pGLO and bacterial genomics

Warm Up (2-17-15)

• What do you know about DNA and how it is replicated?

• Try to be as specific as possible.

Outline

• Objectives• DNA transformation background information• Virtual explorations

Objectives

• IWBAT explain what transformation is and how this process occurs.

DNA review

• DNA– Deoxyribonucleic acid– Found in the nucleus in eukaryotes– Genetic code– Allows for organisms to replicate and reproduce

Warm Up (2-18-15)

• Explain the process of transcription and translation and how these processes occur.

Outline

• Objectives• DNA transformation practice

Objectives

• IWBAT model DNA transformation and demonstrate how a section of DNA is spliced by transposons in order for new information to be inserted into the DNA.

Chapter 8 Notes

• McDougal Littell Biology Book• Stephen Nowicki

KEY CONCEPT DNA structure is the same in all organisms.

DNA is composed of four types of nucleotides.

• DNA is made up of a long chain of nucleotides.• Each nucleotide has three parts.

– a phosphate group– a deoxyribose sugar– a nitrogen-containing base

phosphate group

deoxyribose (sugar)

nitrogen-containingbase

• The nitrogen containing bases are the only difference in the four nucleotides.

Watson and Crick determined the three-dimensional structure of DNA by building models.

• They realized that DNA is a double helix that is made up of a sugar-phosphate backbone on the outside with bases on the inside.

• Watson and Crick’s discovery built on the work of Rosalind Franklin and Erwin Chargaff.

– Franklin’s x-ray images suggested that DNA was a double helix of even width.

– Chargaff’s rules stated that A=T and C=G.

TA

CG

Nucleotides always pair in the same way.

• The base-pairing rules show how nucleotides always pair up in DNA.

• Because a pyrimidine (single ring) pairs with a purine (double ring), the helix has a uniform width.

– A pairs with T

– C pairs with G

• The backbone is connected by covalent bonds.

hydrogen bond covalent bond

• The bases are connected by hydrogen bonds.

KEY CONCEPT DNA replication copies the genetic information of a cell.

Replication copies the genetic information.

• A single strand of DNA serves as a template for a new strand.• The rules of base pairing direct

replication.• DNA is replicated during the

S (synthesis) stage of thecell cycle.

• Each body cell gets acomplete set ofidentical DNA.

Proteins carry out the process of replication.

• DNA serves only as a template. • Enzymes and other proteins do the actual work of

replication.– Enzymes unzip the double helix.– Free-floating nucleotides form hydrogen bonds with the

template strand. nucleotide

The DNA molecule unzips in both directions.

– Polymerase enzymes form covalent bonds between nucleotides in the new strand.

– DNA polymerase enzymes bond the nucleotides together to form the double helix.

DNA polymerase

new strand nucleotide

• DNA replication is semiconservative.

original strand new strand

Two molecules of DNA

• Two new molecules of DNA are formed, each with an original strand and a newly formed strand.

There are many origins of replication in eukaryotic chromosomes.

• DNA replication starts at many points in eukaryotic chromosomes.

Replication is fast and accurate.

• DNA polymerases can find and correct errors.

KEY CONCEPT Transcription converts a gene into a single-stranded RNA molecule.

RNA carries DNA’s instructions.

• The central dogma states that information flows in one direction from DNA to RNA to proteins.

• The central dogma includes three processes.

• RNA is a link between DNA and proteins.

replication

transcription

translation

– Replication– Transcription– Translation

• RNA differs from DNA in three major ways.

– RNA has a ribose sugar.– RNA has uracil instead of thymine.– RNA is a single-stranded structure.

Transcription makes three types of RNA.

• Transcription copies DNA to make a strand of RNA.

• Transcription is catalyzed by RNA polymerase.

– RNA polymerase and other proteins form a transcription complex.

– The transcription complex recognizes the start of a gene and unwinds a segment of it.

start site

nucleotides

transcription complex

– RNA polymerase bonds the nucleotides together.– The DNA helix winds again as the gene is transcribed.

