Exam 4, week 2

True or false: some of us are carrying neanderthal DNA

True

True or false: the U.S. Supreme Court has ruled police can take DNA upon arrest

True

Lytic cycle

Virus takes over immediately; Bacteria dies immediately after virus release; 5 stages- attachment, penetration, biosynthesis, maturation, and release

Viruses

Viruses are not included in the classification of organisms: Non-cellular, called obligate intracellular parasites, are not alive; 2 parts of every virus: Outer capsid- composed of protein subunits and inner core-either DNA or RNA, Viral genome are very small; Some viruses have spikes for attachment to host cell and have outer envelope

Correct statements about viruses

Viruses have an inner core of nucleic acid; Viruses have a protein capsid; Viral genomes may consist of either DNA or RNA

Genetic engineering: Cloning How can we produce large quantities of a protein (such as human insulin)?

We can insert DNA into bacteria and have them do the work

The genetic material of a bacterium include

a circular chromosome, plasmids, and latent bacteriophage DNA

DNA profiling (also called DNA fingerprinting, DNA testing, or DNA typing)

a forensic technique used to identify individuals by characteristics of their DNA. A DNA profile is a small set of DNA variations that is vey likely to be different in all unrelated individuals, thereby being as unique to individuals as are fingerprints (hence the alternate name for the technique). DNA profiling should not be confused with full genome sequencing. First developed and used in 1985, DNA profiling is used in, for example, parentage testing and criminal investigation, to identify a person or to place a person at crime scene, techniques which are now employed globally in forensic science to facilitate police detect work and help clergy paternity and immigration disputes. Although 99.9% of human sequences re the same in every person, enough of the DNA is different that it is possible to distinguish one individual from other, unless they are identical twins. DNA profiling uses repetitive sequences that are highly variable, called variable number tandem repeats(VNTR), in particular short tandem repeats. VNTR loci are very similar between closely related humans, but they are so variable that unrelated individuals are extremely unlikely to have the same VNTRs

DNA polymerase III

add DNA nucleotides to new strands

Explain the structure and function of flagella, capsules, and endopores in bacteria

bacteria have ribosomes but not membrane-bounded organelles; motiles bacteria generally have flagella but never cilia-not like eukaryotic flagella; outer cell wall strengthened by peptidoglycan: prevents bursting or collapsing and may have addition capsule outs cell wall

Therapeutic cloning

can produce specialized cells to treat human disease

Enveloped virus

capsid, nucleic acid, envelope

What means of genetic recombination in bacteria often makes use of pili?

conjugation

Typical Virus lifecycle

1) attachment (absorption) 2)Penetration (injection of viral particle, protein coat remains outside) 3) Synthesis of nucleic acid and protein 4) Assembly and packaging 5) release (lysis) - now mature virus particles

Retroviruses

Contain reverse transcriptase

Who owns genes?

The company president says they have invested more than 500 million to study and isolate the BRCA genes; opponents say genes are made by nature and can't be patented; doctors and patients say they should be able to access tests at a reasonable cost in order to prescribe relevant treatments; The courts opinion was that "a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated"

True or False: Condo associations can use DNA to identify the proper owner of a poop sample on another homeowner's lawn

True

True or False: DNA-based computers may one day hold more data than our fastest server today

True

True or False: You can pay to save a sample of your dog's or cat's DNA for future cloning

True

DNA technology

a set of methods for studying and manipulating genetic material

Conjugation

donor cell passes DNA to recipients

____________ Bacteria have a cell wall

most

Primase

synthesizes RNA primer

Biotechnology

the manipulation of organisms or their components to make useful products

DNA can be synthesized from scratch

An automated DNA synthesizer machine can quickly and accurately produce customized DNA molecules up to lengths of a few hundred nucleotides

Naked virus

Capsomer, capsid (composed of capsomers), nucleic acid

Polymerase chain reaction (PCR) copies target DNA quickly and precisely

Heating splits apart DNA helix into two complementary strands; a heat-stable DNA polymerase (enzyme that synthesizes DNA) is used to build new strands; Billions of gene copies are generated in just a few hours; using PCR, one drop of blood can provide enough DNA for analysis

DNA can be visualized using nucleic a dic probes

In order to find a gene of interest a researcher can use a nucleic acid probe; a complementary molecule made using radioactive or fluorescent building blocks will bind with DNA

Unlike lytic phage, lysogenic phage are able to

Insert themselves into the host genome

Lysogenic cycle

Phage lies latent until triggered to enter lytic cycle; Bacteria does not die until phage integrates into host chromosome as a prophage; Trigger causes phage to enter lytic cycle with biosynthesis, maturation, and release

Cutting and pasting DNA is an important step in genetic engineering

Restriction enzymes: proteins that cut DNA at specific nucleotide sequences; the resulting fragments are called restriction fragments;

What shapes are found among microorganisms?

