovered

the double helix structure of DNA they recognized immediately how DNA could copy itself

• The strands are complementary• If you could separate the two strands,

the rules of base pairing would allow you to reconstruct the base sequence of the other strand

Replication• When the DNA splits into 2

strands, then produces 2 new strands following the rules of base pairing

Semiconservative Replication• Parental strands of DNA separate, serve

as templates, and produce DNA molecules that have one strand of parental DNA and one strand of new DNA.

How Replication Occurs1. Unwinding

2. Synthesizing

3. Joining

Getting Started

Origins of replication- short stretched of DNA having a specific sequence of nucleotides.– The place where DNA replication begins.

Replication fork- Y-shaped region where the parental strands of DNA are being unwound.

1. Unwinding

• Replication is carried out by enzymes

• Before DNA replicates, the double helix must unwind and unzip.

• DNA Helicase-enzyme that is responsible for unwinding and unzipping the double helix.

1. Unwinding• When the double helix unwinds/unzips the

H+ bonds between the bases are broken, leaving single strands of DNA.

• Then, proteins called single-stranded binding proteins associate with the DNA to keep the strands separate during replication.

• As the helix unwinds, another enzyme, RNA Primase, adds a short segment of RNA, called RNA primer on each DNA strand.

1. Unwinding

• The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.

Topoisomerase- helps relieve this strain by breaking, swiveling, and rejoining DNA strands.

1. Unwinding

Helicase

2. Synthesizing

• Within a bubble, the unwound sections of parental DNA strands are available to serve as templates for the synthesis of new complementary DNA strands.

• As the helix unwinds, another enzyme, RNA Primase, adds a short segment of RNA, called RNA primer on each DNA strand.

2. Base PairingDNA Polymerase:• Joins individual nucleotides to produce a DNA

molecule, which is a polymer• The nucleotides are added to the 3’ end of the new

strand.

• Also proof reads each new DNA strand

2. Base Pairing• DNA polymerase continues adding new DNA

nucleotides to the chain by adding to the 3’ end of the DNA strand.

• A binds with T / C binds with G

• This allows for identical copies to be made

Leading Strand: elongated as the DNA unwinds– Continuously added to 3’ end

Lagging Strand: elongates away from fork– Done by adding small fragments. (Okazaki fragments)

3. Joining

• When the DNA polymerase comes to an RNA primer on the DNA, it removes the primer and fills in the place with DNA nucleotides.

• When the RNA primer has been replaced, DNA ligase links the two sections.

Do NowPlace the following steps of

Replication in order.

DNA unwinds DNA Unzips

The bases attach from a supply in the cytoplasm

Sugar and phosphate groups form the side of each new strand

Do NowPlace the following steps of

Replication in order.

DNA unwinds

DNA Unzips

The bases attach from a supply in the cytoplasm

Sugar and phosphate groups form the side of each new strand

1.

2.

3.

4.

DNA replication results in 2 DNA molecules

a. Each with two new strands

b. One with two new strands and the other with two original strands

c. Each with one new strand and one original strand

d. Each with two original strands

12 – 3 RNA and Protein Synthesis

Genes• Coded DNA instructions that

control the production of proteins

• DNA never leaves the nucleus, therefore the code must be copied into

• RNA, or ribonucleic acid

• There are 3 main differences between RNA and DNA

1. It has the sugar ribose, instead of deoxyribose

2. RNA is single stranded

3. RNA contains uracil in place of thymine

• RNA is like a disposable copy of a segment of DNA

• RNA is like a working copy of a single gene

Types of RNA1. Messanger RNA (mRNA)• Serve as messangers from DNA to

the rest of the cell2. Ribosomal RNA (rRNA)• Type of RNA that makes up parts of

ribosomes3. Transfer RNA (tRNA)• Transfers each amino acid to the

ribosome as it is specified by the mRNA

Types of RNA

Transcription• RNA molecules are produced by copying

part of the DNA sequence into RNA

• Transcription requires an enzyme known as RNA polymerase

• During transcription, RNA polymerase binds to DNA and separates the DNA strands. RNA polymerase then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA.

• Q: How does RNA polymerase “know” where to start and stop making a RNA copy of DNA?

• A: promoters

• Signals in DNA that indicate to the enzyme where to bind to make RNA

• Similar signals in DNA cause transcription to stop

RNA Editing• Remember, a lot of DNA doesn’t

code for proteins

• Introns – not involved in coding for proteins

• Exons – code for proteins

• The introns get cut out of the RNA molecules before the final mRNA is made

The Genetic Code

• Proteins are made by joining amino acids into long chains called polypeptides

• Each polypeptide contains a combination of any or all of the 20 different amino acids

• The properties of proteins are determined by the order in which different amino acids are joined together

• The language of mRNA instructions is called the genetic code

• The code is read three letters at a time

• Each 3 letter “word” is called a codon

• Each codon corresponds to an amino acid that can be added to the polypeptide

UCGCACGGUThis sequence would be

read three bases at a time as:

UCG-CAC-GGUThe codons represent the

different amino acids:UCG-CAC-GGU

Serine-Histidine-Glycine

Translation• The sequence of nucleotide

bases in an mRNA molecule serves as instructions for the order in which amino acids are joined to make a protein

• Proteins are put together on ribosomes

Translation• Decoding mRNA into a protein

Steps of Translation1. mRNA is transcribed from DNA in the

nucleus and released into the cytoplasm

2. mRNA attaches to a ribosome

3. as each codon of the mRNA molecule moves through the ribosome, the proper amino acid is transferred to the growing amino acid chain by tRNA

• tRNA carries only one kind of amino acid and three unpaired bases called the anticodon

4. The amino acid chain continues to grow until the ribosome reaches a stop codon on the mRNA molecule

The Roles of RNA and DNA• You can compare the different roles played by DNA and

RNA molecules in directing protein synthesis to the two types of plans used by builders. A master plan has all the information needed to construct a building. But builders never bring the valuable master plan to the building site, where it might be damaged or lost. Instead, they prepare inexpensive, disposable copies of the master plan called blueprints. The master plan is safely stored in an office, and the blueprints are taken to the job site. Similarly, the cell uses the vital DNA “master plan” to prepare RNA “blueprints.” The DNA molecule remains in the safety of the nucleus, while RNA molecules go to the protein-building sites in the cytoplasm—the ribosomes

Genes and Proteins• Q: If most genes contain nothing

more than instructions for assembling proteins, what do proteins have to do with traits?

• A: Everything, proteins are microscopic tools designed to build or operate a component of a living cell

12 – 4 Mutations

Mutations• Changes in the genetic material

Point mutations• Changes in one or a few

nucleotides

Ex.) substitutions, insertions, deletions

Frameshift mutations• Mutation that shifts the “reading”

frame of the genetic message by inserting or deleting a nucleotide

Chromosomal Mutations

Significance of Mutations• Most mutations don’t do anything

• Mutations that cause drastic changes in proteins produce defective proteins that disrupt normal biological activities

• Mutations are also a source of genetic variability which can be beneficial

Polyploidy• When plants produce triploid (3N)

or tetraploid (4N) organisms

• These plants are often larger and stronger

Do Now

• Look at the bottom strand of DNA on the window blinds

• Suppose the second T was changed to a C

• How would this specifically alter the resulting amino acid chain?

• What kind of mutation is this?

Do Now #2

• What if we got rid of the first G in the bottom strand of DNA

• How would this specifically alter the amino acid chain produced?

• What kind of mutation is this?

Do Now #3

• How are substitution/point mutations and frameshift mutations similar?

• How are they different?