Lesson Overview 12.2 The Structure of DNA.

Lesson Overview 12.2 The Structure of DNA

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Read Pages What are the four kinds of nitrogenous bases in DNA? Explain Chargaff’s rule. What does that mean to you? What did Rosalind Franklin accomplish? What did Watson and Crick accomplish? Could they have done so without Franklin? What does “anti parallel? Strands mean Define Base Pairing

THINK ABOUT IT The DNA molecule must somehow specify how to assemble proteins, which are needed to regulate the various functions of each cell. What kind of structure could serve this purpose without varying from cell to cell? Understanding the structure of DNA has been the key to understanding how genes work.

The Components of DNA What are the chemical components of DNA?

The Components of DNA What are the chemical components of DNA?
DNA is a nucleic acid made up of nucleotides joined into long strands or chains by covalent bonds.

Nucleic Acids and Nucleotides
Nucleic acids are long, slightly acidic molecules originally identified in cell nuclei. Nucleic acids are made up of nucleotides, linked together to form long chains. The nucleotides that make up DNA are shown.

Nucleic Acids and Nucleotides
DNA’s nucleotides are made up of three basic components: a 5-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base.

Nitrogenous Bases and Covalent Bonds
The nucleotides in a strand of DNA are joined by covalent bonds formed between their sugar and phosphate groups.

DNA has four kinds of nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). The nitrogenous bases stick out sideways from the nucleotide chain.

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

Solving the Structure of DNA
What clues helped scientists solve the structure of DNA?

Solving the Structure of DNA
What clues helped scientists solve the structure of DNA? The clues in Franklin’s X-ray pattern enabled Watson and Crick to build a model that explained the specific structure and properties of DNA.

Chargaff’s Rules Erwin Chargaff discovered that the percentages of adenine [A] and thymine [T] bases are almost equal in any sample of DNA. The same thing is true for the other two nucleotides, guanine [G] and cytosine [C]. The observation that [A] = [T] and [G] = [C] became known as one of “Chargaff’s rules.”

Franklin’s X-Rays In the 1950s, British scientist Rosalind Franklin used a technique called X-ray diffraction to get information about the structure of the DNA molecule.

Franklin’s X-Rays X-ray diffraction revealed an X-shaped pattern showing that the strands in DNA are twisted around each other like the coils of a spring. The angle of the X-shaped pattern suggested that there are two strands in the structure. Other clues suggest that the nitrogenous bases are near the center of the DNA molecule.

The Work of Watson and Crick
At the same time, James Watson, an American biologist, and Francis Crick, a British physicist, were also trying to understand the structure of DNA. They built three-dimensional models of the molecule.

Early in 1953, Watson was shown a copy of Franklin’s X-ray pattern. The clues in Franklin’s X-ray pattern enabled Watson and Crick to build a model that explained the specific structure and properties of DNA.

Watson and Crick’s breakthrough model of DNA was a double helix, in which two strands were wound around each other.

The Double-Helix Model
What does the double-helix model tell us about DNA?

What does the double-helix model tell us about DNA? The double-helix model explains Chargaff’s rule of base pairing and how the two strands of DNA are held together.

A double helix looks like a twisted ladder. In the double-helix model of DNA, the two strands twist around each other like spiral staircases. The double helix accounted for Franklin’s X-ray pattern and explains Chargaff’s rule of base pairing and how the two strands of DNA are held together.

Antiparallel Strands In the double-helix model, the two strands of DNA are “antiparallel”—they run in opposite directions. This arrangement enables the nitrogenous bases on both strands to come into contact at the center of the molecule. It also allows each strand of the double helix to carry a sequence of nucleotides, arranged almost like letters in a four-letter alphabet.

Hydrogen Bonding Watson and Crick discovered that hydrogen bonds could form between certain nitrogenous bases, providing just enough force to hold the two DNA strands together. Hydrogen bonds are relatively weak chemical forces that allow the two strands of the helix to separate. The ability of the two strands to separate is critical to DNA’s functions.

Base Pairing Watson and Crick’s model showed that hydrogen bonds could create a nearly perfect fit between nitrogenous bases along the center of the molecule. These bonds would form only between certain base pairs—adenine with thymine, and guanine with cytosine. This nearly perfect fit between A–T and G–C nucleotides is known as base pairing, and is illustrated in the figure.

Base Pairing Watson and Crick realized that base pairing explained Chargaff’s rule. It gave a reason why [A] = [T] and [G] = [C]. For every adenine in a double-stranded DNA molecule, there had to be exactly one thymine. For each cytosine, there was one guanine.

DNA, genes, and chromosomes compose the molecular basis of heredity.
A chromosome is a structure in the nucleus of a cell that consists of one long molecule of DNA that is condensed and tightly coiled around associated proteins. Each chromosome consists of hundreds of genes that code for proteins or RNA molecules. Each cell in an organism’s body contains a complete set of chromosomes. The number of chromosomes varies with the type of organism. For example, humans have 23 pairs of chromosomes; dogs have 39 pairs; and potatoes have 24 pairs. One pair of chromosomes in an organism determines the sex (male, female) of the organism; these are known as sex chromosomes. All other chromosomes are known as autosomes. Cells (except for sex cells) contain one pair of each type of chromosome.

Each pair of chromosomes has genes that code for the same proteins
Each pair of chromosomes has genes that code for the same proteins. One chromosome in each pair was inherited from the male parent and the other from the female parent. In this way traits of parents are passed to offspring. A gene is a specific location on a chromosome, consisting of a segment of DNA that codes for a particular protein or RNA molecule that has a function in an organism. Genes are cellular units of information that determine how organisms inherit characteristics from their parents. The particular protein or RNA molecules coded by each gene determine the characteristics of an organism

DNA, which comprises an organism’s chromosomes, is considered the “code of life” (genetic code) because it contains the instructions for building each protein that an organism needs. DNA provides the blueprint for the synthesis of proteins via the sequence of nucleotides that make up the DNA strand. Each individual organism has unique characteristics that arise because of the differences in the nucleotide sequences found in the organism’s DNA. Organisms that are closely related share more genes (with similar nucleotide sequences) than organisms that are less closely related. For example red maple trees have many of the same genes as other red maple trees. Furthermore, red maple trees have more genes in common with oak trees than with earthworms.