Rods, cocci, spirals, stars, and squares

Why do you think PCR uses a DNA polymerase from a microbe first discovered in the hot springs of Yellowstone National Park?

Thermus aquaricus is a species of bacterium that can tolerate high temps, one of several thermophilic bacteria that belong to the Deinococcus-thermus group. It is the source of the heat-resistant enzyme Taq DNA polymerase, one of the most important enzymes in molecular biology because of its use in the polymerase chain reaction (PCR) DNA amplification

STR analysis: Compare 13 sites within the human genome

These sites vary so widely that no two humans have ever had the same number of repeats at all 13 sites (except identical twins); The current method for generating a DNA profile relies on STR analysis, a comparison of the lengths of short tandem repeat sequences at 13 predefined sites within the human genome; At each site, a four-nucleotide sequence is repeated between 3 to 50 times in a row; TO perform an ST analysis, a forensic scientist obtains DNA from two or more samples and then uses the polymerase chain reaction (PCR) to produce large quantities for comparison. Here, the process is simplified to include just 2 STR sites

Archaea

1 of the 3 domains; eukarya evolved from these organisms-share some characteristics; Structure: plasma membranes contain unusual lipids allowing them to function at high temperatures; Diverse cell wall types- no peptidoglycan

Lytic Cycle

1) Attachment: Capsid combines with receptor 2) Penetation: Viral DNA enter host 3)Biosynthesis: Viral components are synthesized 4) maturation: Viral components are assembled 5) Release: New viruses leave host cells

Lysogenic Cycle

1) Attachment: Capsid combines with receptor 2) Penetration: viral DNA enters hots 3) integration: cloning of viral DNA 4) Biosythesiss: Viral components are synthesized 5)Maturation: viral components are assembled 6) Release: New viruses leave host cell

Reproduction of HIV

1) attachment 2) fusion and entry 3)Uncoating- Viral DNA and reverse transcriptase 4) Reverse trancription- single-stranded DNA 5)Replication: double stranded DNA 6)Integration:host DNA and provirus DNA 7) Biosynthesis: viral DNA and ribosomes 8)Maturation 9) release

If a bacterial population has 1000 cells and a doubling time of 30 minutes, how many cells will there be in two hours?

16,000

which of the following DNA sequences is complementary to 3' CTAGTCAGT 5'?

5' GATCAGTCA 3'

DNA can be isolated from a cell and put into a genomic library

A genomic library is a collection of cloned DNA fragments that includes an organims's entire genome; once created, a genomic library can be used to hunt for and manipulate any gene from the starting organism

List of emerging viruses

AIDs, Bird flu, Ebola, SARS

What of the following is used by a bacterium to carry out aerobic metabolism of glucose?

ATPase Cell membrane Citric acid cycle Glycolysis Pyruvate oxidation Electron transport system

Clones

Biologist can artificially manipulate cell division to produce clones; clones are genetically identical individuals born of a single parent; has several uses in agriculture and medicine; Nuclear transplantation can be used to produce a cloned embryo. This embryo can be used to produce a new individual (reproductive cloning) or it can be used to produce stem cells (therapeutic cloning)

Bacteria: structure

Capsule: gel-like coating outside the cell wall Plasma membrane: sheet that surrounds the cytoplasm and regulates entrance and exit of molecules cell wall: structure that provides support and shapes the cell ribosomes: site of protein synthesis Cytoplasm: semifluid solutions surrounded by the plasma membranes; contains nuclei and ribosomes Flagellum: rotating filament that propels the cell COnjugation pilus: elongated, hollow appendage used to transfer DNA to other cells Nucleoid: location of bacterial chromosome Fimbriae: hairlike bristles that allow adhesion to surfaces

Emerging Viruses

Causation agent of a disease that only recently has infected large numbers of people' HIV, West Nile virus, SARS virus, Ebola virus, avian influenza (H5N1); Emerge in several ways: transported to new location, able to infect new species, and new mode of transmission

Viruses that cause cancer?

Cervical cancer-papilloma virus; Liver cancer-Hepatitis B and C; Kaposi's sarcoma-HIV; Epstein-Barr virus-Burkitt lymphoma

Bacterial nutrition: photoautotrophs

Cynanobacteria; use solar energy and carbon dioxide to make food; like plants

Examine the following figure and fill in the blanks. An organism's genetic information is stored within the sequence of ___________. This information is transcribed into a sequence of ____________, which are then translated into a sequence of ___________.

