Topic 9 Notes/Study Guide

Part 1:

DNA & RNA Structure

DNA Structure

Video about DNA Structure

DNA is a long molecule made up of units called NUCLEOTIDES.

Each nucleotide is made up of three basic components:

a 5-carbon sugar called deoxyribose
a phosphate group
a nitrogenous (nitrogen-containing) base

The BACKBONE of a DNA chain is formed by the sugar and phosphate groups of each nucleotide.

The nitrogenous bases are found in the center of the DNA molecule.

The nucleotides can be joined together in any order, meaning any sequence of bases is possible.

There are four kinds of nitrogenous bases in DNA:

PURINES:

Two of the nitrogenous bases, ADENINE (A) & GUANINE (G), belong to a group of compounds known as PURINES.

Purines have TWO rings in their structures.

PYRIMIDINES:

The remaining two bases, CYTOSINE (C) & THYMINE (T), are known as PYRIMIDINES.

Pyrimidines are made up of only ONE ring.

DNA is made up of NUCLEOTIDES. Each nucleotide has three parts: a deoxyribose molecule, a phosphate group, and a nitrogenous base.

There are four different bases in DNA: adenine (A), guanine (G), cytosine (C), and thymine (T).

The DNA in eukaryotic cells is packed tightly into structures called CHROMOSOMES.

Eukaryotic chromosomes contain DNA wrapped around histone proteins that tightly pack together to form a substance called CHROMATIN.

HISTONES are the proteins that DNA is tightly coiled around.

Together, the DNA and histone molecules form a beadlike structure called a NUCLEOSOME. Nucleosomes pack with one another to form a thick fiber, which is shortened by a system of loops and coils. Nucleosomes fold enormous lengths of DNA into the tiny space available in the cell nucleus.

Discovering DNA

Erwin Chargaff

Erwin Chargaff, an American biochemist, had discovered that the percentages of guanine (G) and cytosine (C) bases were almost equal in any sample of DNA. The same was true for the other two nucleotides, adenine (A) and thymine (T).

The observation that A = T and G = C became known as CHARGAFF'S RULES.

These rules are also referred to as DNA Base Pairing Rules as they state how the nitrogenous bases pair with each other in a DNA molecule.

In DNA Adenine (A) will always pair with Thymine (T), and vice versa. And Guanine (G) will always pair with Cytosine (C), and vice versa.

Click HERE to watch a video Rosalind Franklin

Rosalind Franklin

In the early 1950s, a British scientist named Rosalind Franklin began to study DNA. She used a technique called X-ray diffraction to get information about the structure of the DNA molecule. The result of her work was X-shaped X-ray photographs of DNA.

The X-shaped pattern in the photograph shows that the strands in DNA are twisted around each other like the coils of a spring, a shape known as a HELIX. The angle of the X suggests that there are two strands in the structure as well.

Watson & Crick

At the same time that Franklin was continuing her research, Francis Crick, a British physicist, and James Watson, an American biologist, were trying to understand the structure of DNA by building three-dimensional models of the molecule. Watson and Crick eventually built a structural model that explained the puzzle of how DNA could carry information and how it could be copied.

Watson and Crick's model of DNA was a DOUBLE HELIX, in which two strands of DNA were wound around each other. A double helix looks like a twisted ladder or a spiral staircase.

They then discovered that HYDROGEN BONDS could form between certain nitrogenous bases and provide just enough force to hold the two stands together.

Hydrogen bonds can form only between certain base pairs - adenine and thymine, and guanine and cytosine.

Once they saw this they realized that this principle, called BASE PAIRING, explained Chargaff's rules. Now there was a reason that A = T and G = C. Because for every adenine in a double-stranded DNA molecule. there had to be exactly one thymine molecule. And for every cytosine molecule, there had to be one guanine molecule.

Watson and Crick developed the double-helix model of the structure of DNA.

DNA is a DOUBLE HELIX in which two strands are wound around each other. Each strand is made up of a chain of nucleotides. The two strands are held together by hydrogen bonds between adenine and thymine and between guanine and cytosine.

Part 2:

DNA Replication

DINB Slide 17 - "DNA Replication: Why does it happen" DINB Help!

Cells duplicate their DNA when they are preparing for cell division - this happens to grow or repair the organism. When the cell divides, each cell needs to have its own copy of DNA as this controls the activities of the cell, so it doubles it in advance of cell division (mitosis).

Before a cell divides it duplicates its DNA in a copying process called DNA REPLICATION.

