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Biochem Mcat - Comprehensively covers every Chapter and

includes pictures. I think this will
MCAT - Kaplan book notes (Johns Hopkins University)

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Chapter 1: Aminos Peptides and Proteins

Chp 1.1 Proteogenic amino acids
● All amino acids contain an amino group (-NH2) and a carboxyllic acid group
(-COOH) connected by an alpha carbon
● Aminos are categorized by their R group which confers particular properties
●

● All aminos with long alkyl side chains (Alanine, Isoleucine, Leucine, Valine,
and Phenylalanine) are ercely hydrophobic so are only in protein interiors
● All charged aminos (Lysine, Arginine, Histidine, Aspartic Acid, and Glutamic
Acid) are ercely hydrophilic so are only on protein exteriors

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● All aminos are L aminos which generally correspond to S conguration,

except Cystine which is L but has an R absolute conguration
● All aminos’ alpha carbon is a chiral center except Glycine whos R group is H
● Proline is the only Cyclic amino since its R chain loops around to bind the
amino nitrogen. This structure decrease exibility when in a protein.
● 3 aminos contain aromatic rings; Phenylalanine which is alanine with a
phenyl group attached, Tyrosine which is Phenylalanine with a hydroxyl
group attached making it polar and Tryptophan is the largest of all with a
double ring system
Chp 1.2 Acid and Bases and Aminos
● All non charged animos have a positive charge at super low pH and a negative
charge at super high pH
○ Low pH: carboxylic acid is protonated and neutral, Amino is
protonated and positive
○ Biological pH (7.4): carboxylic acid is deprotonated and negative, Amino
is protonated and positive. Charges cancel so amino is zwitterionic
○ High pH :carboxylic acid is deprotonated and negative, Amino is
deprotonated and neutral
● Isoelectric point (non charged aminos), the pH at which all aminos exist in
neutral zwitterionic form

○
● Isoelectric point for Charged aminos

○Acid (negative) →
○Base (positive) →
Chp 1.3 Peptide bonding
● Proteins exist as peptides. Oligo peptides are those of 20 aminos or fewer
and polypeptides are longer chains’
● Peptide bond formation is a condensation reaction between the 3rd H on the
amino group and the Hydroxyl on carboxylic acid
○ Amino group is nucleophile, Carboxylic carbon is electrophile and
hydroxyl is the leaving group
● Peptide bonds share double bond character with the carbonyl so they are
rigid while bonds to the alpha carbon are more exible
● Peptides are stable but can be broken down by enzyme catalyzed hydrolysis

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in which a H is added to the amide nitrogen, an OH is added to the carbonyl

carbon resulting in the peptide bond being broken
○ Trypsin: cleaves carboxyl ends of arginine and lysine
○ Chymotrypsin cleaves carboxyl end of phenylalanine, tryptophan, and
tyrosine (the aromatics)
Chp 1.4-1.6 Protein structure
● Primary structure
○ Linear arrangement/order of aminos
○ Contains all information for rest of protein structure levels
● Secondary structure
○ Stabilized by hydrogen bonds between carbonyl oxygens and amide
hydrogens
○ Alpha helicies
■ Rod structure where hydrogen bonding occurs between every
fourth atom
■ Residues point away from interior
■ Proline will kink the helix and thus generally is found at
beginning of helicies or in an intramembranous region
○ Beta sheets
■ Peptide strand lay along each with amides from one strand h
bonding to carbonylls of another to create pleated sheet
■ Residues stick out above and below sheet
■ Prolines do not exist in sheets but are often found at turn
regions between strands participating in sheet
● Tertiary Structure
○ The 3 dimensional folding of a protein
○ Proteins are brous or globular
○ Proteins are folded based on hydrophobic/phillic interactions to
minimize ordering of solute molecules in the solvation layer
○ Disulde bonds (oxidized cystine residues where S’s are bound to each
other as opposed to H’s), h bonds, and acid base interactions also help
to stabilize tertiary structure
● Quaternary structure
○ Protein that contain more than one subunit
○ These serve the purpose of increasing stability by further reducing
surface area, increase the efciency of limited amount of DNA, and

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bring catalytic site closer together

○ Cooperativity: quaternary structure allows the changing of one
subunits conrmation to regulate the function of another sub unit
● Conjugated proteins: some proteins contain prosthesis groups like metals,
nucleic acids, lipids or carbs that effect function of protein
○ coenzymes/cofactors are small tightly bound prosthesis groups which
are necessary for enzyme function
● Denaturation: the breaking down of 3rd and 4th structure
○ Two main causes are temperature or solute
■ Temperature increases kinetic energy of aminos causes them to
overpower the H-bond
■ Solutes directly interfer with the forces that hold proteins
together
● SDS can disrupt non covalent bonds (hbonds and acid
base interactions)

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Chapter 2: Enzymes
Chp 2.1 Classes
● Enzymes are molecules that increase reaction rate by lowering the Activation
energy thus making the transition state a lower energy and more achievable
● Enzymes have specic function and act on specic substrate. 6 Classes exist
with the mnemonic LILHOT
○ Ligase: catalyze addition or synthesis reaction between large
molecules and often require atp
■ Most frequently seen in nucleic acid synthesis and repair
○ Isomerase: rearrange bonds within molecules to convert
sterochemistry and/or conguration
○ Lyase: catalyze the cleavage of 1 molecule into 2 w/o extra reactants
■ Enzymes can also do the reverse rxn sometimes so it is common
to see lysases doing synthesis rxns between small molecules
○ Hydrolyase: catalyze hydrolysis
○ Oxioreductase: catalyze redox rxns
■ Often have NAD+ or NADP+ as electron carrier cofactors
○ Transferases: catalyze the movement of a functional group from one
molecule to the other
■ These include kinases which often transfer phosphate from ATP
Chp 2.2 Enzyme Mechanisms
● Induced t model: as opposed to the lock and key theory active site dont
perfectly mirror their substrate but instead when substrate is near the active
site is relaxed so that the substrate can squeeze in
○ Its thought that in an endergonic process the substrate bends the
active site, but their is still specicity because only the proper
substrate will be able to make a favorabled enough transition state to
allow for induced binding
● Cofactors and coenzymes: some enzymes require a little help so they
include these in their active sites
■ The most common role of the prosthesis groups is charge
carrying through ionization, protoantion or deprotonation
■ Enzymes missing their helper are apoenzymes while bound
enzymes are ironically called holoensymes
■ Cafactors are minerals and metals which coenzymes are
vitamins and their derivatives like NAD+, FAD and coenzyme Q