What are our three types of RNA? What does each type do?
Bell work 10/27/16 What are our three types of RNA? What does each type do?

Lesson Overview 13.1 RNA

THINK ABOUT IT DNA is the genetic material of cells. The sequence of nucleotide bases in the strands of DNA carries some sort of code. In order for that code to work, the cell must be able to understand it. What, exactly, do those bases code for? Where is the cell’s decoding system?

The Role of RNA How does RNA differ from DNA?

The Role of RNA How does RNA differ from DNA?
There are three important differences between RNA and DNA: (1) the sugar in RNA is ribose instead of deoxyribose, (2) RNA is generally single-stranded and not double-stranded, and (3) RNA contains uracil in place of thymine.

The Role of RNA Genes contain coded DNA instructions that tell cells how to build proteins. The first step in decoding these genetic instructions is to copy part of the base sequence from DNA into RNA. RNA, like DNA, is a nucleic acid that consists of a long chain of nucleotides. RNA then uses the base sequence copied from DNA to direct the production of proteins.

Comparing RNA and DNA Each nucleotide in both DNA and RNA is made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base. There are three important differences between RNA and DNA: (1) The sugar in RNA is ribose instead of deoxyribose. (2) RNA is generally single-stranded and not double-stranded. (3) RNA contains uracil in place of thymine. These chemical differences make it easy for the enzymes in the cell to tell DNA and RNA apart.

Comparing RNA and DNA The roles played by DNA and RNA are similar to the master plans and blueprints used by builders.

Comparing RNA and DNA A master plan has all the information needed to construct a building. Builders never bring a 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.

Comparing RNA and DNA Similarly, the cell uses DNA “master plan” to prepare RNA “blueprints.” The DNA molecule stays safely in the cell’s nucleus, while RNA molecules go to the protein-building sites in the cytoplasm—the ribosomes.

Functions of RNA You can think of an RNA molecule, as a disposable copy of a segment of DNA, a working copy of a single gene. RNA has many functions, but most RNA molecules are involved in protein synthesis only. RNA controls the assembly of amino acids into proteins. Each type of RNA molecule specializes in a different aspect of this job.

Functions of RNA The three main types of RNA are messenger RNA, ribosomal RNA, and transfer RNA.

Messenger RNA 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): They carry information from DNA to other parts of the cell.

Ribosomal RNA Proteins are assembled on ribosomes, small organelles composed of two subunits. These ribosome subunits are made up of several ribosomal RNA (rRNA) molecules and as many as 80 different proteins.

Transfer RNA When a protein is built, a transfer RNA (tRNA) molecule transfers each amino acid to the ribosome as it is specified by the coded messages in mRNA.

RNA Synthesis How does the cell make RNA?

RNA Synthesis How does the cell make RNA?
In transcription, segments of DNA serve as templates to produce complementary RNA molecules.

Transcription Most of the work of making RNA takes place during transcription. During transcription, segments of DNA serve as templates to produce complementary RNA molecules. The base sequences of the transcribed RNA complement the base sequences of the template DNA.

Transcription In prokaryotes, RNA synthesis and protein synthesis take place in the cytoplasm. In eukaryotes, RNA is produced in the cell’s nucleus and then moves to the cytoplasm to play a role in the production of proteins. Our focus will be on transcription in eukaryotic cells.

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

Transcription RNA polymerase binds to DNA during transcription and separates the DNA strands.

Transcription RNA polymerase then uses one strand of DNA as a template from which to assemble nucleotides into a complementary strand of RNA.

Promoters RNA polymerase binds only to promoters, regions of DNA that have specific base sequences. Promoters are signals in the DNA molecule that show RNA polymerase exactly where to begin making RNA. Similar signals in DNA cause transcription to stop when a new RNA molecule is completed.

RNA Editing RNA molecules sometimes require bits and pieces to be cut out of them before they can go into action. The portions that are cut out and discarded are called introns. In eukaryotes, introns are taken out of pre-mRNA molecules while they are still in the nucleus. The remaining pieces, known as exons, are then spliced back together to form the final mRNA.

RNA Editing Biologists don’t have a complete answer as to why cells use energy to make a large RNA molecule and then throw parts of that molecule away. Some pre-mRNA molecules may be cut and spliced in different ways in different tissues, making it possible for a single gene to produce several different forms of RNA.

RNA Editing Introns and exons may also play a role in evolution, making it possible for very small changes in DNA sequences to have dramatic effects on how genes affect cellular function.

On a blank sheet of paper use the following words to make a Venn diagram Comparing DNA and RNA
Deoxyribose Ribose Single Stranded Double Stranded Guanine, Adenine, Thymine, Cytosine, Uracil A nucleotide containing phosphate, sugar, and a nitrogenous base. Inside nucleus Outside nucleus

Lesson Overview 12.3 DNA Replication

Look at the Assignment board – Copy it down or take a picture.
Your Pogil will be due tomorrow. If you haven’t yet turned your gizmo in, you need to do so by Wednesday. On Thursday all of the work you’ve done out of your books for this unit is due – we’ve done two sections already (12.2 & 13.1), and will be doing two more by Thursday. You will have a test on Friday, and you will have a study guide due then. **** The syllabus states – all work is due by the due date. For each day late the assignment will have 10% of the points subtracted from it. After day 5 the assignment will result in a zero. ****If you miss my class you need a readmit for me to give you any missing work.