DNA Replication ensures that each resulting cell will have a complete set of DNA molecules.

During DNA replication, the DNA molecule separates into two strands and then produces two new complementary strands following the rules of base pairing.

Each strand of the double helix of DNA serves as a TEMPLATE, or model, for the new strand. That's because each strand of the DNA double helix as all the information needed to reconstruct another half of the DNA molecule by following base-pairing rules.

Because each strand can be used to make the other strand, the two new DNA strands that are made at the end of DNAP replication are said to be COMPLEMENTARY.

Where does it Happen?!

PROKARYOTIC CELLS...(No Nucleus so this process occurs in the cytoplasm)

In most prokaryotes, DNA replication begins at a single point in the chromosome and proceeds in two directions until the entire chromosome is replicated.

EUKARYOTIC CELLS...(Remember, DNA is found in the NUCLEUS of these cells)

In the larger eukaryotic chromosomes, DNA replication occurs at hundreds of places. Replication then proceeds in both directions until each chromosome is completely copied.

The sites where replication occurs are called the REPLICATION FORKS.

During DNA replication the two strands of the double helix separate, allowing two replication forks to form. As each new strand forms, new bases are added following the rules of base pairing.

For example, a strand that has the bases TACGTT produces a strand with the complementary bases ATGCAA. The result is two DNA molecules identical to each other and to the original molecule.

Each of these new DNA strands will have one original strand and one new strand.

What Happens?!

Who Does it?!

DNA replication is carried out by a series of enzymes.

HELICASE is the enzyme that "unzips" a molecule of DNA.

The unzipping occurs when the hydrogen bonds between the base pairs are broken and the two strands of the molecule unwind. Each strand serves as a template for the attachment of complementary bases.

The principal/main enzyme involved in DNA replication is called DNA POLYMERASE because it joins individual nucleotides to produce a DNA molecule (a polymer).

DNA polymerase also "proofreads" each new DNA strand, helping to maximize the odds that each molecule is a perfect copy of the original DNA.

Slide 19 - Unzipping DINB Help!

An enzyme called HELICASE unzips the double-STRANDED DNA, seperating in into two SINGLE strands. To do this, it has to break the HYDROGEN bonds between the complementary base pairs. The Y-shaped structure is called a REPLICATION FORK.

Slide 20 - Priming DINB Help!

To begin replicating the DNA, it requires a STARTING point. This is created by an enyme called RNA PRIMASE. It attaches an RNA PRIMER to an exposed DNA BASE. This gives DNA polymerase (shown in the next step) something to ATTACH to so it can begin to build the second strand.

Slide 21 - Building DINB Help!

DNA POLYMERASE associates with the DNA and BUILDS the new strands by adding DNA NUCLEOTIDES one at a time.

Slide 22 - Proofreading DINB Help!

It is very IMPORTANT that DNA is replicated with 100% accuracy - i.e. that each nitrogenous base is paried correctly: adenine with THYMINE and guanine with CYTOSINE. DNA POLYMERASE proofreads the new strand - exonuclease cuts out any erroneous bases and they are then REPLACED.

Check Out These Videos to learn more about DNA Replication!

Part 3:

Protein Sythesis

RNA Structure & Types of RNA

RNA's main function/role is to assist with protein synthesis (the making of proteins).

This is because the assembly of amino acids (the monomer of proteins) into proteins is controlled by RNA.

RNA, like DNA, consists of a long chain of nucleotides.

Just like DNA each nucleotide is made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base.

There are three main differences between RNA and DNA:

The sugar in RNA is RIBOSE instead of deoxyribose
RNA is generally SINGLE-STRANDED not double-stranded.
RNA contains the nitrogenous base URACIL in place of thymine.

RNA is... a single-stranded nucleic acid.

Each RNA nucleotide contains... a phosphate group, a ribose sugar and a nitrogenous base.

The four bases found in RNA are:

Adenine
Uracil
Guanine
Cytosine

These form base pair as follows:

Adenine pairs with Uracil
Guanine pairs with Cytosine

Slide 27 - DINB Help: RNA

TRANSCRIPTION

RNA molecules are produced by copying part of the nucleotide sequence of DNA into a complementary sequence of mRNA. This process is called TRANSCRIPTION.

RNA Polymerase

Transcription requires an enzyme known as RNA Polymerase that is similar to DNA 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.

How does RNA polymerase know where to start and stop making an RNA copy of DNA?