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Chp 2.3 enzyme kinetics

●
● Michaelis-menten plot/equation relate reaction velocity and substrat conc.
○ As substrate concentration increases present enzymes become more
booked up until all enzymes are constantly bound
○ Saturation is when all enzymes are bound so the reaction is occurring
with a velocity of Vmax. This means that the only way to increase
Vmax is to increase [E]
■ Vmax = [E]Kcat where Kcat is the rxn rate for ES → E
+ P
○ Km is the concentration of substrate at which Vo=½Vmax. After this
point increasing [S] will have increasingly diminishing returns.
■ Km is used to assess enzyme efciency
■ Kcat/Km is referred to as catalytic efciency so small Km or big
Kcat means more efcient enzyme

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●
● Cooperitivity
○ Enzymatic cooperativity (the binding of one substrate increasing the
afnity for further substrate bind) bens the michaelis metten plot into
a signmoidal shape
■ When one substrate binds one subunit, it induces conrmation
change in other subunits to switch from the Tense position to
the relaxed position which has higher binding afnity
■ This can alos happen the other way around where binding one
subunit makes the other subunits tense
■ Hill coefcient is a measure to determine the level of
cooperativity (>1) or anticooperativity (<1)
■ As more subunits bind substrate afnity continually
increases/decreses
Chp 2.4 Local Condition effects
● Tempurature: most human enzymes have optimal temp around 37 degrees
○ Enzymatic function slowly grows as temp increase until its too hot and
sharp drop in activity occurs do to denaturation
● Salinity: high solute environment can interfer with bonds holding enzyme
together thus denaturatin
● pH: theres a bell curve around optimal pH with is 7.4 (gastric region its more
acidic and in pancreatic its more basic) since aberrant pHs can denature

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enzyme or ionize active site

Chp 2.5 Regulation

● Feedback inhibition more common than feedback activation since it
maintains homeostasis
● Feedforward regulation is when preceding intermediated regulate the
enzymatic pathway
● Irreversible inhibition: is when an inhibitor makes an enzyme non functional
and new enzymes must be made to restore activity
● Reversible inhibition: inhibitors only temporarily block function
○ Line burke weaver plot: linearized michaelis meten plot that featured
1/Vmax as the Y intercept and -1/Km as X intercept
○

○ Competitive: inhibitor directly binds active site blocking substrate

binding meaning in order to reach Vmax, [S] must be much greater to
overwhelm the inhibitor
○ Uncompetitive: inhibitor binds allosteric site only when substrate is
bound to the enzyme which locks it inplace. This increases stability
thus increasing afnity but decreases the amount of enzyme can bind
○ Noncompetivie: inhibitor binds allow steric site either when the
substrate is bound or no with the same afnity so it has no effect on
Km but it does decrease the maximum efciency

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○ Mixed inhibition: similar to competitive but the inhibitor has a

preference for binding either ES or E. If E is preferred then Km
increases (lower afnity) and if ES is prefers then Km decreases
(increased afnity)
● Allosteric binding can also serve to activate enzymes
● Covalent modifcations like phosphorylations can active or inhibit enzyme
function and glycosylation can direct cellular transport of enzyme as well as
alter activity level or selectivity
● Zymogens: some enzymes are very dangerous in their active form so are
secreted with a regulator group that blocks the active site and is cleaved in
the activation process

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Chapter 3: Nonenzymatic Protein

Chp 3.1 Protein types
● Structural proteins: brous proteins that have super secondary structure
(repetitive units of secondary structure)
○ Collagen: primary ECM protein that provides strength and exibility
○ Elastin: component of th ECM that provides stretch and recoil
○ Keritin: makes structures like hair and nail, and is present in epithelial
cells providing some regulatory function and compression resistance
○ Actin: interacts with the enzymatically active motor protein myosin to
create muscle contractions and uni directional cell transport
○ Tubliun: makes up greater structures know as microtubules which
provide structure and intearsct with 2 headed motor proteins
■ Kinesins: play a role in aligning chromosomes during metaphase
and depolarizing them during anaphase. Also transport vesicles
to the positive ended of microtubules AKA cell periphery
■ Dyneins: responsible for cilia and agella functions as well as
vesicle transport to negative end aka the nucleus
● Binding proteins: stabilize molecules within the cell
○ DNA regulation : Tfs are binding proteins
○ Sequesting function: high afnity to clump many of the same molecule
○ Transport function: Varying afnity to allow bind in one area and
release in anothe enviorment
● Cell Adhesion Molecules: CAMs are membrane integrated proteins which
bind cells to ECM or other cells
○ Cadherins: groups of glycoproteins that mediate calcium dependent
cell adhesion. They hold together cells of the same type so there are
different species for each cell type they are present in
○ Selectins: weakly bind carbohydrate projections from other cells and
are important in host defense
○ Integrins: Bind the ECM and are important for cell-cell signaling. They
are involved in processes like platelet clotting, white blood cell
migration and stabilization of basement membrane
● Imunoglobins: antibodies are talked about in bio

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3.2 Biosignaling
● Ion Channels: pathways through the membrane that allow for passive
facilitated diffusion of large polar or charged molecules down a
concentration gradient
○ 3 major kinds: ungated (always open), Ligand gate (ligand binding
causes channel to open or close), voltage gated (the conrmation
depends on surrounding membrane potential)
● Enzyme linked receptors consist of a transmembrane, binding and catalytic
domain and are often involved in secondary messenger cascade.
○ Ligand binding induces conrmational change of catalytic domain that
triggers its enzymatic activity. Think RTKs.
● G-coupled protein receptors: transmembrane proteins that transduce signals
in response to EC ligand binding and are associated with G-protein which
bind GDP in the inactive state and GTP in their active state
○ Ligand binding increase the proteins receptor’s afnity for G-proteins
○ 3 main kinds
■ Gq activates phospholipase C which cleave PIP2 off of the
membrane which cascades into IP3 that can open calcium
channels on the ER
■ Gs stimulates adenylate cyclase which increases cAMP
■ Gi inhibits adenylate cyclase which decrease cAMP

○
○ Binding of GTP, stimulated by the ligand binding the receptor, cause B
and gamma subunits to pop off at which point the G protein activates
and can stimulate adenylate cyclase. Once P is broken off gamma nd B