THINK ABOUT IT Before a cell divides, its DNA must first be copied.
How might the double-helix structure of DNA make that possible?

Copying the Code What role does DNA polymerase play in copying DNA?

Copying the Code What role does DNA polymerase play in copying DNA?
DNA polymerase is an enzyme that joins individual nucleotides to produce a new strand of DNA.

Copying the Code Base pairing in the double helix explained how DNA could be copied, or replicated, because each base on one strand pairs with only one base on the opposite strand. Each strand of the double helix has all the information needed to reconstruct the other half by the mechanism of base pairing. Because each strand can be used to make the other strand, the strands are said to be complementary.

The Replication Process
Before a cell divides, it duplicates its DNA in a copying process called replication. This process ensures that each resulting cell has the same complete set of DNA molecules.

During 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.

The two strands of the double helix separate, or “unzip,” allowing two replication forks to form.

As each new strand forms, new bases are added following the rules of base pairing. If the base on the old strand is adenine, then thymine is added to the newly forming strand. Likewise, guanine is always paired to cytosine.

The result of replication is two DNA molecules identical to each other and to the original molecule. Each DNA molecule resulting from replication has one original strand and one new strand.

The Role of Enzymes The principal enzyme involved in DNA replication is called DNA polymerase. DNA polymerase is an enzyme that joins individual nucleotides to produce a new strand of DNA. DNA polymerase also “proofreads” each new DNA strand, ensuring that each molecule is a perfect copy of the original.

Telomeres The tips of chromosomes are known as telomeres.
The ends of DNA molecules, located at the telomeres, are particularly difficult to copy. Over time, DNA may actually be lost from telomeres each time a chromosome is replicated. An enzyme called telomerase compensates for this problem by adding short, repeated DNA sequences to telomeres, lengthening the chromosomes slightly and making it less likely that important gene sequences will be lost from the telomeres during replication.

Replication in Living Cells
How does DNA replication differ in prokaryotic cells and eukaryotic cells?

How does DNA replication differ in prokaryotic cells and eukaryotic cells? Replication in most prokaryotic cells starts from a single point and proceeds in two directions until the entire chromosome is copied. In eukaryotic cells, replication may begin at dozens or even hundreds of places on the DNA molecule, proceeding in both directions until each chromosome is completely copied

The cells of most prokaryotes have a single, circular DNA molecule in the cytoplasm, containing nearly all the cell’s genetic information. Eukaryotic cells, on the other hand, can have up to 1000 times more DNA. Nearly all of the DNA of eukaryotic cells is found in the nucleus.

Prokaryotic DNA Replication
In most prokaryotes, DNA replication does not start until regulatory proteins bind to a single starting point on the chromosome. This triggers the beginning of DNA replication. Replication in most prokaryotic cells starts from a single point and proceeds in two directions until the entire chromosome is copied.

Prokaryotic DNA Replication
Often, the two chromosomes produced by replication are attached to different points inside the cell membrane and are separated when the cell splits to form two new cells.

Eukaryotic DNA Replication
Eukaryotic chromosomes are generally much bigger than those of prokaryotes. In eukaryotic cells, replication may begin at dozens or even hundreds of places on the DNA molecule, proceeding in both directions until each chromosome is completely copied.

Eukaryotic DNA Replication
The two copies of DNA produced by replication in each chromosome remain closely associated until the cell enters prophase of mitosis. At that point, the chromosomes condense, and the two chromatids in each chromosome become clearly visible. They separate from each other in anaphase of mitosis, producing two cells, each with a complete set of genes coded in DNA.

The process of DNA replication ensures that every new cell that results from mitotic division has identical DNA. Enzymes facilitate the replication process: The first enzyme unzips the two strands of DNA that compose the double helix, separating paired bases. Each base that is exposed can only bond to its complementary base. Each of the separated strands serves as a template for the attachment of complementary bases, forming a new strand, identical to the one from which it was “unzipped”. The result is two identical DNA molecules.

13.2 Ribosomes and Protein Synthesis
Lesson Overview 13.2 Ribosomes and Protein Synthesis

THINK ABOUT IT How would you build a system to read the messages that are coded in genes and transcribed into RNA? Would you read the bases one at a time, as if the code were a language with just four words—one word per base? Perhaps you would read them as individual letters that can be combined to spell longer words.

The Genetic Code What is the genetic code, and how is it read?

The Genetic Code What is the genetic code, and how is it read?
The genetic code is read three “letters” at a time, so that each “word” is three bases long and corresponds to a single amino acid.

The Genetic Code The first step in decoding genetic messages is to transcribe a nucleotide base sequence from DNA to RNA. This transcribed information contains a code for making proteins.

The Genetic Code Proteins are made by joining amino acids together into long chains, called polypeptides. As many as 20 different amino acids are commonly found in polypeptides.

The Genetic Code The specific amino acids in a polypeptide, and the order in which they are joined, determine the properties of different proteins. The sequence of amino acids influences the shape of the protein, which in turn determines its function.

The Genetic Code RNA contains four different bases: adenine, cytosine, guanine, and uracil. These bases form a “language,” or genetic code, with just four “letters”: A, C, G, and U.

The Genetic Code Each three-letter “word” in mRNA is known as a codon.
A codon consists of three consecutive bases that specify a single amino acid to be added to the polypeptide chain.

How to Read Codons Because there are four different bases in RNA, there are 64 possible three-base codons (4 × 4 × 4 = 64) in the genetic code. This circular table shows the amino acid to which each of the 64 codons corresponds. To read a codon, start at the middle of the circle and move outward.

How to Read Codons Most amino acids can be specified by more than one codon. For example, six different codons—UUA, UUG, CUU, CUC, CUA, and CUG—specify leucine. But only one codon—UGG—specifies the amino acid tryptophan.