– Nucleotides pair with one strand of the DNA.

DNA

RNA polymerase moves along the DNA

– The RNA strand detaches from the DNA once the gene is transcribed.

RNA

• Transcription makes three types of RNA.

– Messenger RNA (mRNA) carries the message that will be translated to form a protein.

– Ribosomal RNA (rRNA) forms part of ribosomes where proteins are made.

– Transfer RNA (tRNA) brings amino acids from the cytoplasm to a ribosome.

The transcription process is similar to replication.

• Transcription and replication both involve complex enzymes and complementary base pairing.

• The two processes have different end results.– Replication copies

all the DNA;transcription copiesa gene.

– Replication makesone copy;transcription canmake many copies.

growing RNA strands

DNA

onegene

KEY CONCEPT Translation converts an mRNA message into a polypeptide, or protein.

Amino acids are coded by mRNA base sequences.

• Translation converts mRNA messages into polypeptides.• A codon is a sequence of three nucleotides that codes for an

amino acid.codon formethionine (Met)

codon forleucine (Leu)

• The genetic code matches each codon to its amino acid or function.– three stop

codons– one start

codon, codes for methionine

The genetic code matches each RNA codon with its amino acid or function.

• A change in the order in which codons are read changes the resulting protein.

• Regardless of the organism, codons code for the same amino acid.

Amino acids are linked to become a protein.

• An anticodon is a set of three nucleotides that is complementary to an mRNA codon.

• An anticodon is carried by a tRNA.

• Ribosomes consist of two subunits.– The large subunit has three binding sites for tRNA.– The small subunit binds to mRNA.

• For translation to begin, tRNA binds to a start codon and signals the ribosome to assemble.

– A complementary tRNA molecule binds to the exposed codon, bringing its amino acid close to the first amino acid.

– The ribosome helps form a polypeptide bond between the amino acids.

– The ribosome pulls the mRNA strand the length of one codon.

– The now empty tRNA molecule exits the ribosome.– A complementary tRNA molecule binds to the next

exposed codon.– Once the stop codon is reached, the ribosome

releases the protein and disassembles.

KEY CONCEPT Gene expression is carefully regulated in both prokaryotic and eukaryotic cells.

Prokaryotic cells turn genes on and off by controlling transcription.

• A promotor is a DNA segment that allows a gene to be transcribed.

• An operator is a part of DNA that turns a gene “on” or ”off.”

• An operon includes a promoter, an operator, and one or more structural genes that code for all the proteins needed to do a job.– Operons are most common in prokaryotes.– The lac operon was one of the first examples of gene regulation

to be discovered.– The lac operon has three genes that code for enzymes that

break down lactose.

• The lac operon acts like a switch. – The lac operon is “off” when lactose is not present.– The lac operon is “on” when lactose is present.

Eukaryotes regulate gene expression at many points.

• Different sets of genes are expressed in different types of cells.

• Transcription is controlled by regulatory DNA sequences and protein transcription factors.

• Transcription is controlled by regulatory DNA sequences and protein transcription factors.

– Most eukaryotes have a TATA box promoter.– Enhancers and silencers speed up or slow down the rate

of transcription.– Each gene has a unique combination of regulatory

sequences.

Warm Up (2-19-15)

• Does all DNA code for specific genes? If not, what is the importance of the noncoding sequence?

Outline

• Objectives• Gene notes• DNA notes

Objectives

• Students will be able to explain the importance of gene sequencing and why the splicing of DNA can be so beneficial.

Warm Up (2-20-15)

• Explain the difference between introns and exons and explain what process involves the removal of introns from an RNA sequence

Outline

• Objectives• Chapter 8 notes – DNA replication,

transcription, and translation

Objectives

• Students will be able to explain mRNA processing and explain the alignment of genes on a strand of DNA and RNA

• Students will be able to identify which genes are coding sequences and which genes are noncoding sequences.

• RNA processing is also an important part of gene regulation in eukaryotes.

• mRNA processing includes three major steps.

• mRNA processing includes three major steps.

