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Potential Energy
energy associated with position
Kinetic Energy
energy associated with motion; molecularly - thermal energy
Change in G = Change in H - T Change in S
Change in G - free energy change
Change in H - change in enthalpy (heat content)
T - temperature
Change in S - change in entropy (level of disorder - disorder in being in a state of lower energy)
Exergonic Reaction
- releases energy
- heat out
- spontaneous
Endergonic Reaction
- requires energy for the reaction to occur
- heat in
- non-spontaneous
Energetic Coupling
exergonic reactions drive endergonic reactions
Oxidation Reaction
a molecule loses electrons (exergonic) and has the potential to pick electrons
Reduction Reaction
a molecule gains electrons (endergonic) and has the potential to donate electrons
Transfer of High Electrons (Redox Electrons)
involve the lose or gain of electrons
Transfer of a Phosphate Group (ATP Hydrolysis)
- ATP stores a large amount of potential energy of potential energy which is released when ATP is hydrolyzed
- the phosphate group that is released during hydrolysis covalently bonds to another molecule activating it
Enzymes
they catalyze reactions
Active Site
a region of the enzyme that has a high affinity to bind to substances
Induced Fit
reorientates the substrates and binds them tighter to them tighter to the active site
Stages of Enzymes Catalyzing Reactions
Initiation - reactants bind to the active site in a specific orientation forming the enzyme substrate complex
Transition State Facilitation - interactions between the enzyme and the substrate lower the activation energy needed for the reaction to occur
Termination - products have lower affinity for the active site and are released; the enzyme is unchanged after the reaction
Competitive Inhibition
another molecule binds to the active site that the substrates bind too making it so that the substrates cannot bind
Allosteric Activation
active site becomes available when a regulatory molecule binds to another site on the enzyme
Allosteric Inhibition
active site becomes unavailable when a regulatory molecule binds to a different site on the enzyme
Regulation through Phosphorylation
- phosphorylation changes the shape and activity of proteins
- unphosphorylated - inactive
- phosphorylated - active
Cascade
proteins are phosphorylated and then go and phosphorylate other proteins
Feedback Inhibition
can regulate metabolic pathways when an enzyme in a pathway is inhibited by the product of the reaction sequence
Cellular Respiration
C6H12O6 (glucose) + 602 (oxygen) → 6CO2 (carbon dioxide) + 6H20 (water) + energy (ATP)
Glycolsis
- occurs in the cytosol
- yields 2 pyruvate
- ATP yield
gross - 4 ATP
net - 2 ATP
Fermentation
- occurs in cytosol
- occurs when no oxygen in present
- produces lactic acid in animals
- produces ethanol in plants
Processing Pyruvate
- occurs in the mitochondria matrix
- turns pyruvate into 2acetyl CoA
The Citric Acid Cycle
- occurs in the mitochondria matrix
- produces 6 NADH
- produces 2 FADH2
- produces 2 ATP
Oxidative Phosphorylation (The Electron Transport Chain)
- occurs in the innermembrane system
- Typical
10 NADH
2 FADH2
Proton Motive Force
the gradient created along the electron transport chain
Photosynthesis
light energy (photons) + 6H20 (water) + 6CO2 (carbon dioxide) = C6H12O6 (glucose) + 6O2 (oxygen)
Photosynthetic Pigments Absorb Light
the correlation between the Pigment Absorption Spectra and Photosynthetic Action Spectrum
Chlorophyl A
if functional group is methyl
Chlorophyl B
if functional group is carbonyl
Pigment
absorbs different wave lengths
“Excited” electrons
- electrons are in excited states meaning they have moved further away from the protons
- can cause them release energy when they return back to a lower state of energy or the electron can get picked up by an electron carrier
Light Capturing Reactions
Photosystem II - occurs in the thylakoid interior
Photosystem I - occurs in the stroma
Produces ATP and NADPH
The Calvin Cycle
- occurs in stroma