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can rebind.
Chp 3.3 Protein Isolation
● Electrophoresis: the generation of a current makes proteins travels across a
slightly porous polyacrylamide gel.
○ Different protein travel at different speeds stratifying them by mass
shape and charge
○ V = Ez/f
■ V is travel velocity, E is electric eld, z is molecular charge and f
is a friction coefcient which increase with size and mass
○ SDS-Page straties proteins on mass alone because it denatures the
protein so they all have the same shape and coats them in neg charge
● Isoelectric focusing: proteins are placed in a gel that has an acidic to basic pH
gradient with a negative cathode on the basic side and a positive anode on
the acidic side. The proteins will migrate until they are neutralized by the gel.
The pH where to proteins stop moving will be equal to the IP
● Chromatography: homogenized mixture are fractionated by interaction with
a stationary and mobile phase based on their afnity for each phase
○ Colum chromatography: a column is lled with silica or alumina beads
and the sample is placed on top. Solvent is poured through the column
and the sample straties by molecular size (and polarity). The solvents
pH, salinity or polarity can inuence which solutes elute faster for
example a nonpolar solvent will not elute a polar sample.
○ Ion exchange: in this case the beads are coated with a charged
substance so that oppositely charged molecules will elute slower.
Stuck molecules can be eluted with a graduating salt mobile phase
○ Size exclusion: these beads have little dimples that trap and slow down
small proteins so larger ones elute rst
○ Afnty: coating nickel beads in binding partners of specic molecules
can allow you to extract them from a sample into the stationary phase.
Later you can wash it with free binding partners to extract the protein
of interest
Chp 3.4 Protein analysis
● Protein structures can be determined by NMR or X-ray crystallography
● Edman degradation sequentially digest proteins from the N-termius and we
can tell what was cleaved off by mass spectroscopy.
○ This only works with peptides below a max of 70 aminos so larger

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molecules must rst be cut into sections using proteases

● Bradford Protein Assay can tell us the concentration of a solution: coomassie
brilliant dye changes from brown to blue as it gives up protons to aminos
which it binds in solution. Greater concentrations will produce bluer
solutions which can be measure against know concentraions

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Chapter 4: Carbohydrates
Chp 4.1 Classication
● Subunits are monosacarhies and end with -ose
● Monosaccharides have -OH attached to all carbons unless carbonyl is
present
○ Sugars with aldehydes are aldoses while sugars with ketones are
ketoses
● Aldoses can act as substituents by bonding via the aldehyde carbon
participating in glycosidic linkages
●

● Sugars are classied by D and L steriochemistry which is determined by the

direction of the hydroxyl on the highest number carbon.
○ Positioned with #1 carbon on top the highest number hydroxyl should
be facing the right for D sugars and on the left for L sugars
○ D and L sugars are always enantiomers
● Special types of diasteriomers are called epimers which have varying
absolute conguration at only 1 chiral center
Chp 4.2 Cyclic sugar molecules
● Aldoses and ketoses can undergo self addition rxns since they have a
nucleophile in the alcohol groups and an electrohile in the carbonyl groups
○ Rxns between these form oxygen containing rings
○ Only ve (furanose) or 6 (pyranose) member rings are stable
● Carbonyl carbon is made a chiral center in this process and referred to as the
anomeric carbon meaning there are two resulting sterochemically distinct
product due to the orientation of nucleophilic attack.
○ The beta anomer is formed if the C1 subtitent is equatorial up (cis to

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the highest order C)

○ The alpha anomer is formed if the C1 subtitent is axial down (trans to
the highest order C)
■ Less stable in solution so less prevalent
● Mutarotation: rings will spontaneously open allowing rotation of the C-1
carbon. They will close either as alpha or beta but alpha will reopen quicker
making it less prevent in solution by about 50%
Chp. 4.3 Monosacchrides Reactions
● Oxidation: since hemiacetals spend time in the open chain form they can be
oxidized into aldonic acids
○ The ring form of aldonic acids are lactones, a cyclic ester with a
maintained adjacent carbonyl
● Reducing sugar: since hemiacetals can be oxidized they are considered
reducing sugars. Ketoses also are reducing sugars since they can tautomerize
to create and alcohol bound to a double bonded carbon. It’s called an enol.
○ Reducing sugar detection
■ Tollens reagent: Ag2O is dissolve in ammonia to make
Ag(NH3)2^+. In the presence of aldehydes this will be reduced
making a mirror color
■ Benedicts reagent: Cu(OH)2 can also be used since it will
produce a red precipitate
● Reduced sugars: aldoses can be reduced to only containing a -OH and then
are called alditols which can be further reduced by removing the Hydroxyl
making a deoxy sugar.
● Esterication: ester formation using an alcohol and a carboxylic acid (or its
derivative). All present alcohols will be oxidized into esters.
○ This is a similar process as phosphorylation preformed by kinases
● Glycoside formation: an alcohol reacts with an anomeric alcohol to make a
ether. Both alpha and beta anomers will be produced.
○ This is a condensation rxn so breaking the bond is hydrolysis
Chp 4.4 Complex Carbohydrates
● Def: sugars containing more than one monosaccharide
● Disaccharides are formed through glycosidic bones between the anemeric
carbon and the hydroxyl of the 2, 4 or 6 carbon
○ Different combinations of anomers create different molecules
○

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● Polysaccharides are longer sugar chains

○ When made of only one type of monosaccharide they are called
homosaccharides, and when made of more than one they are
heteropolysaccharides
○ Branching occurs when more than 1 glycocidic bond is formed by a
single monosaccharide
● 3 main polysaccharides are all made of D-glucose
○ Cellulose: linear molecule with B,1-4 glycosidic bonds and is
strengthened by repetitive H-bonds
○ Starches: can be linear and called amylose (a 1,4 bonds) or branched
and called amylopectin(a 1,4 bonds with 4% a 1,6 bonds)
■ Amylopectin requires special enzymes to breakdown branched
structure
■ B-amalyse chops the straight chain into maltose molecules
specically at the non reducing end of the chain (the anameric
carbon which is bound to ether)
■ A-amalyse is much less specic and cleaves glycosidic bonds
randomly along the chain
○ Glycogen: like amylopectin but much higher 1,6 bond content at
around 10% decreasing the surface area of the molecule thus making it
more solualizable and better for storage
■ Glycogen phosphorylase: cleaves glycogen into glucose at
anameric end via phosphorylation in order to produce glucose
1-phosphate molecules

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Chapter 5: Lipids
Chp 5.1 Structural
● Membranes are made up of amphipathic lipids meaning they have both a
hydrophobic and hydrophilic region
● Phospholipds: have a polar head comprised of a phosphate and an alcohol
which is bound to one or more fatty acids through phosphodiester linkage
○ Saturated tails only have single bonds and form straight chains
■ This allows them to bemore compact giving way to the
prevalence of van der Waals forces increasing stability
■ Solid at room temperature
○ unSaturated tails have at least 1 double bonds and form Kinked chains
■ Make up more uid membrane regions
■ Liquid at room tempurature
● Glycerophospholipids: class of phospholipds which specically are
structured as a phosphate bound to a glycerol bound to two fatty acids using
ester bonds
○

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○ Important for cell recognition, signaling and binding

