Cluster of functionally related genes under coordinated control by one on-off "switch"

Consists of operator within promoter

Series of nucleotides to which an active repressor can attach

Binding of repressor prevents RNA polymerase from attaching to promoter and transcribing of genes 

Proteins that turn off operons

Bind to operator, block RNA polymerase and stop transcription 

Operons switched off by active form of repressor

Two Types 

Repressible Operons

Inducible Operons 

Usually on (repressor NOT bound); repressor binds to operator and stops tanscription

Tryp  

If Tryptophan is present, it binds to the trp repressor activating it, allowing it to bind to operator and turn operon off

E. Coli doesn't maky tryp id it doesn't need it  

Usually off (repressor usually bound); inducers bind and inactivate repressors, turning on transcription

Lac

 Inducer inactivates the repressor to turn lac operon on

Made when chemical is present  

A mutation that inactivates the repressor of an operon under negative gene regulation would result in

a) continuous transcription of the operon

b) complete inhibition of tanscription of the operon

c) inactivation of RNA polymerase

d) both B and C 

Proteins are acitvators of transcription

Activators attach to promoter, increasing levels of transcription 

Eukaryotes regulate gene expression through chromatin structure

Genes within highly packed regions are usually not expressed 

Chemical modifications to histones and DNA influence gene expression 

Segments of noncoding DNA that help regulate transcription

 To initiate transription, eukaryotic RNA polymerase requires transcription factors 

Giant protein complexes that bind protein molecules and degrade them

Viruses are not cells

Viruses consist of a nucleic acid in a protein coat and, in some cases, a membraneous envelope 

The protein shell that encloses the viral genome

Can have various structures  

Some viruses have viral envelope that surround capsids and help then infect their hosts

Most common in animal viruses

Derived from the host cell's membrane and contain a combination of viral and cobination of viral and host cell molecules  

They can reproduce only within a host cell

Each one has a "host range", a limited number of host cells that it can infect 

Once inside cell makes viral proteisn

Uses host enzymes, ribosomes, tRNAs, amino acids, and ATP

Viral nucleic acid and protein molecules assemble into new viruses  

Also called bacteriophages

Viruses that infect bacteria

Best understood of alll viruses

Two reproductive mechanisms: lytic and lysogenic cycle 

Kills the host cell

Produces new phages, digests the host's cell wall, releasing new viruses

Virulent Phage- Reproduces only by the lytic cycle

Bacteria have defenses against the phages, including restriction enzymes that recognixe and cut up phage DNA 

Recognizes and cuts phages

Cuts at a specific nucleotide sequence (restriction sites) 

Replicates the phage genome without destroying the host

Viral DNA incorporated into the host cell's chromosome

 Known as Prophage

Everytime host cell divides it copies the phage DNA and passes the copies to daughter cells  

Environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to lytic mode  

RNA virus that reproduces by transcribing its RNA into DNA and inserting the DNA into a cellular chromosome

Uses Reverse Transcription

HIV is a retrovirus that causes AIDS 

Enzyme encoded by certain viruses that uses RNA as a template for DNA synthesis

Retroviruses use reverse transcriptase to copy their RNA  

Viral DNA integrated into host genome

Remains permenant resident of host cell

Host's RNA polymerase transcribes the proviral DNA into mRNA

RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from cell 

Slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals

Spread by converting normal proteins into prion version

Ex. Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob dises in humans 

• Identify and diagnose of human gentic diseases
• Forensic evidence and paternity cases
• Modified microorganisms for environmental cleanup
• Improve agricultural productivty and food quality
• Gene therapy-insertion of genes to treat dieases 

Involves using bacteria to make multiple copies of a gene

Cloned genes are useful for making many copies of a particular gene and for producing a lot of their corresponding proteins 

 Gene --> plasmid --> bacterium

Small circular DNA molecules found in bacteria

Foreign DNA inserted into a plasmid, and the plasmid is inserted into bacterium

Bacterial division results in cloning of the plasmid including foreign DNA

Result: Multiple copies of a single gene  

Cloning: HOW?