- takes 6 turns to produce glucose
- rubisco protein
- three phases
fixation - fixes CO2 (incorporates CO2)
reduction -
ATP → ADP + P
NADPH → NADP+
regeneration - 5×3 C → 3×5 C
Rubisco Protein
- 16 subunits
- 8 active sites
- photosynthesis - reaction with CO2
- photorespiration - reaction with O2 (used to produce CO2 to drive photosynthesis)
Stomata
- made up of multiple stroma
- O2 and CO2 pass through the stomata
closes off at night
open during the day
Guard Cells
- form pores
- stiffen when greater H2O - open pore
- go limp when less H20 - close pore
C4 Plants
- make a 4 carbon sugar
- Can briefly open during the day and use PEP carboxylase to quickly bind to CO2 and then close to prevent losing water
PEP carboxylase
- fixes CO2
- higher affinity for CO2 than rubisco
C4 Compound
stores CO2 that can be later used in the Calvin Cycle, even when they stomata is closed
CAM plants
stomata are closed on hot days and are only open at night (only occurs in the most extreme environments)
Unreplicated Chromosome
single strand of DNA wound around a histone (protein)
Gene
small length of DNA that makes up chromosomes
Replicated Chromosome
- makes a copy of the unreplicated chromosome
- single thread of DNA is now loose, not wrapped around a histone
Condensed Replicated Chromosome
- wound tight around the histone protein
- now known as sister chromatids
Four Phases of the Cell Cycle
- G1 phase - cell is bringing in materials to sustain itself (cells is growing)
- S phase - DNA replicates
- G2 phase - cell prepares to divide
- M phase - cell divides
Interphase
- includes G1, S, and G2 phases
- chromosomes start to condense and the cell prepares to divide
Mitosis
m phase
Centrioles
microtubule organizing center (MTOC)
Prophase
- centrioles move toward the poles of cells and chromosomes continue to condense
- early spindle apparatus - microtubules start to form
Prometaphase
- nuclear membrane begins to break down and chromosomes become really condensed
- formation of kinetochore microtubules - attach to the kinetochore
- formation of polar microtubules - do not attach to a chromosome; opposed to one another which causes them to overlap
Metaphase
- chromosomes line single file in the middle of the cell
- formation of astral microtubules - connect to the membrane of cell
Anaphase
- cell begins to extend out at the poles caused by the microtubules pushing the cell outward
- sister chromatids are being pulled apart; cohesions split caused by kinetochore breaking the bonds between the two sister chromatids (tubulin)
- astral microtubules keep MTOC in place at the poles
Telophase
- nuclear membrane reforms around the chromosomes
- actin and myosin cross each other which causes the cell to begin to pinch and split
- mitosis is complete
Cytokinesis
- Parent cell divides into two daughter cells
cleavage furrow (animals)
cell plate (plants) - made up of callose (carbohydrate)
Binary Fussion
- bacteria replication
DNA is copied
Protein structure that extends across the cell guides the new copy of DNA to migrate across the cell at the pole
Cytokinesis - cleavage furrow is formed
G0
- possible path for cell
- cell will be stuck in G1
G1 Checkpoint
- cells passes through if
it is the right size
has enough nutrients
the social signals are appropriate
DNA is undamaged
P53
- tumor supressor
- can tell cell to go through apoptosis (programmed cell death)
G2 Checkpoint
- cell passes through if
chromosomes have replicated properly
DNA is undamaged
activated MPF is present
MPF
- metaphase promoting factor
- hetero dimer
- regulatory phosphate group - protein is not activated when this is attached
- activating phosphate group - must be attached for protein to be active
- ubiquitin tag - transports MPF to be deconstructed
M Phase Checkpoint
- cell passes through if
chromosomes have attached spindle apparatus
chromosomes have properly segregated
MPF is absent
Cancer
cancer is uncontrolled cell growth
Benign Tumor
tumor cells continue to divide but do not spread from the tumor
Malignant Tumor