○ The head R group can be positive negative or neutral but must be
highly polary
● Shpingolipids: have a single fatty acid tail and a polar head group attached to
a sphingoid back bone

○
○ The simplest sphingolipid is a ceremide which simple has a Hydrogen
for its R group in the polar head
○ Sphinogolypids can either be glycolipids, meaning their polar head is
bound to the backbone through glycosidic linkages to sugars, or
phospholipids, meaning their polar head is bound to the backbone
through phosphodiester bonds to phosphates or phosphate derivatives
○ There are 3 major classes of sphingolipids
■ Sphingomyelins: phospholipids containing phosphocholine or
phosphoethanolamine as polar heads
● Produce myelin so they exist in ogliodendryctyes and
schwann cells
● Non net charge
■ Glycoshpingolipids: are glycolipids with not net charge
● Cerebrosides have one sugar where as globosides have
more than one
■ Gangliosides: are glycolipids with oligosaccharides with sialic
acid functional groups as polar heads
● Negatively charged
● Play major roles in cell interaction, recognition and signal
transduction
○

Chp 5.2 Signaling lipids

● Lipids serve as coenzymes for ETC

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● Terpenes: made up of 5 carbon isoprene units these are important

precursors of steroids and Terpenoids

○
○ A monoterpentene has 2 isoprenes
○ Triterpente is precursor for steroids including cholesterol
● Terpenoids: the major difference is that terpeniods are more
complex/modied and often have oxidized carbons
● Steroids: posses the basic structure of 3 6 membered rings and 1 ve member
ring sequentially bound
○ Many hormones like aldesterone, estrogen, cortisol, and testosterone
are steroids
○ Cholesterol is a steroid thats in the membrane regulating its uidity
■ Prevalent solidication at low temps and prevents collapse and
permeability at high temps
■ Important precursor for other steroid hormones, bile acids, and
vitamin D
● Prostaglandins: 20 carbon unsaturated carboxylic acid which contains a 5
member ring that is derived from arachidonic acid
○ They regulate the cAMP synthesis
○ Signaling molecule for both paracrine and autocrine functions
○ Effect sleep wake cycle, smooth muscle function, and body
temperature in regards to fever and pain
● Fat soluble vitamins: must be consumed in diet but cause body aint
producing them
○ K: quinone family which undergoes redox cycles during formation of
prothrombin, which is a precursor to the thrombin clotting factor. Also
introduce calcium binding sites on some calcium dependent molecules
○ A: also known as carotene, this is an unsaturated hydrocarbon which is
imperative for site in its aldehyde form retinal but also important in
growth and development when oxidized to retinoic acid, and is
important for immune function
○ D: convert to calcitrol by the kidney/liver which increases Ca and K
uptake and in turn results in bone production

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○ E: called tocopherols and tocotrienols are a characterized by aromatic

ring substituents that react with free radicals to prevent oxidative
damage
Chp 5.3 Storage
● Free fatty acids with carboylic acids yet to be esteried can circulated in the
blood when carried by serum albumin
● Triacylglycerols: are nonpolar/hydrophobic molecules consisting of 3
(normally different) fatty acids ester linked to a glycerol
○ They travel bidirectionally between the liver and adipose fat cell but
are primarily stored in the adipose
○ They serve as depot of energy to be used when fuel is low
○ Sopanocation of triacylglycerols make soaps
■ act as surfactant lowering surface tensions
■ Form micelles which emulsify fate soluble vitamins and complex
fats like lecithin helping our body absorb them
● Micelles are also how fatty acids and bile salts are
secreted by the gallbladder

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Chapter 6: DNA
Chp 6.1 Structure
● Nucleosides: Pentoses which are covalently linked to a nitrogenous base on
their C-1’
● Nucleotides: a nucleoside with one or more phosphate groups attached to
their C-5’ whose high energy is due to repulsion between the phosphates’
neagitive charges which are inclose proximity
● DNA’s monomer’s are deoxyriboses where are RNAs are riboses the diffence
being the substitution of an -OH for an -H on C-2’
● The sugar-phosphate backbone is consstructed out of 3’ carbons linked to an
oxygen off of the prior sugars 5’ phosphate group by phosphodiester bonds
○ Dna is read an written 5’ to 3’ which matter since it is a polar molecule
● Purines (A and G) contain two rings while pyrimidines (T, C, U) conatin one
○ Both are heterocylic aromatic structures meaing they are stablizied
through delocalized P orbitals and contain more than 1 type of atom
○ Huckels rule: in order to be aromatic a ring must have 4n+2 pi electron
● Watson-Crick model
○ DNA is double helix that runs anti parallel
○ Backone is on the exterior while the bases are within the helix
○ Complementary base pairing rules: A pairs with T (or U) and G pair
with C making 3 bonds as opposed to 2 so have stronger connect
■ Its is the H-bond and hydrophobic interactions between bases
which stabilize the double helix
○ Chargaffs rule: purines content = pyrimidine content
● B-DNA: as opposed to Z-DNA which is biologically inactive, B-DNA turns
every 3.4 nm (a span of about 5 bps) makes major and minor binding curves
● Denaturation: heat, alkaline pH and chemicals like formaldehyde and urea
separate DNA helixes which can be reannealed if the denaturant condition is
slowly removed
Chp 6.2 Chromosome Organization
● Nucleoprotein: proteins which bind DNA
○ Most are acid solluable transcription factors
○ Histones also are this kind of protein and exist in 5 major variants
■ H2A, H2B, H3, H4 which form an octomer and spool up 200 bps
into a nucleosoe
■ H1 binds DNA before and after nucleosome to seal it off

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● Heterochomatine vs Euchromatin
○ H: high nucleosome content making it remain compacted in
interphase. Has repetitive sequences and is transcriptionally inactive
○ E: lower nucleosome content making it disperse in interphase. is
transcriptionally active
● Telomere: TTAGGG sequence repeating at the end of the chromosomes. High
G-C content makes it able to prevent unraveling. Sequence is lost at the end
of replication from the lagging strand but telomerase can restore it. Over
time we loose teleomerase activity contributing to aging
● Centromere: located centrally in the chromosome it holds sister chromatids
together
Chp 6.3 Replication
● Origin of replication: specic sections of DNA where Replisome binds to
create replication bubble
● Replication Complex:
○ Helicase: unwinds DNA and cause DNA supercoiling in the process
○ ssDNA binding protein: bind to unraveled strand to stablizes fork
preventing degradation by nucleases or reassociation of bases
○ DNA topoisomers: introduce negative suercoils by working ahead of
the helicase, nicking strands, allowing relaxation of torsional pressure
then resealing nicked strands
○ DNA Ligase: seals gaps between okizaki fragments on lagging strand
■ Lack proofreading so lagging strand is more mutated
○ Primase: syntehsizes RNA primer for Polymerase to bind to
○ Polymerase: read template strand 3’ to 5’ and synthesize 5’ to 3’
■ Pol III (prokaryotes) and Pols alpha delta and epsilon
(eukaryotes) synthesize daughter strands
■ Pol I (pro) and RNaseH (eu) removes primer
■ Pol I (pro) and Pol delta (eu) synthesizes DNA where primer was
■ Pol gamma (eu) replicate mitochondrial DNA
■ Pol beta and delta (eu) are involved in DNA repair
○ Sliding clamp: trimeric structure of PCNA protein which strengthens
interactions between polymerase and the template strand
Chp 6.4 DNA repair
● DNA polymerase possesses proofreading function: incorrect base pair have
unstable H-bond which can be detected causing the bases to be excised and