Start and Stop Codons The genetic code has punctuation marks.
The methionine codon AUG serves as the initiation, or “start,” codon for protein synthesis. Following the start codon, mRNA is read, three bases at a time, until it reaches one of three different “stop” codons, which end translation.

Translation What role does the ribosome play in assembling proteins?

Translation What role does the ribosome play in assembling proteins?
Ribosomes use the sequence of codons in mRNA to assemble amino acids into polypeptide chains.

Translation The sequence of nucleotide bases in an mRNA molecule is a set of instructions that gives the order in which amino acids should be joined to produce a polypeptide. The forming of a protein requires the folding of one or more polypeptide chains. Ribosomes use the sequence of codons in mRNA to assemble amino acids into polypeptide chains. The decoding of an mRNA message into a protein is a process known as translation.

Steps in Translation Messenger RNA is transcribed in the nucleus and then enters the cytoplasm for translation.

Steps in Translation Translation begins when a ribosome attaches to an mRNA molecule in the cytoplasm. As the ribosome reads each codon of mRNA, it directs tRNA to bring the specified amino acid into the ribosome. One at a time, the ribosome then attaches each amino acid to the growing chain.

Steps in Translation Each tRNA molecule carries just one kind of amino acid. In addition, each tRNA molecule has three unpaired bases, collectively called the anticodon—which is complementary to one mRNA codon. The tRNA molecule for methionine has the anticodon UAC, which pairs with the methionine codon, AUG.

Steps in Translation The ribosome has a second binding site for a tRNA molecule for the next codon. If that next codon is UUC, a tRNA molecule with an AAG anticodon brings the amino acid phenylalanine into the ribosome.

Steps in Translation The ribosome helps form a peptide bond between the first and second amino acids—methionine and phenylalanine. At the same time, the bond holding the first tRNA molecule to its amino acid is broken.

Steps in Translation That tRNA then moves into a third binding site, from which it exits the ribosome. The ribosome then moves to the third codon, where tRNA brings it the amino acid specified by the third codon.

Steps in Translation The polypeptide chain continues to grow until the ribosome reaches a “stop” codon on the mRNA molecule. When the ribosome reaches a stop codon, it releases both the newly formed polypeptide and the mRNA molecule, completing the process of translation.

The Roles of tRNA and rRNA in Translation
Ribosomes are composed of roughly 80 proteins and three or four different rRNA molecules. These rRNA molecules help hold ribosomal proteins in place and help locate the beginning of the mRNA message. They may even carry out the chemical reaction that joins amino acids together.

The Molecular Basis of Heredity
What is the “central dogma” of molecular biology?

What is the “central dogma” of molecular biology? The central dogma of molecular biology is that information is transferred from DNA to RNA to protein.

Most genes contain instructions for assembling proteins.

Many proteins are enzymes, which catalyze and regulate chemical reactions. A gene that codes for an enzyme to produce pigment can control the color of a flower. Another gene produces proteins that regulate patterns of tissue growth in a leaf. Yet another may trigger the female or male pattern of development in an embryo. Proteins are microscopic tools, each specifically designed to build or operate a component of a living cell.

Molecular biology seeks to explain living organisms by studying them at the molecular level, using molecules like DNA and RNA. The central dogma of molecular biology is that information is transferred from DNA to RNA to protein. There are many exceptions to this “dogma,” but it serves as a useful generalization that helps explain how genes work.

Gene expression is the way in which DNA, RNA, and proteins are involved in putting genetic information into action in living cells. DNA carries information for specifying the traits of an organism. The cell uses the sequence of bases in DNA as a template for making mRNA.

The codons of mRNA specify the sequence of amino acids in a protein. Proteins, in turn, play a key role in producing an organism’s traits.

One of the most interesting discoveries of molecular biology is the near-universal nature of the genetic code. Although some organisms show slight variations in the amino acids assigned to particular codons, the code is always read three bases at a time and in the same direction. Despite their enormous diversity in form and function, living organisms display remarkable unity at life’s most basic level, the molecular biology of the gene.

When a particular protein is needed, the cell must make the protein through the process of transcription and translation. DNA molecules (which contain the code) do not leave the nucleus of the cell. Protein synthesis occurs on ribosomes located outside of the nucleus. Therefore, the code must be carried from the nucleus to the cytoplasm. Transcription is the process by which a portion of the molecule of DNA is copied into a complementary strand of RNA. The process of transcription takes place as follows: 1. An enzyme attaches to the DNA molecule at the gene of interest. 2. The two strands of DNA separate at that location. 3. Complementary RNA nucleotides bond to the nitrogenous bases on one of the separated DNA strands. 4. The chain of RNA nucleotides forms a single-stranded molecule of RNA by using the DNA strand as a template. 5. When a stop codon is reached, the RNA strand separates from the DNA molecule, leaves the nucleus and goes through the nuclear membrane into the cytoplasm. 6. The two DNA strands rejoin.

Translation is the process by which the genetic message, carried by the mRNA, is used to assemble a protein. The mRNA attaches to a ribosome, which contains proteins and ribosomal RNA (rRNA). The function of ribosomes is to assemble proteins according to the genetic message Each three-base nucleotide sequence on the mRNA is called a codon. Each codon specifies a particular amino acid that will be used to build the protein molecule. For example, if the DNA sequence was GAC, then the RNA sequence becomes CUG (transcription) and the amino acid that is coded is Leucine (translation). Another type of RNA, transfer RNA (tRNA), brings amino acids to the ribosome in the order specified by the codon sequence on the mRNA. At one end of each tRNA is the anticodon, a region that consists of three nucleotide bases that are complementary to the codon of mRNA. The other end of the tRNA molecule binds to the specific amino acid that is determined by the mRNA codon.

