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· Reducing Atmosphere
o Reduced molecules have higher energy than oxidized moleculesReduced molecules are required for creation of the organic molecules
o : Oxygen hogs more electrons, bonds are stronger, molecule has less potential to break apart, has lower potential energy
o Energy storage (metabolizing sugars results in energy to run reactions of the cell)
o Structural component in DNA and RNA
o Fats, steroids and phospholipids
o Have hydrocarbon tails that vary in length attached to other chemical groups and do not dissolve in water
o Phospholipids make up the cell membrane and organelle membranes
o If the structure changes/is messed up/ whatever, the protein will NOT work
o STRUCTURE IS IMPORTANT
o Made of amino acids
o Fold into really complex shapes
o Structure determines function
What do proteins do?
§ Transport other molecules (hemoglobin)Enzymes (catalyze rxn)
· Started with CH + H +N + other small reduced molecules, water
o A, T, G, C, and U
o Polymer of A, T, G, and C
stable and less complex than RNA
1. Must contain information
2. Must be able to be copied
3. Be able to catalyze reactions (would have to have been able to replicate itself)Facilitate Evolution
1. Contain information
2. Can catalyze reaction
3. BUT… cannot be copied. There is no code!
1. DNA contains information
2. It can be copied, act as a template
3. BUT, it would not have be able to catalyze reactions (too stable)
1. Contains information
2. Can be copied.
3. And, it is able to catalyze reactions!
DNA to RNA to Protein
§ Concentrate reactants so chemical reactions are more efficient
§ Make the internal environment different from the external (ex. Maintains temp., pH, and other conditions)
§ SELECTIVELY keeps out damaging compounds, admit needed compounds, and allow unneeded ones to leave
§ 3 classes of lipids: steroids, fats, and phospholipids
§ CELL MEMBRANES ARE MADE OF PHOSPHOLIPIDS
o Polar head: very charged, love water
o Non-polar tail: no charge, hate water
Factors that determine if a molecule will permeate the cell membrane:
1. Polarity/charge of the molecule
2. Size of the molecule
3. Properties of the membrane itself
*The combination of polarity and size determines the permeability
Saturated: all H’s that can be there are there
Unsaturated: not all H’s there, double bond causing kink in tail
(more passable… more space due to kink)
1. (simple) is the diffusion of molecules that pass freely through the
1. diffusion of molecules that cannot pass freely through the
membrane. Charged or large polar particles pass through a specialized protein embedded in the cell membrane.
o Water moves down it’s concentration gradient OR against the concentration gradient of a solute
o Water is always moving in a direction to achieve equilibrium
o Sometimes this is with or against the movement of the solute
· If the solute concentration is higher inside the cell than outside the cell
o The cell is in a HYPOTONIC environment
o The cell is HYPERTONIC to the environment
· If the solute concentration is higher outside the cell than inside the cell
o The cell is in a HYPERTONIC environment
o The cell is HYPOTONIC to the environment
o Allows molecules through that cannot freely pass
o Powered by movement down the concentration gradient (no energy input!)
o Move from High to low
o Ion channels: most channels selective, only admit one kind of ion
o This selectivity is determined by the specific amino acids of the channel
o Channel is triggered to open by charge, then opens.
o EX. Glucose transporters
o What makes ATP a high energy molecule?
o phosphate group make it unstable/ reactive
o Releases energy= EXERGONIC reaction
Ø ADP+ PHOSPHATE+ ENERGY= ATP
§ C H O is a reduced molecule
§ This means it has a lot of energy stored in it, stored in those carbon bonds
§ That energy is released when the bonds are broken
§ Electrons have to go somewhere, to another molecule
§ This molecule is the electron acceptor (oxygen)
§ Sugar is the electron donor
GLUCOSE + 2ATP+ 2 NAD+ à PYRUVATE + 4 ATP + 2 NADH
What goes in What comes out
1 glucose 2 PYRUVATE
2 ATP 4 ATP
2 NAD+ 2 NADH
1. CELL RESPIRATION (if Oxygen is available)
2. FERMENTATION (if NO oxygen is available)
· Glycolysis makes pyruvate
· Pyruvate accepts electrons from NADH (oxidizing NADH TO NAD+)
· That NAD+ feeds back into glycolysis where it is used to generate more ATP
· Some organisms use fermentation as a back-up when oxygen is not available (ex. Humans)
STEP 2: Citric Acid Cycle
STEP 3: Electron Transport Chain
STEP 1: Pyruvate to acetyl coA
1. If oxygen is present, pyruvate is converted to acetyl coA which enters the Citric Acid Cycle
**Pyruvateà-> CO2 + NADH + Acetyl coA-> Citric Acid Cycle
Citric Acid Cycle
Acetyl coA-> CO2 + NADH +FADH + ATP
Ø CO2 released, used for photosynthesis
Ø NADH= electron carriers
Ø ATP- can be used immediately for energy
§ BIG IDEA= a lot of oxidation reactions
o Glycolysis and fermentation occur in cytosol
o Citric acid cycle and electron transport chain occur in mitochondria
1. ELECTRON TRANSPORT CHAIN
o Chain refers to a series of molecules that receive electrons which brings them to a higher energy level, then pass off those electrons
o final electron acceptor is OXYGEn
o So without it, NADH will not be oxidized to NAD+ because no electron acceptor to accept NADH’s electron and this is why fermentation would happen when we run out of oxygen
water is a by-product of cell respiration
o The first organisms to do photosynthesis were bacteria but photosynthesizing bacteria were not the first bacteria.