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resynthesized
○ Polymerase can tell which strand has the correct base since the
template strand is older and thus more heavily methylated
● MSH2 and MLH1 are the genes responsible for mismatch repair
● Nucleotide excision Repair: useful when UV light causes thymine dimers. The
dimer bulge is detected by proteins which recruits decision endonuclease to
nick either side of the dimer which is removed and replace subsequently by
DNA polymerase at which point ligase seals new fragment to the old strand
● Base excision repair: useful when cytosine deamination ( loss of cytosine and
replacement by uracil) results from too much thermal energy. Glycosylase
removes base leaving behind AP or abasic site that is recognized by AP
endonuclease the removes the damaged sequence. DNA polymerase
resynthesizes the sequence at which point ligase seals new the fragment to
the old strand
6.5 Biotechnology
● Restricition enzymes: recognize palindromic sequences and make ds cuts
○ Many cuts are offset resulting in sticky ends which help when trying to
create recombinant DNA
○ Were derived from bacteria which used them to degrade viral DNA
● DNA cloning: process to isolate and amplify a specic DNA sequence from a
heterogenous mixture
● Genomic library: possess large fragments of the entire genome (coding and
non coding regions) by way of DNA cloning
○ Contains all genetic material but randomly fragmented
● cDNA library: produced from reverse transcriptase action of the
metaproteome
○ Only contains expressed gene
● Southern Blot: the results of a gel electrophoresis are transferred onto a
membrane at which point a probe is introduced which hybridizes to detec
the presence or absence of a particular gene
● Gene therapy: a gene can be packaged in to a virus which will infect someone
with a defective gene and incorporate the health vector into the geneome to
restore WT function
● Transgenic/KO lines: clone gene is injected into gametes and is
incorporated into DNA

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Chapter 7: RNA and Genetic code

Chp 7.1 Genetic code
● Messenger RNA: only RNA to carry info specifying amino acid sequence of
proteome
○ Transcribed and post transcriptionally modied in the nucleus
○ Eukaryotic mRNA is monocistronic meaning it only encodes 1 protein
while prokaryotic mRNA is polycistronic because starting translation
at different points can yield different, active proteins
● Transfer RNA: binds amino acids to attach them to to peptides
○ Aminoacyl-trna synthase breaks two high energy phosphate bonds to
make a high energy bond betwixt the amino and the tRNA CCA binding
sequence
○ The high energy of this bond is used to attach the amino to the
peptide during translation
○ Mature tRNAs exist in the cytoplasm
○ The anticodon is reverse and complementary to the codon
● Ribosomal RNA: makes up part of the ribosome and has enzymatic activity to
catalyze peptide bonds
○ Formed in the nucleolus and important in its own splicing
● Codons: 64 possible codons provide unambiguous nucleotide to amino code
○ Degenerate: meaning every amino but met and trp have multiple
codons
○ 3 position wobble: many codons that code the same protein vary only
at the third position
Chp 7.2 Transcription:
● RNA polymerase I: locates in the nucleolus and synthesizes 28s 18s and 8s
rRNA in a single transcript
● RNA polymerase II: located in the nucleus and synthesizes hnRNA
(preprocessed mRNA) and some small RNAs
● RNA polymerase III: located in the nucleus and synthesizes tRNA and 5s Rrna
● All RNA polymerases synthesize from the template strand in the 3’ to 5’
direction
● TATA box: located about 25 bases upstream from transcription start cite this
region is the location of polymerase binding
○ This binding is aided by transcription factors
● Post Transcriptional modication: must occur to make mRNA ready to leave

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nucleus
○ 5’ cap: occurs during transcription process, 7-methylguanylate
triphosphate cap is added to 5’ end to protect against degradation
once in cytoplasm
○ Splicing: snRNA is coupled with snRNPs to make a spliceosome.
■ Removes introns by excising them into lasso shape called lariat
■ Recognizes 5’ and 3’ intron ends to make cuts
■ Alternative splicing can cut out certain exons to make a wider
array of proteins from limited hnRNAs
○ Poly a tail: acts as a fuse of addenisines that begins degrading the
moment it exits the nucleus meaning that once the tail is gone the
protein wont be produced
7.3 Translation
● Occurs in the cytoplasm and after transcription (as transcription is
happening for prokaryotes) and mRNA has exited nuclear pore
● Ribosomal structure:
○ 40s (30 for pro) Small subunit is the 5s and 18s bits
○ 60s (50 for pro) large subunit is the 5.8s and 28s subunit
○ Has A, P and E binding sites
● Initiation:
○ Small subunit binds rst (shine dalgarno region in prokaryotes, 5’ cap
in eukaryotes)
○ Initiator tRNA binds AUG start codon at P binding site
○ Initiation factors help large subunit to connect with small
● Elongation:
○ Ribosome move 5’ to 3’ direction synthesizing from n to c terminus
○ A site accepts next up t-RNA
○ p site hold tRNA with the amino which is about to be added to the
chain. Peptidyl transferase which is contained in the large subunits
catalyzes this transfer
○ The now inactive tRNA pauses at the E site before exiting the ribosome
○ Elongation factors assist by recruiting tRNAs GTP as well as remove
GDP once its been used
○ If the protein is to be secreted the ribosome moves to the ER where it
can synthesize directly into the ER
● Termination:

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○ Once the stop codon moves into the A site release factor is recruits
and binds to the termination codon add H2O to the chain end
○ Peptyl transferase a termination factors hydrolyze the completed
polypeptide chain from the nal tRNA
Chp 7.4 Prokaryotic Gene Expression control
● The most common for of gene expression control in prokaryotes is the
operon which can be both inducible or repressible
● Jacob-Monod model: basic model to describe structure/function of operon
○ They contain structural gene (expressed gene) down stream of
operator site both of which are downstream of the promoter site
○ Upstream in the genome is the regulator gene that can bind the
operator site
● Inducible system: the repressor is expressed under normal conditions
blocking the expression of the gene of interest. However if the repressor is
removed the promoter has the ability to start transcription
○ Lac operon is a basic example where lactase is produced under high
lactose low glucose level. Low glucose stimulates the binding of CAP to
cAMP. This induces a conformational change that allows CAP to act as
a tf for the promoter. Lactose will bind the repressor gene product
removing it from operator site and lactase will be transcribed
● Repressible system: in this system the gene of interest is normally
exppressed but under certain circumstances (normally a negative feedback
situation in which gene of interest acts a corespressor) the respressor will be
able to bind the opporator site
○ Common example is the trp operon. The respressor is always
expressed but when trp is at high levels it will bind the respressor as a
corepressor. Together they bind the opperator and tamp down
expression.
Chp 7.5 Eukaryotic Gene Expression control
● Heterochromatin vs Euchromatin: inactive vs active but can be remodeled
● Methylation: DNA methylases will attach methyls to A and C which hinder
transcriptional machinery access (more methylation in heterochromatin)
● Acetylation: acetyl groups on histone tale decrease positive charge of histone
making the dna more loosely bound allowing for txn or remodeling
○ Deactylase do the opposite and silence genes
● Transcription factors: search DNA for particular binding motifs

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○ Activation domain recruit RNA polymerase and acetylases to aid in

heterochromatin remodeling
○ DNA-binding domains exist in promoter regions and binding
encourages Txn machinery recruitment
● Enhancers: generally far upstream of promoter regions but help amplify a
product
○ Often loop around to get closer in space to gene of interest. Several
response elements for tf binding may exist near each other in
enhancers which allow multiple cell inputs to produce the same
product thus increasing its yeild
● Gene duplication: another form of amplication can exist where multiple
copies of a gene a produced in series or parallel by DNA polymerase

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Chapter 8: Biological membranes

Chp 8.1 uid mosacic model
● The cell membrane is a semipermiable phsopholipid bilayer
● It is lled with various lipids proteina and carbs w/ varying degrees of udity
● Lipid rafts are distinct clusters of specic lipid and proteins and are often
sights for sognaling and other biomolecule attachments
● Carbohydrates are bound to the mebrane and are hydrophillic so create a
water based glycoprotein coat
● While the topology of mebranes are generally maintain leafs of the
membrane can be ipped by the enzymatic function of ipases
Chp 8.2 Membrane compentents
● Fatty acids: unsatuarated increase uidit whil satuarted fats decrease it
○ Some fatty acids like linoleic and alpha linoleic acid are essential
meaning they must be in our diets and transported to our cells as
tryacylglycerols in chylomicrons while some our bodies produce
● Cholesertol: stabilize adjacent phospholipids which can make our
membranes stiffer in high heat but also exist between phospholipid breaking
up any crystal structure which would form therefor is nessecary for
membrane uidity
○ By mass = 20% by molarity = 50%
● Waxes: composed of long chain fatty acid bound to long chain alcohol these
molecules very rare in animals but more common in plants
○ Provide stability and rigidity and even have extracellular functions like
water proong
● Carbohydrates: generally hydrophillic for form coat round cells and also act
as signalling and recognition molecules. For instance, abo antigens are the
carbohydrate components of sphingolipids.
● Membrane proteins: either embedded, peripheral (associated through
electrostatic interactions), or transmembrane. Protein serve roles in
attachment, signaling and membrane transport
○ Membrane receptors: tend to be transmembrane proteins
○ CAM also tend to be transmembrane proteins
● Cell-Cell junctions: comprised of CAMs which allow cells to recognize, bind
and differentiation from each other
○ Gap junctions: composed of 6 molecule ring made out of connexin
proteins. These junctions permit movement of water and some solutes

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directly from cell to cell

○ Tight junctions: completely surround cells to prevent solutes from
leaking into intercellular gaps
○ Desmosomes: direct cells attachment site from cytoskeleton of one
cell to another by transmembrane proteins linking intermediate
laments
■ Often found at borders of two epithelial identities
■ Hemidesmosoes are similar but create epithelial cell to ECM
binding like at the basement membrane
Chp 8.3 Membrane transport
● Passive transport: spontaneous process in which something ows from a
high to low concentration
○ Simple diffusion substrates which can pass through membrane move
across it to create net ow down a concentration gradient
○ Osmosis: simple diffusion of water to generate isotonic conditions
■ Osmotic pressure is a sucking pressure which equal =iMRT
■ Hypotonic condition is when solute concentration is higher
within the cell so water rushes in
■ Hypertonic condition is when solute concentration is lower
within the cell so water rushes out
○ Facilitated diffusion: transmembrane proteins enable the movement or
large, polar or charged molecules to move down their concentration
gradient
■ Carrier proteins are transporters that are open to only one side
of the membrane. Oben binding they induced conrmational
chanin to the occulded stated before the open up on the other
side of the membrane releasing their binding protein
■ Channel: can be open or closed an let particle ow through
● Active transport: expend energy to move solute up it concentration gradient
○ Primary: the use of energy molecules like atp pushes something up the
gradient
○ Secondary transport two molecules at a time moving one up the
concentration gradient using the energy generated by moving the
other down
■ Movement in the same direction is symport while opposite
directions is antiport

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● Endocytosis (pino for lq and phago for large solids) and endo cytocsis utilize
vescicels to take thing into and out of cells
Chp 8.4 Special membranes
● Some cells like neuron must maitian membrane poteintials

○
○

● Sodium-Potssium pump: maintains low Na and high K intracellularly which is

hard since leak channels allow movent to eq but do so by puming 3 Na out for
every 2 K in utilizing Na/K ATPase
● Mitochondrial membranes:
○ Outer has larger pores allowing for passage of ions and smallproteins
into the intermitochondrial membrane space
○ Inner has many infolds called cristae to maximize surface area for ETC
and much more restricted permeability to prevent contents leaking

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Chapter 9: Carbohydrate metabolism 1