– Introns are removed and exons are spliced together.– A cap is added.– A tail is added.

KEY CONCEPT Mutations are changes in DNA that may or may not affect phenotype.

Some mutations affect a single gene, while others affect an entire chromosome.

• A mutation is a change in an organism’s DNA.• Many kinds of mutations can occur, especially during

replication.• A point mutation substitutes one nucleotide for another.

mutatedbase

• Many kinds of mutations can occur, especially during replication. – A frameshift mutation inserts or deletes a nucleotide in

the DNA sequence.

• Chromosomal mutations affect many genes.

– Chromosomal mutations affect many genes.– Gene duplication results from unequal crossing over.

• Chromosomal mutations may occur during crossing over

• Translocation results from the exchange of DNA segments between nonhomologous chromosomes.

Mutations may or may not affect phenotype.

• Chromosomal mutations tend to have a big effect. • Some gene mutations change phenotype.

– A mutation may cause a premature stop codon.– A mutation may change protein shape or the active site.– A mutation may change gene regulation.

blockage

no blockage

• Some gene mutations do not affect phenotype.

– A mutation may be silent.– A mutation may occur in a noncoding region.– A mutation may not affect protein folding or the active

site.

• Mutations in body cells do not affect offspring. • Mutations in sex cells can be harmful or beneficial to

offspring.• Natural selection often removes mutant alleles from a

population when they are less adaptive.

Mutations can be caused by several factors.

• Replication errors can cause mutations.

• Mutagens, such as UV ray and chemicals, can cause mutations.

• Some cancer drugs use mutagenic properties to kill cancer cells.

Warm Up (2-23-15)

• What is the importance of being able to splice out genes within the DNA?

Outline

• Objectives• DNA replication video• DNA manipulatives

Objectives

• Students will explain the importance of DNA replication

• Students will identify the steps that must occur in order for DNA replication to happen

DNA manipulatives

• http://www.dnai.org/b/index.html

Interesting article

• http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397

DNA Transformation Background

• http://www.dnalc.org/resources/animations/transformation1.html

Warm Up (2-24-15)

• Explain what the process is of splicing a gene. Can the DNA be cut anywhere? Be specific.

Outline

• Objectives• Chapter 9 notes – biology book

Objectives

• Students will explain the process of DNA fingerprinting

• Students will identify how DNA can be used in modern technology

KEY CONCEPT Biotechnology relies on cutting DNA at specific places.

Scientists use several techniques to manipulate DNA.

• Chemicals, computers, and bacteria are used to work with DNA.

• Scientists use these tools in genetics research and biotechnology.

Restriction enzymes cut DNA.

• Restriction enzymes act as “molecular scissors.” – come from various types of bacteria– allow scientists to more easily study and manipulate

genes– cut DNA at a specific nucleotide sequence called a

restriction site

• Different restriction enzymes cut DNA in different ways.

– each enzyme has a different restriction site

– some cut straight across and leave “blunt ends”

– some make staggered cuts and leave “sticky ends”

Restriction maps show the lengths of DNA fragments.

• Gel electrophoresis is used to separate DNA fragments by size.– A DNA sample is cut with restriction enzymes.– Electrical current pulls DNA fragments through a gel.

– Smaller fragments move faster and travel farther than larger fragments.

– Fragments of different sizes appear as bands on the gel.

• A restriction map shows the lengths of DNA fragments between restriction sites.

– only indicate size, not DNA sequence

– useful in genetic engineering

– used to study mutations

KEY CONCEPT DNA fingerprints identify people at the molecular level.

A DNA fingerprint is a type of restriction map.

• DNA fingerprints are based on parts of an individual’s DNA that can by used for identification.– based on noncoding regions of DNA– noncoding regions have repeating DNA sequences– number of repeats differs between people– banding pattern on a gel is a DNA fingerprint

DNA fingerprinting is used for identification.

• DNA fingerprinting depends on the probability of a match.– Many people have the

same number ofrepeats in a certainregion of DNA.

– The probability that two people share identicalnumbers of repeats inseveral locations isvery small.

