BIO 3

10/18/2021

- Metabolism: all chemical reactions in a cell

- Catabolic: release energy by breaking down molecules
- Anabolic: consume energy to build molecule
- Energy: capacity to cause change
 Kinetic energy-moving objects perform work
 Thermal energy-molecular movement felt as heat
 Potential energy-potential to do work or release heat based on location or structure
- Energy cannot be destroyed or created, just changed from one form to another
- Free energy: energy in a system available to do work (G)
- Exergonic reaction: spontaneous, energy released, products have lower potential energy,
ΔG negative
- Endergonic reactions: not spontaneous, energy input required, products have higher potential
energy, Δ positive
ENZYMES
- Enzymes: most chemical reactions are too slow to support life (even spontaneous ones);
enzymes are proteins that act as catalysts (speed up reactions, not consumed by the reaction)
- Transition state: an intermediate state where the reactants have a combination of old and new
bonds
- Activation energy: the amount of energy needed to reach the transition state
- Enzymes: lower activation energy (bring together molecules, stabilize transition state), very
specific for substrate(s) (substrate: reactant the enzyme acts on), usually very efficient (can
make reactions 1,000,000Xfaster), NOT USED UP IN THE REACTION (same amount at the end
then you did at the beginning)
- Generally global molecules, tertiary structure of enzyme important to function!!, contain an
active site (a place on the enzyme where substrates bind and interact)
3 steps of enzyme action
1) Initiation- substrates bind to active site, enzyme changes shape (induced fit)
2) Transition state facilitation- the transition state is stabilized via interactions with active site
3) Termination- reaction products are released (products don’t fit as well in active site),
enzyme returns to original shape
- Environmental factors- temperature & pH affect enzyme activity (enzymes function best at an
optimal pH & temp)
- At high temp the pH starts denaturing, at lower temps they start moving slower, not going to
read the enzyme as quickly
- Enzyme regulation- activation (substances bind to enzymes to stabilize structure, many vitamins
act as cofactors for enzymes), inhibition (substances bind to enzyme to destabilize structure
(allosteric inhibitors) or compete with substrate for active site) Allosteric- binds somewhere
other than active site
- Scurvy
 Vitamin C- cofactor for an enzyme that functions in collagen synthesis
 Vit C deficiency- loose teeth, bleeding gums, bone lesions, swollen joints, weakness &
irritability, skin lesions & hemorrhaging
 Caused by poor nutrition (treatment with supplements, change in diet)
BIO 3

- What affects an enzymes activity? temperature, salinity, pH, presence of cofactors, activators or
inhibitors, substrate or enzyme concentration, enzymes affinity for the substance
- Substrate concentration: as substrate concentration increases, more active sites are occupied,
enzymes are “saturated” with substrate & cant bind more (reaches maximum speed of reaction)
- Enzyme affinity for substrate
 High affinity: substrates bind quickly and easily, enzymes function at maximum speed even
when there isn’t much substrate present
 Low affinity: substrates don’t bind as quickly, substrate concentrations need to be high in
order for enzyme to function at maximum rate
- Examples of enzyme affinity for substrate
 Alcohol dehydrogenase (ADH)- enzyme that converts ethanol to acetaldehyde

 Different people have variations of ADH genes, with different affinities for ethanol
 High affinity ADH results in rapid buildup of acetaldehyde which causes facial flushing,
nausea, rapid heart rate

10/20/2021

- Adenosine Triphosphate: 3 neg charged phosphate groups, hydrolysis of ATP is exergonic

- Making ATP: attach P to ADP, ADP->ATP, endergonic
- Using ATP: P transferred to another molecule, ATP->ADP, exergonic
- Phosphorylation: energy is used to transfer phosphate group to another molecule or protein
(shape change or energy coupling to endergonic reactions)
- Phosphorylation causes shape change -> mechanical work
- Energetic coupling: ATP fuels endergonic reactions (transfer of a phosphate group from ATP to a
protein is exergonic, can be used to drive endergonic reactions) an exergonic process is used to
drive an endergonic protein
- When a protein is phosphorylated, the exergonic phosphorylation reaction is paired with an
endergonic reaction (reactant molecules are phosphorylated, the phosphorylated reactant is
less stable than the original reactant, second reactant displaces the phosphate group)
- Enzymes are necessary for the many chemical reactions needed to convert ATP to ADP
- Enzymes facilitate energetic coupling