The translation process takes place as follows:
1. The anticodon of the tRNA, with its attached amino acid, pairs to the codon of the mRNA, which is attached to a ribosome. 2. When a second tRNA with its specific amino acid pairs to the next codon in sequence, the attached amino acid breaks from the first tRNA and is bonded to the amino acid of the second tRNA. 3. The ribosome forms a peptide bond between the amino acids, and an amino acid chain begins to form. 4. The empty tRNA moves off and picks up another matching amino acid from the cytoplasm in the cell. 5. This sequence is repeated until the ribosome reaches a stop codon on the mRNA, which signals the end of protein synthesis.

In your groups, build a protein Each group member is responsible for one protein
Your group will be given multiple strands of DNA – each coding for a different protein. Each group member must complete one protein. First you must complete transcription. On a blank sheet of computer paper you must transcribe your DNA into RNA. From there you need to label each codon. Provide each anti codon Using the key in your book on page 367 decipher each codon sequence into its respective amino acid. Make sure to keep in mind start and stop codons. On your computer paper make sure you label your mRNA, rRNA, and tRNA. When you think you’ve finished, check with your group, and then bring it to me. Also, make sure you’ve labeled your Protein with the name I gave you. **** Pages 368 and 369 in your book have a very good illustration of all three RNA’s as well as the translation process.

3rd – These are your groups, sit at desks with these groups.
Shamar, Alexis, DJP, Eddy Willy B, Bret, Devon, Hannah Curren, Adrien, Rita, Ambrosia Carson, Ethan, Nevaeh, Carneisha Elijah, Kelly, Camille, Darren Elliot, Maddy, Nydia, Cameron

4th – These are your groups, sit at a group of desks together.
Grace, Taylor, Tyrese, Tanner Alan, Auston, Chloe, Jessie Sean, Jennifer, Jack, Amaya Caroline, Kyle, Joseph, Taniah Kaziah, Sydney, Luke, Holden Chase, Mason, Jamie, Noah

13.3 pages 372-376 Define 5 highlighted words
Explain the difference between chromosomal mutations and point mutations What are the three types of point mutations? Give an example of a good mutation and a bad one. Give an example of polyploidy

Lesson Overview 13.3 Mutations

THINK ABOUT IT The sequence of bases in DNA are like the letters of a coded message. What would happen if a few of those letters changed accidentally, altering the message? What effects would you predict such changes to have on genes and the polypeptides for which they code?

Types of Mutations What are mutations?

Types of Mutations What are mutations?
Mutations are heritable changes in genetic information.

Types of Mutations Now and then cells make mistakes in copying their own DNA, inserting the wrong base or even skipping a base as a strand is put together. These variations are called mutations, from the Latin word mutare, meaning “to change.” Mutations are heritable changes in genetic information.

Types of Mutations All mutations fall into two basic categories:
Those that produce changes in a single gene are known as gene mutations. Those that produce changes in whole chromosomes are known as chromosomal mutations.

Gene Mutations Mutations that involve changes in one or a few nucleotides are known as point mutations because they occur at a single point in the DNA sequence. They generally occur during replication. If a gene in one cell is altered, the alteration can be passed on to every cell that develops from the original one.

Gene Mutations Point mutations include substitutions, insertions, and deletions.

Substitutions In a substitution, one base is changed to a different base. Substitutions usually affect no more than a single amino acid, and sometimes they have no effect at all.

Substitutions In this example, the base cytosine is replaced by the base thymine, resulting in a change in the mRNA codon from CGU (arginine) to CAU (histidine). However, a change in the last base of the codon, from CGU to CGA for example, would still specify the amino acid arginine.

Insertions and Deletions
Insertions and deletions are point mutations in which one base is inserted or removed from the DNA sequence. If a nucleotide is added or deleted, the bases are still read in groups of three, but now those groupings shift in every codon that follows the mutation.

Insertions and Deletions
Insertions and deletions are also called frameshift mutations because they shift the “reading frame” of the genetic message. Frameshift mutations can change every amino acid that follows the point of the mutation and can alter a protein so much that it is unable to perform its normal functions.

Chromosomal Mutations
Chromosomal mutations involve changes in the number or structure of chromosomes. These mutations can change the location of genes on chromosomes and can even change the number of copies of some genes. There are four types of chromosomal mutations: deletion, duplication, inversion, and translocation.

Deletion involves the loss of all or part of a chromosome.

Duplication produces an extra copy of all or part 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.

Effects of Mutations How do mutations affect genes?

Effects of Mutations How do mutations affect genes?
The effects of mutations on genes vary widely. Some have little or no effect; and some produce beneficial variations. Some negatively disrupt gene function. Mutations often produce proteins with new or altered functions that can be useful to organisms in different or changing environments.

Effects of Mutations Genetic material can be altered by natural events or by artificial means. The resulting mutations may or may not affect an organism. Some mutations that affect individual organisms can also affect a species or even an entire ecosystem.

Effects of Mutations Many mutations are produced by errors in genetic processes. For example, some point mutations are caused by errors during DNA replication. The cellular machinery that replicates DNA inserts an incorrect base roughly once in every 10 million bases. Small changes in genes can gradually accumulate over time.

Effects of Mutations Stressful environmental conditions may cause some bacteria to increase mutation rates. This can actually be helpful to the organism, since mutations may sometimes give such bacteria new traits, such as the ability to consume a new food source or to resist a poison in the environment.

Mutagens Some mutations arise from mutagens, chemical or physical agents in the environment. Chemical mutagens include certain pesticides, a few natural plant alkaloids, tobacco smoke, and environmental pollutants. Physical mutagens include some forms of electromagnetic radiation, such as X-rays and ultraviolet light.