Well, RNA polymerase will only bind to regions of DNA known as PROMOTERS, which have specific base sequences. PROMOTERS are basically signals in DNA that indicate to the RNA polymerase enzyme where to bind to make RNA. Similar signals in DNA cause transcription to stop when the new RNA molecule is completed.

Transcription:

DNA to mRNA

During transcription RNA polymerase uses one strand of DNA as a template to assemble nucleotides into a strand of RNA.

Editing RNA

Like a writer's first draft many RNA molecules require a bit of editing before they are completely ready. Remember that RNA is produced by copying DNA.

In the DNA of eukaryotic genes are sequences of nucleotides called INTRONS that are NOT involved in coding for proteins.

The DNA sequences that do actually code for proteins are called EXONS because they are "EXpressed" during protein synthesis.

When RNA molecules are formed, both the introns and exons are copied from the DNA. But the introns are cut out of RNA molecules while still in the nucleus. The remaining exons are then spliced back together to form the final mRNA. Then a cap and tail are added to form the final mRNA molecule.

Why does this process happen?

Well, some RNA molecules may be cut in spliced in different ways in different body/organ tissues making it possible for a single gene to produce several different forms of RNA.

Introns and exons may also play a role in evolution.

There are three main types of RNA:

Messenger RNA (mRNA)

Ribosomal RNA (rRNA)

Transfer RNA (tRNA)

Ribosomal RNA (rRNA)

Proteins are assembled in ribosomes. Ribosomes are made up of several dozen proteins, as well as a form of RNA known as RIBOSOMAL RNA (rRNA).

Messenger RNA (mRNA)

Most genes contain instructions for assembling amino acids into proteins. The RNA molecules that carry copies of these instructions are known as MESSENGER RNA (mRNA), because they serve as "messengers" from DNA to the rest of the cell.

Transfer RNA (tRNA)

During the construction of a protein, a third type of RNA molecule transfers each amino acid to the ribosome as it is specified by coded messages in mRNA. These RNA molecules are known as TRANSFER RNA (tRNA).

Slide 33 - DINB Help: rRNA & mRNA

What are ribosomes made of?

Ribosomes are made of rRNA and ribosomal proteins. They are composed of 2 subunits.

Why do you think mRNA can leave the nucleus but DNA cannot?

Messenger RNA is smaller than DNA and it is single stranded, so it can fit through nuclear pores.

Slide 34 - DINB Help: tRNA

Each tRNA molecule is associated with a specific amino acid. It uses its anticodon to connect with the correct codon on the mRNA strand, bringing its amino acid into place. The amino acid can then form a peptide bond with the next amino acid, building a polypeptide chain. The tRNA will then detach from the amino acid and leave to bind to another.

TRANSLATION

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 to produce the polypeptide.

The "language" of mRNA instructions is called the genetic code. RNA contains four different bases: A, U, C, and G. Thus the genetic code is written in a language that only has four letters.

The genetic code is read three letters at a time so that each "word" of the coded message is three bases long. Each three-letter "word" in mRNA is known as a CODON. A codon consists of three consecutive nucleotides that specify a single amino acid that is to be added to the polypeptide.

As an example let's look at this RNA sequence: UCGCACGGU

This sequence would be read three bases at a time as: UCG-CAC-GGU

The codons represent the different amino acids: Serine-Histidine-Glycine

Because there are four different bases, there are 64 different possible three-base codons (4 x 4 x 4 = 64). Some amino acids can be specified by more than one codon.

Start and Stop Codons:

There is also one codon "AUG" that codes for "methionine" and can serve as the initiation or START CODON for protein synthesis.

There are also three STOP CODONS. They are "UAG", "UAA", and "UGA". Stop codons act like the period at the end of a sentence; they signify the end of a polypeptide, which will at that point consist of many amino acids.

The sequence of nucleotides bases in an mRNA molecule serves as instructions for the order in which amino acids should be joined together to produce a polypeptide.

In order to create these polypeptides, the cell uses its ribosomes, which serve as small protein factories.

The decoding of an mRNA message into a polypeptide chain (protein) is known as TRANSLATION. During translation, the cell uses information from messenger RNA (mRNA) to produce proteins. The cell uses all three main types of RNA during translation.

Translation takes place in the ribosomes of the cell that are free-floating in the cell's cytoplasm.

Step 1:

Before translation occurs, messenger RNA is transcribed from DNA in the nucleus of the cell, and then enters the cytoplasm where it attaches to a ribosome.

Step 2:

Translation begins when an mRNA molecule in the cytoplasm attaches to a ribosome. As each codon of the mRNA molecule moves through the ribosome, the proper amino acid is brought into the ribosome by Transfer RNA (tRNA). Remember that the first codon that is translated is AUG the start codon.