DNA bases; RNA bases; proteins

Drug control of human viral diseases

Difficult to develop-uses cell's own machinery; Some drugs structurally similar to nucleotides to interfere in viral genome synthesis; some block viral enzymes like reverse transcriptase in HIV

Bacterial nutrition: Chemoautotrophs

Don't use solar energy to reduce carbon dioxide; like deep sea vent bacteria living inside tube worms

Origin of cells

First living cells were prokaryotes; Found in rocks 3.5 billion years ago and may have existed before that but not fossils found yet; conditions on early Earth very different from today; Then, the temperatures high, little free oxygen; Abiotic synthesis of organic molecules with input from energy sources-lightning, sunlight, meteorite impact, volcanic activity, radioactive decay

Kuru

Fore people of Papua New Guinea; Prior to the 1950s, a dead family member was cooked and eaten; Brain most likely to pass kuru

DNA profiling: proves a match between two samples

Imagine that you have a sample of DNA from a crime secene and a second sample from a suspect; how can you prove they match? Entire genome matching is impractical, but we can compare regions of DNA

Bacteria-Structure

Most common 3 shapes-rods (bacilli), spheres (cocci), and spirals (spirilla or spirochetes); some form chains or bunches; no nucleus- single curricular chromosome found in nuclei (region of cell); plasmids-extrachromosomal DNA in some

Bacteria

Most diverse and prevalent organism on earth; ten of thousands of different bacteria identified-likely many more exist;

Viroids

Naked strands of RNA not covered by capsid; Like virus takes over cell to make more viroids; About a dozen crop diseases

Prokaryotes

No nucleus to contain genome; no sealed compartments; no membrane-bounded organelles; far greater metabolic capabilities than more complex organisms; bacteria and archaea

Nuclear transplantation

Nucleus isolated, cell from adult to be cloned, then nucleus removed from egg, egg from donor; isolated nucleus injected into nucleus-free egg; donor nucleus; resulting embryo

What do we call a virus that attacks a bacterium?

Phage

PCR: Amplifies one region of DNA

Primers (forward and reverse: short single stands of DNA) bind to the start and end points of the segment of DNA being amplified

Prions

Proteinaceous infectious particles; Misshaped protein changes normal protein into more misshaped protein; discovered as cause of kuru; also mad cow disease and Creutzfeldt-Jakob disease

Retroviruses

RNA animal viruses with a DNA stage; HIV-causes AIDS; Reverse transcriptase makes DNA from RNA template

The following statements about the flow of genetic information for HIV is true

RNA encodes information that is translated into DNA, and DNA encodes information that is translated into proteins

Animal Viruses

Reproduce similar to bacteriophages; Some, but not all, will have an outer membranous envelope beyond capsid - made from host cell plasma membrane; Herpesviruses (causes cold sores, genital herpes, and chickenpox in humans) are infections that remain latent most of the time- stress can cause them to enter the lytic cycle

DNA profilers: focus on specific sites that are known to vary considerably

Scattered throughout the genome are short tandem repeats (STRs) sites; at each STR site, a four-nucleotide sequence is repeated many times in a row. For example: AGATAGATAGATA

Real-World Case Study: In the 1990s a private company discovered a set of genes that increase the risk of getting breast and ovarian cancers (BRCA1 and BRCA2). They applied for and received a patent for the genes, which means they are the only company that can offer a genetic test for the BRCA1 and BRCA2 genes, earning the company over $400 million in 2012.

Supreme Court case Association for Molecular Pathology et al. v. Myriad Genetics, Inc., et al. The Court's opinion was that "a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated."

PCR uses forward and reverse DNA primers that help synthesize complementary DNA of the targeted sequence. In order to generate complementary strands, when aligned to the genome

The forward primer should align to the leading strand, and the reverse primer should align to the lagging strand, at a higher base pair position than the first one so that they are pointed towards one another.

Variable number tandem repeat (VNTR)

a loctaion in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length between individuals. Each variant acts as an inherited allele, allowing them to be used for personal or parental identification. Their analysis is useful in genetics and biological research, forensics, and DNA fingerprinting

Restriction enzyme or restriction endonuclease

an enzyme that cuts DNA at or near specific recognition nucleotide sequences known as restriction sites; they are commonly classified into three types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix

biofilm

any group of microorganisms in which cells stick to each other on a surface; these adherent cells are frequently embedded within a self-produced matrix of extracellular polymeric substance; Microbes form a biofilm in response to many factors, which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, or in some cases, by exposure of planktonic cells to sub inhibitory concentrations of antibiotics

Reproduction of bacteria

any of a group of bacteria that reproduce by budding; Each bacterium divides following unequal cell growth; the mother cell is retained, and a new daughter cell is formed; in budding, the cell wall grows from one point on the cell (polar growth), rather than throughout the cell; this permits the development of more complex structures and processes; most budding bacteria develop cytoplasmic extrusions, such as stalks, hyphae, and appendages; budding bacteria are most often aquatic and can attach to surfaces by their stalks; others are free-floating

Types of Archaea: Methanogens

chemoautrophs couple production of methane to ATP sythesis, swamps, and animal intestines