(mother) (child 1) (child 2) (father)

– Individual probabilities are multiplied to find the overall probability of two DNA fingerprints randomly matching.

– Several regions of DNA are used to make DNA fingerprints.

1 1 1 1500 90 120 5,400,000 1 chance in 5.4 million peoplex x = =

• DNA fingerprinting is used in several ways.

– evidence in criminal cases

– paternity tests– immigration requests– studying biodiversity– tracking genetically modified crops

KEY CONCEPT DNA sequences of organisms can be changed.

Entire organisms can be cloned.

• A clone is a genetically identical copy of a gene or of an organism.

• Cloning occurs in nature.

– bacteria (binary fission)– some plants (from roots)– some simple animals (budding, regeneration)

• Mammals can be cloned through a process called nuclear transfer.

– nucleus is removed from an egg cell– nucleus of a cell from the animal to be cloned is

implanted in the egg

• Cloning has potential benefits.

– organs for transplant into humans– save endangered species

• Cloning raises concerns.– low success rate– clones “imperfect” and less healthy than original animal– decreased biodiversity

New genes can be added to an organism’s DNA.

• Genetic engineering involves changing an organism’s DNA to give it new traits.

• Genetic engineering is based on the use of recombinant DNA.

• Recombinant DNA contains genes from more than one organism.

(bacterial DNA)

• Bacterial plasmids are often used to make recombinant DNA.

– plasmids are loops of DNA in bacteria

– restriction enzymes cut plasmid and foreign DNA

– foreign gene inserted into plasmid

Genetic engineering produces organisms with new traits.

• A transgenic organism has one or more genes from another organism inserted into its genome.

• Transgenic bacteria can be used to produce human proteins.– gene inserted into plasmid – plasmid inserted into bacteria– bacteria express the gene

• Transgenic plants are common in agriculture.– transgenic bacteria

infect a plant– plant expresses

foreign gene– many crops are now

genetically modified(GM)

• Transgenic animals are used to study diseases and gene functions.

– transgenic mice used to study development and disease

– gene knockout mice used to study gene function

• Scientists have concerns about some uses of genetic engineering.– possible long-term health effects of eating GM foods– possible effects of GM plants on ecosystems and

biodiversity

Boundless Microbiology notes

• Transcription, Translation, Transformation• https://www.boundless.com/microbiology/tex

tbooks/boundless-microbiology-textbook/microbial-genetics-7/genetic-transfer-in-prokaryotes-81/bacterial-transformation-442-6842/

Warm Up (2-25-15)

• What are some thoughts that you have on the manipulation of DNA.

• Think of some advantages as well as some disadvantages that could occur because of these modern advances.

Outline

• Objectives• Gene Splicing interactive

Objectives

• Students will be able to practice splicing out DNA from specific sequences of DNA using the simulation.

Gene Splicing Interactive

• http://www.biotechnologyonline.gov.au/popups/int_splicing.html

Warm Up (2-26-15)

• Write down what you can remember about DNA replication, transcription, and translation.

Outline

• Objectives• DNA replication, transcription, translation quiz• Bacterial DNA information

Objectives

• Students will identify the different stages in DNA replication

• Students will describe the processes involved in DNA replication

• Students will demonstrate mastery of the processes of DNA transcription and translation and replication.

Quiz - DNA

• Replication• Transcription• Translation

Bacterial DNA notes and structure

• Chapter 18 biology

Warm Up (2-27-15)

• Draw and label a picture of the internal structure of bacteria.

Outline

• Objectives• Ch. 18 notes – bacterial structure

Objectives

• Students will be able to explain and identify the structure of bacteria

• Students will use knowledge of DNA to explain how Bacteria and other pathogens can damage cellular DNA if they invade a host organism.

Bacterial DNA notes and structure

• Chapter 18 biology

pGLO lab

• https://www.youtube.com/watch?v=OZyFX9megs8

Lab Bench virtual labs

• http://www.phschool.com/science/biology_place/labbench/lab6/intro.html