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 Halen...or virus philosophy?
Online Quiz #1!
Must be completed by noon today Questions 2 and 5 only allow one answer even though they say "Mark all that apply". If you mark at least one of the one or more correct answers, you will get full credit. Answers will be given this evening. 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". I will drop the lowest quiz grade during the semester.
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
First, an anaerobic prokaryote or protoeukaryote engulfs an aerobic prokaryote
Evolution in the form of plasma membrane invagination (infolding) led to compartmentalization
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 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
Lytic vs. lysogenic viral cycles
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, that's when there are serious concerns, because it could jump species.
Herpesvirus infection confers protection from bacterial infection
a) Virus 1 week before Listeria
b) Virus 4 weeks before Listeria
Erik Barton, Dept. of Bio. 2007
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
Orbital structure determines electrons needed for stable state
Coulomb's Law
F = k Q1 Q2/ r2 Q1 and Q2 are charge in coulombs k=1/4 0 , where 0 is the electric constant The distance between the point charges is r When Q1 and Q2 have the same sign, F is positive (repulsive) and when they have opposite sign, F is negative (attractive). Da-da-da-dut-da-daaaaaa CHARGE!
Qualitative example of Coulomb's law
The key to bonds - sharing
Shared charge in the binding region will tend to attract the nuclei, and in the anti-binding region will repel
A chemical bond is thus the result of the accumulation of negative charge density in the region between the nuclei to an extent sufficient to balance the nuclear forces of repulsion. http://www.chemistry.mcmaster.ca/
Electron charge density is increased between nuclei in a covalent bond (C-C bond in example)
Left: gradient of charge density difference (molecular minus atomic) Solid line: Increased charge density, Dashed line: decreased density Right: Slice of density difference along internuclear axis
http://www.chemistry.mcmaster.ca/
Electronegativity reflects the tendency of an atom to attract an electron
nuclear
More protons, more electronegative More distance of outer electrons from nucleus, less electronegative O, N, Cl, are very electronegative biomolecules (Why?)
Covalent bonds are polar when one atom is more electronegative than the other
Top: Covalent C-C bond, equal charge distribution between atoms. Bottom: Covalent N-B bond, unequal distribution between atoms. Nitrogen is more electronegative.
http://www.chemistry.mcmaster.ca/
A sampling of covalent bond energies (in kcal/mol)
Standard Bond Energies
Single Bonds HH CC NN OO FF SiSi PP * 104.2 83 38.4 35 36.6 52 50 Single Bonds BF BO CN NCO CO OCO CS * 150 125 73 86 85.5 110 65 Multiple Bonds C=C N=N O=O C=N C=O (CO2) C=O (aldehyde) C=O (ketone) * 146 109 119 147 192 177 178
http://www.cem.msu.edu/~reusch/VirtualText/react2.htm
In an ionic bond, there is a complete transfer of charge that is energetically more stable
Top: Covalent C-C bond for comparison. Bottom: Ionic Li-F bond. The highly electronegative F pulled away the electron from the Li which can be (see charge density difference on the right). Now both atoms have complete outer shells and are stable.
The most important polar molecule is water
Oxygen is more electronegative than hydrogen, so the hydrogen are effectively partially positively charged and the oxygen is partially negatively charged.
A very important bond in water and throughout the cell is the hydrogen bond.
When H is covalently bound to an electronegative N, O, or P, it has a partial positive charge that can attract negative or partial negative charged atoms.
Hydrogen bonds are weak (2-5 kcal/mol)
Hydrogen bonds in water form a network and give water its unusual properties
The need to break H-bonds confers high specific heat (energy to raise 1 degree C) Strong cohesion gives strong surface tension Strong hydrogen bonding opposes increase in density during freezing so water expands as it freezes
Water dramatically dampens the strength of ionic bonds by surrounding ions with "hydration shells".
Ionic bonds are only 2-5 kcal/mol in water, but stronger when water is excluded
Strength in numbers: Ionic and Hydrogen bonds
In this example, ionic bonds between the phosphate backbone of the DNA and the amine of the protein are present . Also, hydrogen bonds are what hold the complementary DNA strands together. Why would H bonds be useful? Many H bonds that can easily be broken and reformed give great overall strength of DNA strands holding together yet flexibility to unzip them in specific locations with relatively little energy expenditure.
Things that don't mix
Oil and water Yankees and Red Sox Purdue University and a surfing team 7:30 AM class and attentiveness
Hydrophobic interactions are very important for understanding dynamics in and around lipid membranes
Hydrophobic molecules are non-polar, mainly composed of hydrocarbons with low and comparable electronegativities. Hydrophobic molecules do not dissolve into particles in water, but form aggregates. Hydrophilic molecules are polar and typically have atoms with high electronegativities Hydrophilic molecules dissolve into individual molecules or ions in water.
How do hydrophobic interactions work?
G= H-TS is Gibbs' Free Energy
Chandler 2006
van der Waals forces are remaining non-covalent intermolecular forces
Effects are still electrostatic attractive and repulsive, but based on interactions between transient dipoles in non-polar molecules Very weak individually (0.1-0.3 kcal/mol)
The Lennard-Jones potential function to describe van der Waal forces is often written as:
where
=
is the distance at the minimum of the potential.
Qualitative graphing of van der Waals forces
rmin is typically about 4 angstroms
Van der Waals forces are very important in stabilizing large protein structures
The better the complementarity between two molecular surfaces, the greater the van der Waals contribution