Chp 9.1 Glucose transport
● Dirven based on concentration independent to other solute concentration
which is unlike in the gut
● Normal blood glucose range is 4-6 mM
● 4 GLUT transporters but only 2 and 4 are highly regulated
● GLUT 2: is high afnity (Km =15mM) transporter in hepatocytes (liver) and
Pancreatic cells
○ Capture glucose primarily for storage
○ Once blood glucose drops below 15mM glucose by passes liver and no
more is taken up for storage and rest enter peripheral circulation
○ B-islet cells of pancreas secrete insulin based in part on GLUT2 sensor
capabilities
● GLUT4: has afnity of 5mM=Km so maintains blood glucose average and
exists in adipose and muscles
○ Muscles store excess glucose as glycogen while fat cells convert it to
glycerol phosphate for triacylglycerol production
○ Rate of inux per transporter is constant so the regulation of uptake is
control by exocytotic vesicles inputting more GLUT4 to the plasma
membrane which is stimulated by insulin
Chp 9.2 Glycolysis
● Fermentation: oxidation of NADH to NAD+ allows from energy production
during anaerobic conditions
○ Pyruvate is reduced to lactate and the oxidation of NADH means that
glycolysis can continue to occur even if the critic acid cyclic is non
functional and cant consume the waste
● Low energy yielding conversion of glucose to pyruvate
● Only energy producing pathway for mitochondrial lacking cells like
erythrocytes
● The ve most important enzymes (because they serve energetic function) are
highlighted below
○ 3 of these enzymes are irreversible so that pathway moves in 1
direction
■ Hexokinase/glucokinase
■ Pyruvate kinase
■ PFK-1

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●
○ Hexokinase: phosphorylating glucose prevents it from traveling
backwards through GLUT transporters
■ Glucokinase is used in liver and pancreatic B-islet cells instead
and there are a few differences
● The Km for glucokinase is high so activity is proportional
to glucose present where as for hexokinase its max
velocity is reach at a lower concentration
● Glucokinase acts as an insulin signaler
● Glucokinase is inhibited by insulin where as hexokinase is
inhibited by glucose 6 phosphate
○ Phosphofructokinases: are the enzymes which catalyze the rate
limiting step of adding a second phosphate group to glucose
■ PFK1 is inhibited by ATP and citrate but activated by AMP and
F2,6B-P meaning when energy molecules are high its activity is
turned off but when they are low concentrated it will be on
■ PFK2 makes F2-6B-P and is activated by insulin and inhibited by
glucagon meaning that when energy molecules are sufcient

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but glucose in the blood is high the ATP inhibition of PFK1 can
be overridden to activated glycolysis for storage purposes
○ G3P dehydrogenase: oxidizes substrate adding inorganic phosphate
(Pi) and in turn reduces NAD+ to NADH
○ 3-Phosphoglycerate kinase: transfers Pi from high energy 1,3
bisphosphoglycerate to ADP producing 2 ATP for every 1 glucose
○ Pyruvate kinase: transfers Pi from high energy PEP to ADP producing 2
ATP for every 1 glucose
■ Participates in feed forward activation since F1,6B-P stimulates
its function
● Fructose 1-6 bisphospate is taken out of the glycolysis pathway into hepatic
and adipose tissues to be converted to glycerol with the help of DHAP
● Red blood cells possess bisphosphoglycerate mutase which convert 1,3-BPG
to 2,3-BPG. 2,3BPG is an allosteric binder of hemoglobin A decreasing oxygen
afnity. This allows for oxygen unloading to the rest of the body which does
not have bisphosphoglycerate mutase as well as maternal to fetal blood since
fetal hemoglobin does not bind 2,3BPG

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Chp 9.3 other monosaccharides

● Galactose metabolism
○ Ingested lactose is hydrolyzed into glucose and galactose by lactase
○ Galactose is transported to cells and upon entry is phosphorylated by
galactokinase preventing exit
○ Galactose-1-phosphate uridyltransferase then can convert galactose 1-
p into Glucose 1-P
■ This enzyme is an epimerase meaning that galactose and
glucose are epimers
● Frucotose metabolism:
○ Fructose comes from sucrose which is metabolized into fructose and
glucose by fructase
○ The liver uses fructokinase to phosphorylate and trap fructose in the
cell
○ Aldolase B cleaves fructose 1-P into DHAP and glyceraldehyde
Chp 9.4 Pyruvate Dehydrogenase:
● Complex of enzymes which carry out reactions in rapid succession
● Are responsible for irreversible rxn which converts pyruvate to acetyl CoA
● NADH and CO2 are byproducts
● Requires lipoic acid, NAD+, CoA, FAD, thiamine pyrophosphate
● Activated by insulin (but only in the liver)
● It is inhibited by acetyl CoA so build up causes a shift in pyruvate fate from
TCA to fatty acid synthesis
● Also responsible for active transport into mitochondria since located in
mitochondrial matrix
Chp 9.5 Glycogen
● The branched storage molecule of glucose
○ Stored in liver for maintenance of blood sugar and stored in muscles as
reserves for contractions
○ Stored in granule bound to a protein called glycogenin which exists a
central binding point
■ Glycogen with more linear bonds has greater density near the
core while branched bonds create mor periphery density so that
glucose can be released more rapidly

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●
● Glycogenesis: synthesis of granules
○ Glucose Activation: Glucose molecules are converted from glucose 6-
phosphate to glucose 1-Phosphate. This then interacts with uridine
triphosphate resulting in pyrophosphate by product and activated
UDP-Glucose.
○ Rate limiting step: Glycogen synthase makes straight chain a,1-4
glycosidic bonds
■ Stimulated by insulin and 6-phosphate and inhibited by
epinephrine and glucagon which activate protein cascades the
phosphorylate the enzyme
○ Branching enzyme: responsible for a,1-6 linkages
■ First hydrolyzes 1-4 bond of carbon and moves ogliosaccharide
to new location closer to core
■ Forms new 1-6 bond creating branch
● Glycogenolysis: break down of granules
○ Rate limiting step: Glycogen phosphorylase breaks straight chain a,1-4
glycosidic bonds
■ In the liver its Stimulated by glucagon, in the muscles its
stimulated by epinephrine ans AMP and everywhere its

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inhibited by ATP
○ debranching enzyme: responsible for breaking a,1-6 linkages
■ First hydrolyzes 1-4 bond of carbon adjacent to the carbon
forming the branch point
■ moves ogliosaccharide to new location at the end of the nearest
straight chain
■ Finally cleaves the 1-6 bond creating a single free glucose
Chp 9.6 Gluconeogenesis
● Pathways are activated by glucagon and epinephrin to raise blood glucose
levels and are inhibited by insulin to lower levels
● Liver is biggest player in gluconeogenesis but costs lots of energy
● Fat cells release fatty acids to provide supplies and energy for hepatic
gluconeogenesis
● Lactate (from anaerobic glycolysis), Glucogenic amino acids which are all but
luecine and lysine (from muscle protein) and glycerol 3-phospate/fatty acids
(from adipose tissue) can be enzymatically converted back to a glycolysis
intermediate and then can be pushed up the pathway
○ Lactate is converted to pyruvate by lactate dehydrogenase
○ Alanine is converted to pyruvate by alanine aminotransferase
■ Although many aminos contribute to gluconeogenesis, alanine is
the most common and the other aminos have the own enzymes
○ G3P is converted to DHAP by glycerol-3-phosphate dehydrogenase
● Ketone bodies: ketogenic amino acids and acetyl-CoA can be converted into
ketone bodies. While these cant partake in gluconeogenesis they are
effectual in starving conditions at providing a fuel source
●
● Glucose 6 phosphatase:
○ Found in the lumen of the ER of liver cells
○ Oppose hexokinase/glucokinase by reverting Glucose 6P to glucose
● Fructose 1,6-bisphosphatase:
○ Rate limiting step of gluconeogenesis
○ Enzyme found in cytoplasm
○ Activated by high ATP and inhibited by high AMP or fructose 2,6-
bisphosphate
■ Fructose 2,6-bisphosphate (produced by PFK-2) is a regulator of
glycolysis/gluconeogenesis balance since PFK-2 is activated by