- adhesion proteins of the cell are being compromised and the cells can no longer be together
- cancer spreads from tumor
Hershey Chase Experiment
- which molecule carries DNA - proteins or nucleic acids
- did an experiment where they tagged the proteins and DNA of viruses to see which they left behind while infected bacteria host cell
- discovered nucleic acids hold DNA
DNA
- synthesized from 5’ to 3’
Meselton -Stahl Experiment
- three hypotheses for what happens after DNA is replicated - semiconservative, conservation, dispersive
- tagged the parent and daughter strands with 15n and 14n then used density gradient centrifugation to separate the parent and daughter strands
- determined that replication is through semiconservative replication
Semiconservative
parent strand stays with the daughter strand after replication
Conservative
parent strand leaves the daughter strand and goes back to the other parent strand
Dispersive
the parent and daughter strand mix together and form hybrid strands
DNA Synthesis Proceeds in Two Directions
- bidirectional synthesis - at the same time
leading strand - synthesizes into the fork
lagging strand - synthesizes away from the fork
Helicase
opens the double helix (breaks hydrogen bonds)
Single Stand DNA Binding Proteins (SSBP)
stabilizes the single strands by binding with them and preventing the hydrogen bonds from reforming
Topoisomerase
relieves twisting forces by cutting the DNA and the allowing it to rejoin (prevents supercoiling)
Primase
- synthesizes RNA primer
- RNA primer gives us a little fragment of double stranded nucleic acid
DNA Polymerase III
binds to the RNA primer and starts moving along the single strand of DNA creating a complementary daughter strand
Sliding Clamp
holds DNA polymerase in place
DNA polymerase I
removes the RNA primer and replaces the RNA nucleotides and replaces them with DNA nucleotides
Okazaki Fragments
fragments that occur during the synthesis of the lagging stand
DNA Ligase
closes the gaps between the Okazaki fragments of the lagging strand to connect the fragmented strands
Telomere
non coding segment of DNA the repeats
Telomerase
- occurs in sex cells and cancer cells
- adds more nucleotides to the parent lagging strand
- can extend parent strand to be longer than before
One Gene, One Enzyme Hypothesis; Later One Gene, One Polypeptide Hypothesis
- first believed one gene coded for one enzyme
- worked with red mold and used mutations to make certain proteins non-functional
- determined one gene could code for a polypeptide
- one gene can actually code for multiple proteins
Central Dogma
DNA → mRNA → Protein
Allele
different forms of the same gene
Codon
triplets (sequence of three bases)
The Genetic Code
- is
redundant - amino acids are coded by more than one codon
unambiguous - each codon creates a specific amino acid
non-overlapping
universal (nearly)
conservative - first two bases are the same for the amino acid
Wobble
the third base variable
Start Codon
- starts translation
AUG
- codes for amino acid
Stop Codon
- stops translation
UAA
UAG
UGA
- does not code for amino acid
Coding Strand
- sense strand
- non-template strand
- top strand
Non-Coding Strand
- anti-sense strand
- template strand
- bottom strand
- gets transcribed because the RNA transcribed from it reflects the coded strand
Mutations
permanent changes in DNA
Point Mutations
caused by errors in the replication process of DNA
Silent Point Mutations
- point mutation where the error occurs at the wobble and doesn’t change the amino acid that is coded for
- no effect on phenotype
Missense Point Mutations
- point mutation that causes a different animo acid to be coded which changes the primary structure of the protein
- could be beneficial, deleterious, or neutral
Nonsense Point Mutations
- point mutation where there is an early stop codon which shortens the polypeptide
- typically deleterious
Frameshift Point Mutations
- point mutation where there is an addition or deletion of a nucleotide into the sequence which shifts the reading frame altering the meaning of all codons
- almost always deleterious