Cellular respiration chp 9

- Being alive:
1) Extract energy from food
2) Energy used to make ATP
3) Use ATP to do cellular work (energy coupling, phosphorylation->shape changes)
- 3 ways to make ATP:
1) Aerobic respiration: most eukaryotes and some prokaryotes, uses oxygen, most efficient at
making ATP
2) Anaerobic respiration: some prokaryotes, does not use oxygen (humans don’t do)
3) Fermentation: some eukaryotes and prokaryotes, does not use oxygen
Aerobic respiration
- Catabolism: breakdown of molecules
BIO 3

- C6H12O6+6O26CO2+6H20+energy (glucose from food), (oxygen from inhaling), waste products

- Aerobic respiration overview
1) Catabolic reactions break apart glucose
2) Electrons stripped from glucose give to oxygen (series of redox reactions)
3) Chemical energy from reactions transformed to kinetic energy & heat
4) Kinetic used to make ATP
- Redox reactions: transfer of electrons from one reactant to another, Oxidation: loss of electrons,
Reduction: gain of electrons; oxidation and reduction are always paired together
Oxidation Is Loss Reduction Is Gaining
Molecule that loses e- is OXIDIZED, molecule that loses e- is a REDUCING AGENT, molecule that
gains e- is reduced, molecule that loses e- is oxidized
- C6H12O6+6O26CO2+6H20+energy becomes oxidized, becomes reduced
H+ “follows” the electron
Glucose is oxidized to form carbon dioxide, oxygen is reduced to form water, multiple redox
reactions happen in between,
1) Glycolysis- glucose is oxidized to form pyruvate
2) Pyruvate oxidation- pyruvate is oxidized to from Acetyl CoA & CO 2
3) Citric Acid Cycle- Acetyl CoA is oxidized to form CO 2
4) Electron transport chain- electrons stripped from steps 1-3 are given to oxygen, protons (H+)
pumped across mitochondrial membrane, flow of protons back through membrane is used
to attach P to ADP

10/22/2021

- NAD & FAD: electron carriers (carry electrons to ETC, H+ go with the electrons)
- Oxidized state: NAD+ can accept e-
- Reduced state: NADH can donate e-glu

10/25/2021

Step 1) Glycolysis
- Glucose -> 2 pyruvate molecules (little ATP made, NAD+ reduced to NADH)
- Glycolysis: in cytosol (outside mitochondria), invested of 2 ATP, Glucose OXIDIZED to pyruvate
(many intermediates), NAD+ reduced to NADH, a little bit of ATP produced by Substrate-level
phosphorylation: enzyme transfers P from an intermediate to ATP
- Products of glycolysis include a little ATP and NADH
Step 2) Pyruvate oxidation
- Getting ready for Citric Acid cycle, pyruvate transported into mitochondria matrix, pyruvate
oxidized to Acetyl CoA & CO2, NAD+ reduced to NADH
- Matrix: center of mitochondria
- CO2 produced (byproduct), remaining 2 carbon molecules oxidized to acetate, coenzyme A
attached to make Acetyl CoA
- NAD+ reduced to NADH, No ATP made, Acetyl CoA into Citric Acid Cycle
- Pyruvate was made in glycolysis in the cytoplasm, Pyruvate moves from mitochondria from the
cytoplasm and is then oxidized.
Step 3) Citric Acid Cycle
BIO 3