Mutagens If these mutagens interact with DNA, they can produce mutations at high rates. Some compounds interfere with base-pairing, increasing the error rate of DNA replication. Others weaken the DNA strand, causing breaks and inversions that produce chromosomal mutations. Cells can sometimes repair the damage; but when they cannot, the DNA base sequence changes permanently.

Harmful and Helpful Mutations
The effects of mutations on genes vary widely. Some have little or no effect; and some produce beneficial variations. Some negatively disrupt gene function. Whether a mutation is negative or beneficial depends on how its DNA changes relative to the organism’s situation. Mutations are often thought of as negative because they disrupt the normal function of genes. However, without mutations, organisms cannot evolve, because mutations are the source of genetic variability in a species.

Harmful Effects Some of the most harmful mutations are those that dramatically change protein structure or gene activity. The defective proteins produced by these mutations can disrupt normal biological activities, and result in genetic disorders. Some cancers, for example, are the product of mutations that cause the uncontrolled growth of cells.

Harmful Effects Sickle cell disease is a disorder associated with changes in the shape of red blood cells. Normal red blood cells are round. Sickle cells appear long and pointed. Sickle cell disease is caused by a point mutation in one of the polypeptides found in hemoglobin, the blood’s principal oxygen-carrying protein. Among the symptoms of the disease are anemia, severe pain, frequent infections, and stunted growth.

Beneficial Effects Some of the variation produced by mutations can be highly advantageous to an organism or species. Mutations often produce proteins with new or altered functions that can be useful to organisms in different or changing environments. For example, mutations have helped many insects resist chemical pesticides. Some mutations have enabled microorganisms to adapt to new chemicals in the environment.

Beneficial Effects Plant and animal breeders often make use of “good” mutations. For example, when a complete set of chromosomes fails to separate during meiosis, the gametes that result may produce triploid (3N) or tetraploid (4N) organisms. The condition in which an organism has extra sets of chromosomes is called polyploidy.

Beneficial Effects Polyploid plants are often larger and stronger than diploid plants. Important crop plants—including bananas and limes—have been produced this way. Polyploidy also occurs naturally in citrus plants, often through spontaneous mutations.

A mutation is the alteration of an organism’s DNA
A mutation is the alteration of an organism’s DNA. Mutations can range from a change in one base pair to the insertion or deletion of large segments of DNA. Mutations can result from a malfunction during the processes of mitosis or meiosis or from exposure to a physical or a chemical agent, a mutagen. Most mutations are automatically repaired by the organism’s enzymes and therefore have no effect. However, when the mutation is not repaired, the resulting altered chromosome or gene structure can be passed to all subsequent daughter cells of the mutant cell, which may have negative, positive or no consequences for the cell, organism, or future generations.

If the mutant cell is a body cell (somatic cell), the daughter cells can be affected by the altered DNA, but the mutation will not be passed to the offspring of the organism. Body cell mutations can contribute to the aging process or the development of many types of cancer. If the mutant cell is a gamete (sex cell), the altered DNA will be transmitted to the offspring and may be passed to subsequent generations. Gamete cell mutations can result in genetic disorders. If the mutation affects a single gene, it is known as a gene mutation

For example, the genetic basis of sickle-cell disease is the mutation of a single nucleotide base pair in the gene that codes for one of the proteins of hemoglobin. Other examples of genetic disorders caused by gene mutations are Tay-Sachs disease, Huntington’s disease, Cystic fibrosis, Hemophilia A or albinism. If the mutation affects a group of genes or an entire chromosome, it is known as a chromosomal mutation. Malfunction during meiosis can result in a gamete with an abnormal number of chromosomes. Examples of abnormalities in humans due to an abnormal number of sex chromosomes are Klinefelter’s syndrome (male; XXY genotype) and Turner’s syndrome (female; missing or structurally altered X). An example of an abnormality in humans due to an abnormal number of autosomal chromosomes (refer to H.B.4A.1) is Down’s syndrome.

In some cases mutations are beneficial to organisms
In some cases mutations are beneficial to organisms. Beneficial mutations are changes that may be useful to organisms in different or changing environments. These mutations result in phenotypes that are favored by natural selection and will eventually increase in frequency in a population. Gene mutations that occur during replication may or may not affect the production or function of the protein for which the gene codes. A point mutation is the substitution, addition, or removal of a single nucleotide. In a substitution mutation, one nucleotide replaces another. The new codon may or may not signal the insertion of the wrong amino acid. Sometimes the insertion of the wrong amino acid does not affect protein function because the change does not significantly alter the protein’s structure (shape). The deletion or addition or a nucleotide causes all subsequent codons to be misread (Frameshift mutation) so are likely to have a disastrous effect on the protein’s function.

15.3 Applications of Genetic Engineering
Lesson Overview 15.3 Applications of Genetic Engineering

THINK ABOUT IT Have you eaten any genetically modified food lately?
If you’ve eaten corn, potatoes, or soy products in any of your meals this week, chances are close to 100 percent that you’ve eaten foods modified in some way by genetic engineering.

Agriculture and Industry
How can genetic engineering benefit agriculture and industry?

How can genetic engineering benefit agriculture and industry? Ideally, genetic modification could lead to better, less expensive, and more nutritious food as well as less harmful manufacturing processes.

Almost everything we eat and much of what we wear come from living organisms. Researchers have used genetic engineering to try to improve the products we get from plants and animals. Genetic modification could lead to better, less expensive, and more nutritious food as well as less harmful manufacturing processes.

GM Crops Since their introduction in 1996, genetically modified (GM) plants have become an important component of our food supply. One genetic modification uses bacterial genes that produce a protein known as Bt toxin. This toxin is harmless to humans and most other animals, but enzymes in the digestive systems of insects convert Bt to a form that kills the insects. Plants with the Bt gene do not have to be sprayed with pesticides. In addition, they produce higher yields of crops.