· Removes CO2 from atmosphere.
· Primary Producer of food for all life on earth
o LIGHT energy à CHEMICAL energy
Light energy+ 6CO2+ 6H2O à 6O2 + C6H12O6
o S0… light energy + carbon dioxide+ waterà Oxygen + sugar
Ø Where is photosynthesis happening?
§ Bacteria: no specialized organelles for photosynthesis, happens on membranes found throughout the cytosol
§ Eukaryotes: (plants and protists) Happens in chloroplast
· Photosystem II
o gradual step down of re-dox reactions from high to low energy.
o There is a series of molecules embedded in thylakoid mebrane.
o As they give up electrons they just received, they give off energy because they are becoming oxidized to lower energy state.
H2O split to O2
How is ATP generated in PSII?
o Energy released by electron transport chain used to pump protons into lumen of thylakoid (inside of membranes)
o Proton gradient builds up and movement of protons out of lumen (down the gradient) through ATP synthase releases energy.
· photosystem II generates ATP and photosystem I generates NADPH
§ Uses light energy
§ H2O is split
§ O2 is released
§ Produces ATP
§ Produces NADPH
§ CO2 à Glucose
§ This is a reduction reaction that uses ATP and NADPH from light reactions
§ The cycle continues because some of the intermediate carbon molecules in the cycle are used to make more of the 5 carbon sugar RuBP
o A trait that a certain group of organisms has that do not exist in other organisms
o Ex. Fur is a synapomorphy of mammals
· Why compare sequence for rRNA gene?
o Ribosomal RNA there in ALL organisms
o The DNA that encodes for rRNA in ALL organisms
o This gene happens to be highly conserved (similar) among species but not identical
§ No membrane bound organelles
§ No nucleus
§ Single celled
§ Circular chromosomes
§ Membrane bound organelle
§ Linear chromosomes
· us that eukarya and arhaea are more closely related than either are to bacteria even though bacteria and archaea are both prokaryotes
Why would it be an advantage for a species to have a very different metabolism that uses SO4 instead of O2?
1. This allows bacteria to live in an environment where other organisms cannot reducing competition
2. They can co-exist with other prokaryotic species by “cleaning up each other’s mess” and again- not competing for resources
Why, as a group, are bacteria so well adapted to living in environments that other organisms have not adapted to?
1. Have been on earth a lot longer than any other group of organisms so MORE TIME TO ADAPT
2. They can share their “survival/adaptation” genes with unrelated bacteria so constant gene mixing within bacteria as a groupReproduce at a fast rate
How do temperature extremes effect cells?
o denatured proteins not conducive to life
o how do psychrophiles retain effective enzyme reactions?
§ Enzyme may bind better to substrate. It may not encounter the substrate as often because of cold temps, but when it does, it will have an easier time binding
high temps=more permeable·
low temps= membranes less permeable
saturated and long tails= less permeable
unsaturated and short tails= more permeable
· Prokaryotes VERY diverse
· Been here the longest
· Because of their fast reproduction rate, more opportunities to introduce mutation
· Because of their ability to exchange DNA so easily with others, more opportunities for genetic variation
· Diversity: diff., extreme habitats
o Bacteria take up free DNA released by other bacteria
o DNA transferred from bacterium to bacterium by viruses
o Genetic transfer involving bacterium to bacterium contact
§ Cell membrane folded in to create both nuclear envelope and endoplasmic reticulum
§ Theory of endosymbiosis
ú Eukarya ancestor (which was a prokaryote) used anoxygenic cell respiration of fermentation engulfed/ate/took in/whatever a bacteria that used aerobic respiration
§ have happened in cell after endosymbiosis of mitochondria
§ Endosymbiosis theory proposes a photosynthetic bacteria was engulfed by early non-photosynthetic eukaryote and lived in host
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