- In mitochondria matrix, Acetyl CoA combines with OAA, Acetyl CoA fully oxidized to Co2,
electrons given to NAD+ & FAD
- Products: NADH; FADH2; a little ATP, OAA regenerate (cycle)
- Glucose full oxidized to CO2, CO2 exhaled as waste, a little ATP made, NADH, FADH2 carry
electrons to ETC
- Electron Transport Chain: electrons passed down electron transport chain (negative change in
free energy in small steps), given to oxygen at the end, energy used to pump H+ from matrix
into intermembrane space, H+ flow back through “turbines” to generate mechanical energy to
attach P to ADP
- Chemiosmosis: diffusion of ions across a semipermeable membrane
- Oxidative phosphorylation: phosphorylation powered by redox reactions
- ETC: chain of e- transporters embedded in inner mitochondrial membrane, grouped into large
complexes (I-IV), accept e- from NADH, FADH2, passes e- down chain, final electron acceptor:
oxygen
- Intermembrane space: High H+ concentration
- Matrix: low H+ concentration
- H+ cant cross the lipid bilayer on their own because they are charged. The intermembrane space
is most acidic. If you poked holes in the membrane, the H+ would flow back into the matrix (they
want to go where there are no other H+)
- Proton Motive Force (PMF): potential energy stored in electrochemical gradient of H+ ions
- Oxidation Phosphorylation: phosphorylation powered by redox reactions (chemiosmosis drives
ATP production, protons flow through the ATP synthase, mechanical energy: ADP +Pi -> ATP, 350
revolutions/second)
- If we stop breathing in oxygen, we stop making ATP, then all the things that use ATP very quickly
die first
- Protons flow through ATP synthase like water through a water wheel, water- protons, wheel-
ATP synthase, Gravity- the electrochemical radiant
- If 34% of the potential energy of a glucose molecule is converted to ATP, what happens to the
other 66%. Heat- it maintains body temp
- Oxidation: loss of electrons
- Reduction: gain of electrons
- Substrate-level phosphorylation: transfer of a phosphate group from an intermediate molecule
directly to ADP
- Aerobic respiration redox: big picture
- Glucose is oxidized to form carbon dioxide, oxygen is reduced to form water, multiple redox
reactions happen in between, change in free energy of reactants & products is used to
synthesize ATP from ADP & P

10/27/2021- chapter 9

- During respiration glucose is oxidized

- During glycolysis electrons stripped from glucose are given to NAD+
- Electron transport chain is a series of redox reactions, passes electrons to the final acceptor O2
- ATP synthase harnesses the flow of H+ down their electrochemical gradient to attach P to ADP
- Majority of ATP is made by oxidative phosphorylation
BIO 3

- 3 ways to make ATP

1) Aerobic respiration: most eukaryotes & some prokaryotes, uses oxygen,
- Obligate anaerobes: cant survive in oxygen environment (anaerobic respiration or fermentation,
cant do aerobic respiration)
- Facultative anaerobes: can do both respiration or fermentation depending on conditions
- Anaerobic respiration: very similar to aerobic respiration (glycolysis, pyruvate oxidation, CAC<
ETC), final electron acceptor not oxygen (usually inorganic molecules, sulfate, nitrate, carbon
dioxide, etc)
- Anaerobic bacteria: can cause opportunistic infections & food poisoning (clostridium botulinum,
clostridium tetani, clostridium difficile)
- Bacteria don’t have a mitochondria, they don’t have the same organelles as eukaryotes
- ETC built into plasma membrane of organisms without mitochondria

11/1/2021

- Photosynthesis: uses energy from the sun to convert CO 2 to biomolecules (store energy, cellular
components, fuel respiration)
- 2 steps of photosynthesis
1) Light reactions: use sunlight to make ATP & collect electrons (thylakoid membrane of
cytoplast)
2) Calvin cycle: use ATP & electrons to convert CO 2 to carbohydrates (stroma of chloroplasts)
- Chlorophyll: main photosynthesis pigments (chlorophyll a) (each pigment type absorbs specific
wavelengths)
- Electrons can be “boosted” to a higher energy state (by absorbing just the right amount of
energy, electrons become excited and move to a higher orbital, energy lost as they “fall” back to
their ground state)
- Light reaction: photon strikes chlorophyll & transfers energy (absorbs photons whose energy is
equal to difference between ground state & excited state), raises e- to a higher shell
- Photosystems: in thylakoid membrane, chlorophyll molecules grouped into photosystems
1) Light strikes photosystem
2) Energy passes around light harvesting complex to the reaction center
3) Electron in reaction center gets excited
4) Electron passed to electron acceptor
- Photosystem II generates ATP for Calvin Cycle
- Photosystem I generate electrons for Calvin Cycle (NADP+.NADPH: electron carriers)
- Electron transport chain connects two photosystems- oxidation phosphorylation used to make
ATP
Light reaction
1) Photons strike Photosystem II
2) Photosystem II gives electrons to primary acceptor
3) Electron passed down ETC -> ATP made (H+ pumped into thylakoid space, flow out via ATP
synthase)
4) Electron given to photosystem I
5) Photons strike photosystem I
6) Photosystem I gives electrons to tiny ETC
BIO 3