GM Crops Other useful genetic modifications include resistance to herbicides, which are chemicals that destroy weeds, and resistance to viral infections.

GM Crops A Summary of the Adoption of GM Crops from 1996-2007
The modified traits shown in the graph include herbicide tolerance (HT) and insect resistance (Bt).

GM Crops Some transgenic plants may soon produce foods that are resistant to rot and spoilage. Engineers are currently developing GM plants that may produce plastics for the manufacturing industry.

GM Animals Transgenic animals are becoming more important to our food supply. About 30 percent of the milk in U.S. markets comes from cows that have been injected with hormones made by recombinant-DNA techniques to increase milk production. Pigs can be genetically modified to produce more lean meat or high levels of healthy omega-3 acids. Using growth-hormone genes, scientists have developed transgenic salmon that grow much more quickly than wild salmon.

GM Animals Scientists in Canada combined spider genes into the cells of lactating goats. The goats began to produce silk along with their milk. The silk can be extracted from the milk and woven into a thread that can be used to create a light, tough, and flexible material.

GM Animals Scientists are working to combine a gene for lysozyme—an antibacterial protein found in human tears and breast milk—into the DNA of goats. Milk from these goats may help prevent infections in young children who drink it.

GM Animals Researchers hope that cloning will enable them to make copies of transgenic animals, which would increase the food supply and could help save endangered species. In 2008, the U.S. government approved the sale of meat and milk from cloned animals. Cloning technology could allow farmers to duplicate the best qualities of prize animals without the time and complications of traditional breeding.

Health and Medicine How can recombinant-DNA technology improve human health?

Health and Medicine How can recombinant-DNA technology improve human health? Today, recombinant-DNA technology is the source of some of the most important and exciting advances in the prevention and treatment of disease.

Preventing Disease Golden rice is a GM plant that contains increased amounts of provitamin A, also known as beta-carotene—a nutrient that is essential for human health. Two genes engineered into the rice genome help the grains produce and accumulate beta-carotene. Provitamin A deficiencies produce serious medical problems, including infant blindness. There is hope that provitamin A–rich golden rice will help prevent these problems. Other scientists are developing transgenic plants and animals that produce human antibodies to fight disease.

Preventing Disease In the future, transgenic animals may provide us with an ample supply of our own proteins. Several laboratories have engineered transgenic sheep and pigs that produce human proteins in their milk, making it easy to collect and refine the proteins. Many of these proteins can be used in disease prevention.

Medical Research Transgenic animals are often used as test subjects in medical research. They can simulate human diseases in which defective genes play a role. Scientists use models based on these simulations to follow the onset and progression of diseases and to construct tests of new drugs that may be useful for treatment. This approach has been used to develop models for disorders like Alzheimer’s disease and arthritis.

Treating Disease Recombinant-DNA technology can be used to make important proteins that could prolong and even save human lives. For example, human growth hormone, which is used to treat patients suffering from pituitary dwarfism, is now widely available because it is mass-produced by recombinant bacteria. Other products now made in genetically engineered bacteria include insulin to treat diabetes, blood-clotting factors for hemophiliacs, and potential cancer-fighting molecules such as interleukin-2 and interferon.

Treating Disease Gene therapy is the process of changing a gene to treat a medical disease or disorder. In gene therapy, an absent or faulty gene is replaced by a normal, working gene. This process allows the body to make the protein or enzyme it needs, which eliminates the cause of the disorder.

Treating Disease — One Example of Gene Therapy
To deliver therapeutic genes to target cells researchers engineer a virus that cannot reproduce or cause harm.

The DNA containing the therapeutic gene is inserted into the modified virus.

The patient’s cells are then infected with the genetically engineered virus.

In theory the virus will insert the healthy gene into the target cell and correct the defect.

Treating Disease Gene therapy can be risky.
In 1999, 18-year-old Jesse Gelsinger volunteered for a gene therapy experiment designed to treat a genetic disorder of his liver. He suffered a massive reaction from the viruses used to carry genes into his liver cells, and he died a few days later. For gene therapy to become an accepted treatment, we need more reliable ways to insert working genes and to ensure that the DNA used in the therapy does no harm.

Genetic Testing Genetic testing can be used to determine if two prospective parents are carrying the alleles for a genetic disorder such as cystic fibrosis (CF). Because the CF allele has slightly different DNA sequences from its normal counterpart, genetic tests use labeled DNA probes that can detect and distinguish the complementary base sequences found in the disease-causing alleles. Some genetic tests search for changes in cutting sites of restriction enzymes, while others use PCR to detect differences between the lengths of normal and abnormal alleles. Genetic tests are now available for diagnosing hundreds of disorders.

Examining Active Genes
The same genes are not active in every cell. By studying which genes are active and which are inactive in different cells, scientists can understand how the cells function normally and what happens when genes don’t work as they should. Scientists use DNA microarray technology to study hundreds or even thousands of genes at once to understand their activity levels.

A DNA microarray is a glass slide or silicon chip to which spots of single-stranded DNA have been tightly attached. Typically each spot contains a different DNA fragment. Differently colored tags are used to label the source of DNA.

For example, to compare the genes in cancer cells with genes in normal cells, the mRNA would first be isolated from both types of cells. Enzymes are used to copy the mRNA base sequence into single-stranded DNA labeled with fluorescent colors—red for the cancer cell and green for the normal cell.

Both samples of labeled DNA would be mixed together and they would then compete to bind to the complementary DNA sequences already in the microarray.

If the cancer cell produces more of a particular form of mRNA, then more red-labeled molecules will bind at the spot for that gene, turning it red. Where the normal cell produces more mRNA for another gene, the spot will be green. Where there is no difference between the two cell types, the spot will be yellow because it contains both colors.

