difference The between school and life? In school, you're taught a lesson and then given a test. In life, you're given a test that teaches you a lesson. -Tom Bodett
Life is a source of infection -Van Halenor virus philosophy?
Online Quiz #1 and Web Links
Must be completed by noon Wednesday You must save each answer for them to count. You must submit the quiz before time expires. Time starts as soon as you click Begin Assessment.
Additional web links related to class will be placed in the Web Links folder to the left of the home page. Some movies will be placed in the Movies folder on the home page. These are for your interest only and will not be tested.
Timeline of early cell types-1
1) 2) Initial cells were anaerobic (energy not from oxygen) heterotrophs (had to obtain organic molecules (C,N,O,P,S based) from environment) As availability of environmental organics decreased, some cells became able to use the sun as an energy source and as a way to synthesize organic compounds. Since they didnt depend on preformed environmental compounds and were sun-powered, called photo-autotrophs. Non-photosynthetic eukaryotic cells are generally aerobic (energy mostly obtained using oxygen) heterotrophs. The occurrence of oxygenic photosynthesis fundamentally changed the earth and its evolution. The accumulation of atmospheric O2 led to the formation of the ozone barrier to prevent intense ultraviolet radiation from reaching the earth. This meant organisms could exist over the entire surface of the earth.
3) 4)
Jennifer McDowall, Protein Data Bank Brock Biology of Microorganisms, 5th edition, Madigan et al. Eric J. Chaisson, Wright Center for Science Education
How do we date/verify bacterial fossils?
Carbon date rock Mostly morphological and chemical evidence Casts of bacteria Presence of organic compounds
McLoughlin et al. 2007 Stromatolite
A major increase in atmospheric oxygen and a major decrease in hydrogren precedes the appearance of eukaryotes
Xiong and Bauer 2002
Dietrich et al. 2006
How might we trace the lineage of organisms throughout history? use divergence in genetic code to trace phylogeny, such as ribosomal RNA or DNA
Endosymbiont theory of eukaryotic origin
This is the idea that certain eukaryotic organelles (most notably mitochondria & chloroplasts) have evolved from smaller prokaryotic cells that had taken up residence in the cytoplasm of the larger host It was called the endosymbiont theory because it describes how a single composite cell of greater complexity can evolve from 2 or more separate, simpler cells living in a symbiotic relationship Mutually beneficial to both organisms
http://www.gwu.edu/~darwin/BiSc151/Eukaryotes/Eukaryotes.html
Evidence for the endosymbiont theory
Mitochondria closely resemble extant (currently existing) bacteria. Mitochondria replicate in a fashion that is very similar to that observed in bacteria. The inner membrane of mitochondria bears a strong resemblance to the membranes of prokaryotes, sharing several key proteins and transport systems. Mitochondria have their own DNA (which is circular, like that of prokaryotes), and they possess all of the cellular machinery required to transcribe and translate their genomes, Mitochondrial ribosomes are more similar in behavior, structure, and nucleic acid base sequence to the ribosomes of prokaryotes than they are to eukaryotic ribosomes. For example, there is high sequence similarity between the ribosomal RNA of mitochondria and that of modern endosymbiotic bacteria. Similar arguments can be made for chloroplasts
Evolution in the form of plasma membrane invagination (infolding) led to compartmentalization
Difficulties with the original endosymbiont hypothesis
The main problem is that no currently existing prokaryotes that engulf cells. Initially thought that archezoa, or anaerobic eukaryotes, were missing links for original endosymbionts with aerobic bacteria, but these cells have vestigial bacteria The other main problem is that it is not clear how the nucleus would arise. Suggested that a protoeukaryote existed with an early nucleus and engulfing ability, little but support thus far (from Poole and Penny 2007)
Viruses: the intro
The BAD: Colds, H1N1 (swine flu), SARS, HIV, West Nile, Herpes, Rabies. These are pathogenic and often deadly Would you believe, the GOOD? Herpes, Rabies, Sindbis, Simliki Forest virus. These are used routinely in biology to tranfect cells with DNA sequences of interest so that the cells will express the proteins of interest, such as fluorescent markers.
Virus Structure
At its simplest, a virus is just DNA or RNA with a protein coat. Many more complex variations on shape and life
Example shown here is tobacco mosaic virus, a plant pathogen.
Simple viral life cycle
1) Bind and gain entry into cell 2) Uncoat capsid (protein coat) and if applicable, membranes, around DNA or RNA (if retrovirus) 3) Use viral DNA to alter host DNA such that viral DNA is replicated and mRNA needed to make viral proteins is transcribed 4) The duplicated viral DNA and translated viral proteins exit
From: Molecular Biology of the Cell, Third Edition, Alberts et al
Tracking Viral Movements
Too small to resolve with light microscopy, but can track emitted light Viruses can be labeled with fluorescent markers and tracked as fluorescent dots using a light or confocal microscope Track 1: outside cell Track 2: binding to cell Track 3: entry into cell Track 4: entry into nucleus
Protein coats are often formed by repeating protein subunits that form repeating structures. Genetically efficient, structurally stable
Adenovirus Icosahedral (20-sided)
Lytic vs. lysogenic viral cycles
Most viruses, once they infect the cell, will rupture (lyse) the cell and release viral particles
This infection is known as a lytic infection and is shown by a bacteriophage infection here.
The HIV virus
The protein coat allows it to bind to the host and determines host specificity (host range). When genetic alterations allow a virus to change its host specificity or range, thats when there are serious concerns, because it could jump species.
Membrane coated viruses, such as HIV, enter the cell through endocytosis
Upon exit, the capsid and RNA are coated with the host cells membrane and bud off. This type of virus is a provirus.
http://www.youtube.com/watch? v=9leO28ydyfU
Progression of HIV viral load and CD4+ T cell depletion
CD4+ T helper cells are immune cells that promote the immune response Mechanism of CD4+ death not well understood, but is mainly through apoptosis (programmed cell death) Thought that majority of CD4+ cells killed are uninfected bystanders whose cell death pathways become activated Alimonti et al. 2003
Bacteriophages are complex viruses that infect bacteria.
They consist of: 1) A polyhedral head that contains DNA 2) A stalk through which DNA is injected 3) Tail fibers to attach to bacteria
Cryo-EM can show detailed bacteriophage structure, resolution proportional to acceleration of electron beam
Jiang et al. 2006, Wen Jiang is in Bio. Dept, Purdue University
Herpesvirus infection confers protection from bacterial infection
a) Virus 1 week before Listeria
b) Virus 4 weeks before Listeria
Erik Barton, Purdue Dept. of Bio. 2007
Viruses are commonly used to introduce DNA into cells.
Inserted genes In this example, the Sindbis virus is shown, along with the constructed DNA that has been inserted. Typically, for infection for labeling or for insertion of DNA, some portion of the viral DNA, such as the some of the replication machinery or the recoating with the capsid protein, is disabled so that the virus does not take over.
Sindbis viral DNA (whole circle, 9.95 kilobases DNA in length)
Many viruses specifically target neurons and when combined with fluorescent markers, reveal beautiful neuronal organization and morphology
Ehrengruber et al. 1999 GFP after infection of hippocampal cultures with Semliki Forest virus
Electronegativity --- Buried in Bonds: Better Living Through Biochemistry 1
Four types of biochemicals and their distribution in cells
The structures and reactivities of biomolecules are determined by bonds
Covalent Ionic Hydrogen Van der Waals Related to bonds, hydrophobic interactions