7) Electron given to NAP+

8) ATP & electrons (NADPH) transported to Calvin Cycle
- How are electrons in Photosystem I replaced? Collect electrons from ETC
- How are electrons in Photosystem II replaces? Splitting of a water molecule (O2 is a byproduct)
- If the ETC in between the photosystems is pumping H+ to generate ATP during the light reaction
then: everything is occurring
- Calvin cycle uses CO2, ATP, and electrons to construct carbohydrates

Calvin cycle

- 3 steps: fixation, reduction, & regeneration

- Starts & ends with a 5-carbon molecule called RuBp
- Generates a 3 carbon sugar G3P
- Uses ATP & electron carried by NADHP
1) Fixation: the enzyme Rubisco fixes CO2 onto RuBP
Split immediately into two 3-carbon molecules
2) Reduction: 3-carbon molecules converted to G3P
ATP & electrons used, NAHPH oxidized to NADP+
6 molecules of G3P made for every 3 CO2 molecules that enter the cycle
(1 G3P molecule is used to make glucose & other carbohydrates, 5 G3P molecules go back to
Calvin Cycle)
3) Regeneration: 5 G3P molecules left used to regenerate RuBP
Some ATP used in converting G3P back to RuBP

11/3/2021-cell cycle & mitosis

- Cells divide: replace worn out cells, healing from injury, generate specialized cells, growth of the
whole organism, reproduction
- Mitosis: division of somatic cells
- Meiosis: division of cells to make gametes
- DNA: double stranded, information passed down to cells, gene-region of DNA sequence
containing information for building RNA or protein, genome- all DNA in a cell, human nuclear
genome (3 billion nucleotides, 20,000 genes in human genome, organized into 23 pairs of
chromosomes)
- Chromosome: structure in the cell consisting of one double stranded DNA molecule + associated
proteins (can be either condensed or uncondensed depending on if the cell is in the process of
dividing)
- Chromatin: DNA tightly wrapped around histone proteins (chromosomes are made of
chromatin)
- Ploidy: the number of sets of chromosomes in the cell
- Human somatic cells are diploid: each cell has 2 chromosomes, each cell has 2 copies of each
DNA molecule, each cell has 2 copies of each gene
- Gametes are haploid: 1 chromosome set, 1 copy of each DNA molecule, 1 copy of each gene
- DNA is replicated prior to mitosis & meiosis
- 2 of each type of DNA molecule -> 4 of each type of DNA molecule
BIO 3

- DNA copies stay attached before they are pulled apart during mitosis (sister chromatids)
- Chromosomes are defined as a single unit regardless of the number of DNA copies contained in
that unit
- Chromatid: each DNA copy in a replicated chromosome
- Sister chromatid: chromatids in the same chromosomes, containing exact copies of the same
genetic information
- Centromere: a specialized region of the chromosome at which sister chromatids are most tightly
linked
- Karyotype: image of the full set of chromosomes from a cell
- Humans:46 chromosomes total, 2 of each kind (typically)
Cell cycle
- Orderly series of events that end in cell division
- To divide cells:
 Need to make sure division is needed
 Need to replicate & compact their DNA
 Need to grow
 Need to make more membrane, organelles
 Need to check for problems
 Physically separate components into 2 cells
- Dividing cells cycle between 2 phases
- G1: 2 copies of DNA, go ahead signal, make proteins necessary for DNA replication, make more
organelles
- G2: 4 copies of DNA, prepare for physical division, check for DNA damage, continue cell growth
- S phase: DNA ‘synthesis’, DNA replication,
At the end: 46 chromosomes, each chromosome is composed of 2 sister chromatids, 4 of each
type of DNA molecule

- End of interphase: DNA replicated, extra organelles membrane, signal to proceed to mitosis,
chromosomes still uncondensed, 2 centrosomes
- Centrosome: microtub
- M phase: mitosis
1) Prophase
2) Prometaphase
3) Metaphase
4) Anaphase
5) Telophase
- Cytokinesis: process of physically dividing cell
*READ FIGURE 12.7 ON PG 238-239
- Mitotic spindle: microtubules & associated proteins, attaches to kinetochore: structure of
proteins assembled at centromere, spindle fibers attached to kinetochore shorten during
Anaphase