Each tRNA has an ANTICODON whose bases are complementary to a codon on the mRNA strand. The ribosome positions the start codon to attract its anticodon on the tRNA that has the amino acid methionine bound to it. The ribosome then binds the next codon and its anticodon.

Step 3:

Like an assembly line worker who attaches one part to another, the ribosome forms a peptide bond between the first and second amino acids (which in this case is methionine and phenylalanine) and breaks the bond between methionine and its tRNA. The tRNA that had carried methionine then floats away from the ribosome allowing the ribosome to bind to another tRNA carrying a new amino acid. Now the ribosome can move down the mRNA molecule binding new tRNA molecules and amino acids.

Step 4:

The polypeptide chain continues to grow a until the ribosome reaches one of three possible stop codons on the mRNA molecule. When the ribosome reaches the stop codon, it releases the newly formed polypeptide and the mRNA molecule, completing the translation process.

The BIG Picture: Protein Synthesis

The cell uses the DNA "master plan" as a template to prepare RNA "blueprints."

The DNA "master plan" stays in the nucleus for safekeeping, while the mRNA "blueprints" are brought to the protein "building site" which is the ribosomes in the cytoplasm. Once at the "building site" the codons on the mRNA "blueprints" allow for proteins to be built.

Being able to label a diagram of Protein Synthesis is a great skill!

Check out these 3 Protein Synthesis Diagrams!

Still, Confused?! Check out these videos!

Part 4:

Mutations

Now and then cells make mistakes in copying their own DNA, inserting an incorrect base, or even skipping bases as the new strand is put together. These mistakes are called MUTATIONS.

Mutations are changes in genetic material.

A GENE MUTATION is a mutation that permanently changes the sequence of bases found in DNA.

Those that produce changes in whole chromosomes are known as CHROMOSOMAL MUTATIONS.

Gene Mutations

Click HERE to watch a video on Mutations

The Two Major Types of Gene Mutations:

Point Mutations

(Substitutions)

and

Frameshift Mutations

(Insertions or Deletions)

SUBSTITUTION

One base replaces another base.

These are also known as "POINT MUTATIONS" as they change the DNA Sequence at one point.

INSERTION

An extra base is inserted into a DNA base sequence.

Insertions can cause "FRAMSHIFT MUTATIONS" that shift/change the way the DNA message is read.

DELETION

A base is removed from a DNA base sequence.

Deletions can cause "FRAMSHIFT MUTATIONS" that shift/change the way the DNA message is read.

Types of Point Mutations -

Caused by Base Subsitutions

Nucleotide substitutions may lead to no change in the protein sequence (known as silent mutations), change the amino acid sequence (known as missense mutations), or create a stop codon (known as a nonsense mutation).

Remember, that the genetic code is read in three-base codons...

If a nucleotide is added or deleted, the bases are still read in a group of three, but now these groupings are shifted for every codon following the mutation.

Changes like these are called FRAMESHIFT MUTATIONS because they shift the "reading frame" of the genetic message.

By shifting the reading frame, frameshift mutations may change every amino acid that follows the point of the mutation.

Frameshift mutations can alter a protein so much that it is unable to perform its normal function.

Example of Frameshift mutation caused by the point mutation of deletion.

Chromosomal Mutations

Deletion

The loss of all or part of a chromosome.

Duplication

Produce extra copies of parts of a chromosome.

Inversion

Reverses the direction of parts of a chromosome.

Translocation

Occurs when part of one chromosome breaks off and attaches to another.

Gene Mutations vs. Chromosomal Mutations

YOUR TURN:

Which Karotype is from a male? Which is from a female?

Karyotypes

To analyze our chromosomes scientists photograph cells during mitosis since this is when chromosomes are condensed and easy to see. They then cut out chromosomes from these pictures and group them together in pairs forming a KARYOTYPE.

KARYOTYPE: photograph of chromosomes grouped together in pairs.

The number of chromosomes found in a typical human's karyotype is 46. 23 of these chromosomes coming from the father and the other 23 coming from the mother.

Two of these 46 chromosomes are known as SEX CHROMOSOMES. Females have two copies of the large X chromosome. While males have on X and one small Y chromosome.

AUTOSOMES or AUTOSOMAL CHROMOSOMES are the other 44 chromosomes that are not sex chromosomes.

So in a typical human cell, you will find both autosomes and sex chromosomes. 46, XX for females and 46, XY for males.