Restriction enzymes

Sticky ends

DNA ligase 

Restriction enzymes can be used to cut DNA at specific DNA sequence

Produces fragments with "sticky ends" that bond with complementary sticky ends of other fragments

DNA ligase is an enzyme that seals the bonds between restriction fragments  

A single-stranded end of a double stranded restriction fragment

Bond with complementary sticky ends of other fragments  

Enzyme that seals bong between restriction fragments

Catalyzes 3' end to 5' of another fragment  

Polymerase Chain Reaction

(PCR) 

Involves using an enzymatic reaction to create many copies of a gene

Important in forensics, paternity cases, and for many molecular biology applications

Use DNA or RNA polymerase to make more DNA or turn DNA-->RNA or RNA-->DNA 

PCR: HOW?

Primers

Taq DNA polymerase

Denaturation

Annealing

Replication 

Need: two primers, nucleotides (A,T,C,G), Taq DNA polymerase, and DNA to copy

Three step cycle:

-Denaturation (95º)

Heat-stable protein, derived from hotspring bacterium

Adding new base pairs onto primer, makes actual copies, polymerase can handle higher temps 

Breaks apart weaker bonds, breaks down center not back bone

First stage  

Primer reanneals to template strand

Provides starting place for PCR

DNA Sequencing

What and Why

Involves using an enzymatic reaction to uncover the exact sequence of short segments of DNA

Important for reconstructing evolutionary relationships, diagnosing diseases and can be useul for forensic and paternity cases  

DNA can be sequenced by the dideoxy chain termination method

Similar to PCR, but modified nucleotides called dideoxyribonucleotids (ddNTP) attach to synthesized DNA strands

Each type of ddNTP marked with distinct fluorescent label which identifies nucletide at end of fragment  

• DNA
• Primer-tells enzyme where to add nucleotides
• DNA polymerase- catalyzes reaction
• Deoxyribonucleotides- building blocks of DNA
• Dideoxyribonucleaotids-marked so you can read them and they stop reaction
• Reaction creates an assortment of fragments which are labeled at the end so you can "read" the sequence
• Sperarated into long and short fragments by running through molecular sieve
• Passed through laser to read fragments

Analyzing Transcription: HOW?

 Nucleic Acid Probe

Nucleic Acid Hybridization 

Need nucleic acid probe having a sequence complementary to the gene

Process is calles Nucleic Acid Hybridization

Probes can bind with mRNAs

Probes can be used to idenitfy where or when a gene is transcribed in an organism

Labeled single stranded nucleic acid used to locate a specific nucleotide sequence in a nucleic acid sample

Probe can be synthesized that is complementary to the mRNA of interest

Ex. desired mRNA is

5'GGCUAACUUAGC3'

we would synthesize this probe

3'CCGATTGAATCG5' 

Nucleic Acid Hybridization

In Situ Hybridization

Uses fluorecent dyes attached to probes to identify the location of specific mRNAs in place in the intact organism

If you know gene of interest, make probe bind to gene, can make it give off color

Can find what happens in cell, where it is produced, what it does in cell, or you can insert it into call and see where it shows up 

Founder of taxonomy; the classification of organisms: Genus, species

Interpreted organismal adaptations as evidence that the Creator had designed each species for a specific purpose  

Similarity resulting from common ancestry

Homologous structures: anatomical similarities that represent variations on a structural theme present in a common ancestor  

Ex. Human hand, Cats paw, Whale flipper, Bats wing 

Hypothesized that species evolve through use and disuse and the inheritance of acquired traits

The mechanisms he proposed are unsupported by evidence 

Darwin made two major points:

-All of life is related: current species are ancestors of past species

  -Natural Selection

Describes a population that is not evolving

States that frequencies of alleles and genotypes in a population's gene pool remain constant from generation to generation

Hardy-Weinberg Theorem

Equations 

p+q=1

p2+2pq+q2=1

p2 and q2= frequencies of the homozygotes

2pq= frequency of the heterozygotes 

• No mutations
• No natural selection
• Extremely large population size
• No gene flow
• Random mating

Three major factors alter allele frequencies and bring about most evolutionary change:

• Natural Selection
• Genetic Drift
• Gene Flow 

Describes how allele frequencies fluctuate unpredictably due to small population sizes

Genetic drift tends to reduce genetic variation through losses of alleles  

A sudden change in the environment that may drastically reduce the size of a population

Resulting gene pool may no longer reflect the original population's gene pool 

Occurs when a few individuals become isolated from a larger population and "find" a new population

It can affect allele frequencies in the new population 

Consists of genetic additions or subtractions from a population, resulting from movement of individuals

Causes to population to gain or lose alleles

Tends to reduce differences between populations overtime