Personal Identification
How is DNA used to identify individuals?

How is DNA used to identify individuals? DNA fingerprinting analyzes sections of DNA that may have little or no function but that vary widely from one individual to another.

No individual is exactly like any other genetically—except for identical twins, who share the same genome. Chromosomes contain many regions with repeated DNA sequences that do not code for proteins. These vary from person to person. Here, one sample has 12 repeats between genes A and B, while the second has 9 repeats between the same genes. DNA fingerprinting can be used to identify individuals by analyzing these sections of DNA that may have little or no function but that vary widely from one individual to another.

In DNA fingerprinting, restriction enzymes first cut a small sample of human DNA into fragments containing genes and repeats. Note that the repeat fragments from these two samples are of different lengths. Next, gel electrophoresis separates the restriction fragments by size.

A DNA probe then detects the fragments that have highly variable regions, revealing a series of variously sized DNA bands.

If enough combinations of enzymes and probes are used, the resulting pattern of bands can be distinguished statistically from that of any other individual in the world. DNA samples can be obtained from blood, sperm, or tissue—even from a hair strand if it has tissue at the root.

Forensic Science The precision and reliability of DNA fingerprinting has revolutionized forensics—the scientific study of crime scene evidence. DNA fingerprinting has helped solve crimes, convict criminals, and even overturn wrongful convictions. To date, DNA evidence has saved more than 110 wrongfully convicted prisoners from death sentences.

Forensic Science DNA forensics is used in wildlife conservation as well. African elephants are a highly vulnerable species. Poachers, who slaughter the animals mainly for their precious tusks, have reduced their population dramatically. To stop the ivory trade, African officials now use DNA fingerprinting to identify the herds from which black-market ivory has been taken.

Establishing Relationships
When genes are passed from parent to child, genetic recombination scrambles the molecular markers used for DNA fingerprinting, so ancestry can be difficult to trace. The Y chromosome, however, never undergoes crossing over, and only males carry it. Therefore, Y chromosomes pass directly from father to son with few changes.

Similarly, the small DNA molecules found in mitochondria are passed, with very few changes, from mother to child in the cytoplasm of the egg cell. Because mitochondrial DNA (mtDNA) is passed directly from mother to child, your mtDNA is the same as your mother’s mtDNA, which is the same as her mother’s mtDNA. This means that if two people have an exact match in their mtDNA, then there is a very good chance that they share a common maternal ancestor.

Y-chromosome analysis has helped researchers settle longstanding historical questions. One such question—did President Thomas Jefferson father the child of a slave?—may have been answered in 1998. DNA testing showed that descendants of the son of Sally Hemings, a slave on Jefferson’s Virginia estate, carried his Y chromosome. This result suggests Jefferson was the child’s father, although the Thomas Jefferson Foundation continues to challenge that conclusion.

Biotechnology utilizes biological processes, organisms, cells or cellular components to develop new technologies. New tools and products developed by biotechnologists are useful in research, agriculture, industry and the medicine. Genetic Engineering is the deliberate modification of the characteristics of an organism by manipulating its genetic material. The goal is to add one or more new traits that are not already found in that organism. Genetic engineering is accomplished by taking specific genes from one organism and placing them into another organism. Genetic engineering is possible because the genetic code is shared by all organisms. Examples of genetically engineered products currently on the market include human insulin produced by genetically modified bacteria, plants with resistance to some insects, plants that can tolerate herbicides.

An organism that is generated through genetic engineering is considered to be a genetically modified organism (GMO). Techniques used to manipulate DNA Restriction enzymes are used to cut DNA at precise locations. Because it is a very long molecule, DNA needs to be cut into smaller pieces to facilitate studying and working with it. Restriction enzymes are enzymes that cut DNA at particular nucleotide sequences. Each of the many restriction enzymes cuts DNA at a different restriction site.

Gel electrophoresis is used to separate segments of DNA according to length.
After DNA has been cut with a restriction enzyme, the pieces must be separated from one another. For gel electrophoresis, an electric current is applied to a small tray containing a flat slab of gelatin. One end of gel is positively charged and the other is negatively charged. A solution of cut-up DNA is placed in the negative end of the gel. Because DNA has a negative charge, the segments are pulled to the positive end of the gel. Small pieces move through the gel faster than large pieces. A dye is used to be able to see the DNA on the gel slab. Clumps of DNA made up of a certain length segment appear on the gel as bands or lines. Scientists can use the pattern of bands to identify the location of a gene or in DNA fingerprinting.

DNA fingerprinting A genome is the complete genetic material contained within an individual organism. Except for in identical twins, every person’s genome (DNA sequence) is unique. The specific patterns of bands produced by gel electrophoresis create a DNA fingerprint. Because the probability of two individuals having the same DNA fingerprint is extremely small, it provides compelling forensic evidence and can also provide evidence of family relationships.

Bacterial plasmids are used to create recombinant DNA
Recombinant DNA is DNA that contains genes from more than one organism A bacterial plasmid is a tiny ring of DNA carried in the cytoplasm. They are separate from the bacteria’s chromosome and replicate on their own inside the cell. A restriction enzyme is used to cut a desired gene from a strand of “foreign” DNA (i.e. from a different organism than the bacteria from which the plasmid was taken). An example of a desired gene is the human DNA sequence that codes for the protein hormone insulin. The circular bacterial plasmid is cut with the same restriction enzyme. The piece of foreign DNA, with the desired gene, is attached to the open ends of the plasmid DNA. The plasmid and the foreign DNA are bonded together to form recombinant DNA. In the insulin example, the plasmid could be reintroduced into bacterial cells, which would then multiply rapidly and produce insulin in large amounts and at low cost.

Lesson Overview 12.2 The Structure of DNA.

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Lesson Overview 12.2 The Structure of DNA.

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