Types of Archaea: Thermoacidophiles

extremely hot, acidic environment like hot springs and submarine thermal vents; survive best about 80 degree C; grows best a pH 1 or 2

Gel electrophoresis provides comparison of DNA samples

gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA, and proteins) and their fragments, base on their size and charge. It is used in clinical chemistry to separate proteins by charge and/or size (IEF agarose, essentially size independent) and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge. Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through a matrix of agarose or other substances. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving .Proteins are separated by charge in agarose because the pores of the gel are too large to sieve proteins. Gel electrophoresis can also be used for separation of nanoparticles. Gel electrophoresis uses a gel as an anticonvective medium and/or sieving medium during electrophoresis, the movement of a charged particle in an electrical field. Gels suppress the thermal convection caused by application of the electric field, and can also act as a sieving medium, retarding the passage of molecules; gels can also simply serve to maintain the finished separation, so that a post electrophoresis stain can be applied. DNA Gel electrophoresis is usually performed for analytical purposes, often after amplification of DNA via PCR, but may be used as a preparative technique prior to use of other methods such as mass spectrometry, RFLP, PCR, cloning, DNA sequencing, or Southern blotting for further characterization.

Bacteria (and archaea) reproduce asexually by binary fission

genetic diversity due to 3 process; conjugation, transformation, and transduction

Single-strand binding proteins

holds DNA strand apart

Cloned embryos can be used to produce a new individual

in reproductive cloning the embryo must be transplanted into a surrogate; embryo produced via nuclear transplantation injected into surrogate mother

Cloned embryos can be used to produce stem cells

in therapeutic cloning, stem cells are harvested from the cloned embryo

Unlike lytic phage, lysogenic phage are able to

insert themselves into the host genomes

Eukaryotic cell strucutre

nuclear membrane, endoplasmic reticulum and golgi apparatus, cytoskeleton, cilia and flagella, mitochondria in most, chloroplast is some, most are unicellular

Bacteria disease in humans

pathogens are able to produce a toxin and/or adhere to surfaces and sometimes invade organs or cells; toxin are small organic molecules or pieces of bacteria released when bacteria die; often toxins cause more problems than growth of the microbe itself; Clostridium tetani causes tetanus (lock jaw); soil bacteria thrives in puncture wounds; bacteria never leave site of injury but toxin circulates in blood; Toxin prevents muscle relaxation; Person suffocates when diaphragm can no longer relax; Antibiotics generally either inhibit protein synthesis or inhibit cell wall production

Cyanobacteria are important producers as

photoautotrophs

Transformation

picks up free DNA from environment

Criminal profiling provides a great basis for a variety of TV shows! It allows investigators to determine with certainty whether two samples of DNA came from the same individual. Which process allows this to happen?

polymerase chain reaction (PCR) analysis

Origin of the first cells

protocells to origin of genetic code = cell

topoisomerase

relieves strains caused by unwinding

DNA polymerase 1

removes RNA primer and replaces with DNA

Types of Archaea: Halophiles

require high salt concentrations to grow; use pigments to absorb light energy to pump chloride and to synthesize ATP

All viruses

require host cells for reproduction

DNA produced from a cell's mRNA

reverse transcriptase can synthesize DNA rom the mRNA within the cell; The result is complementary DNA (cDNA) representing the genes that were being transcribed in the cell at the time

Prokaryotes vs. Eukaryotes

smaller and often less complicated structure; single celled (but many in biofilms); often grow faster; more of them (number and biomass); more diverse (evolutionarily, genetically, and metabolically)

A chain of spherical bacterial cells is called a

streptococcus

Bacterial nutrition: Chemoheterotrophs

take in organic molecules as source of energy and carbon; first cells most likely this; like animals; saprotrophs- send enzymes into environment to digest food

Plant viruses

tend to enter through damaged tissues; move through plasmodesmata; Tobacco mosaic virus is a good example; Until recently, the only way to control viruses way to destroy symptomatic plants and control insect vector (if there is a vector); with bioengineering, possible to transfer genes for disease resistance between plants- the creation of transgenic papaya plants in Hawaii resistant to PRSV

Genetic engineering

the direct manipulation of genes for practical purposes; It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. New DNA may be inserted in the host genome by first isolating and copying the genetic material of interest using molecular cloning methods to generate a DNA sequence, or by synthesizing the DNA, and then insetting this construct into the host organism. Genes may be removed, or "knocked out", using a nuclease. Gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations

Binary fission

two equal daughter cells are produced from the unilateral growth and division of the mother cell, is typical to most bacteria

helicases

untwists and separates strands

Ligase

joins DNA fragments together

Which of the following is not an application of polymerase chain reaction?

linking two DNA molecules together

Transduction

phage carries DNA to new cell

Retroviruses are called retro because

they make DNA from their RNA genome