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insulin and supressed by glucagon, its product is a marker for

available energy supply
○ Oppose phosphofructokinase-1 by reverting glucose 1,6p to glucose 6p
● Phosphoenolpyruvate Carboxykinase (PEPCK):
○ Present in cell cytoplasm
○ Changes OAA to PEP with energy supplied by GTP
○ Induced by glucagon and cortisol which act to raise blood sugar
● Pyruvate Carboxylase:
○ Changes pyruvate to OAA using energy from burning fatty acids
○ Activated by acetyl-CoA
Chp 9.7 Pentose phosphate pathway:
● Produces ribose 5-phosphate and NADPH
○ Ribose 5-phosphate is precursor for amino acids
○ NADPH (distinct form the oxidizing agent NAD+) is a potent reducing
agent which is important for:
■ Biosynthesis of fatty acids and cholesterol
■ Cellular bleach production for bactericidal activity
■ And production of glutathione which is an antioxidant
●
○ In the rst step the rate limiting enzyme G6PD regulates the
conversion of glucose 6-P to Ribulose 5-P while producing NADPH as a
byproduct
■ G6PD activity is induced by insulin so that the incoming sugar
can be shunted toward storage but inhibited by NADPH
○ In the second step the conversion of ribulose to ribose (and other
sugars) is reversible
■ These sugars can be converted to gylcolitic intermediates (and
vis versa) using the enzymes transaldolase and transketolase

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Chapter 10: carb metabolism II: aerobic

respiration
Chp 10.1 Acetyl CoA Production:
● Pyruvate Dehydrogenase reaction

●
○ Acetyl CoA is an acetyl group participating in a thiol ester
● First 3 Steps of Pyruvate Dehydrogenase Complex Function to Convert
Pyruvate to Acetyl CoA

○ Pyruvate Dehydrogenase: Utilizes thiamine pyrophosphate to hold the

2 carbon acetyl group after CO2 is cleaved off of pyruvate. Also
requires Mg^2+
○ Dihydrolipoyl Transacetylase: 2 carbon molecule is oxidized by lipoic
acid’s disulde group causing the 2 carbon molecule to be transfered
to the liopic acid. Then Dihydrolipoyl Transacetylase catalyzes CoA-SH
to steal acetyl group from lipoic acid forming the thioester linkage
while reducing lipoic acid

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○ Dihydrolipoyl Dehydrogenase: FAD reoxidizes lipoic acid and NAD+

steals the protons from the reduced FADH2
● Fatty Acid Oxidation Can Contribute to Acetyl-CoA Production

○ FA activation: occurs in the cytosol and sees FA bind Acetyl CoA via
thioester bond. Then transesterication transfers FA to carnetine
allowing FA to cross the membrane
○ Once in the matrix FA carnitine undergoes a second transesterication
reproducing FA-CoA which can be converted into Acetyl CoA
● Alcohol Conversion: Alcohol dehydrogenase and acetaldehyde
dehydrogenase can convert alcohol to acetyl CoA however it cause NAPDH
build up inhibiting the Krebs Cycle
● Amino Acid catabolism: Ketogenic amino acids can lose there amino group
via transamination at which point their carbon backbones become ketone
bodies which can be converted to Acetyl CoA through reverse ketogenesis

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Chp 10.2 citric acid cycle

● The citric acid cycle is a reaction which takes place in the mitochondrial
matrix under aerobic conditions and produce the majority of electron
carriers to be used in the ETC from energy production while spitting out
CO2 as a byproduct
● From 1 pyruvate molecule PDH and the TCA will yield 12.5 ATP
○ 1 from GTP
○ 1 NADH from PDH and 3 NADH from TCA which each make 2.5 ATP
○ 1 FADH2 which yields 1.5 ATP
● TCA is a complex 8 step cycle depicted below
●
1. Citrate formation:
a. acetyl-CoA and oxaloacetate undergo condensation to make citryl CoA
intermediate
b. Hydrolysis of Citryl-CoA catalyzed by citrate synthase produces
citrate and CoA-SH
i. Synthases catalyze exergonic rxns so the nature of this steps
encourages the cycle to not reverse
2. Citrate isomerized to Isocitrate:
a. Citrate binds aconitase enzyme (which requires FE^2+) at all three
COO-
b. Water is lost from citrate yielding cis-aconitase
c. Water is added back to form one of four possible isocitrates
3. Alpha ketoglutarate and CO2 formation:
a. Isocitrate is oxidize to oxalosuccinate by isocitrate dehydrogenase
reducing rst of 3 NAD+ to NADH in the process
i. This oxidation is the rate limiting step of TCA
b. Oxalosuccinate is decarboxylated to produce Alpha ketoglutarate/CO2
4. Succinyl-CoA and CO2 formation:
a. Alpha ketoglutarate dehydrogenase complex reduces NAD+ to NADH
and reacts Alpha ketoglutarate with CoA-SH to form CO2 and
Succinyl-CoA

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i. Requires TPP, lipoic acid and Mg^2+ (similar to PDH)

5. Succinate Formation:
a. The thioester bond of Succinyl-CoA is hydroylized producing CoA-SH
and succinyl as the coupled rxn of GDP to GTP occurs
i. Succinyl-CoA synthetase is the enzyme responsible so as with
all synthetases (unlike synthases) the rxn is endergonic
b. GTP then transfers phosphate to ADP yielding ATP through the
enzymatic function of nucleosidediphosphate kinase
6. Fumarate Formation:
a. Succinate is oxidized to fumarate as FAD is reduced to FADH2 reliant
of the catalytic function of succinate dehydrogenase
i. This part of the cycle takes place in the inner membrane
7. Malate Formation:
a. Fumarase catalyzes hydrolysis of alkene bond in fumarate making
malate
8. Oxaloacetate Reformation:
a. Malate dehydrogenase oxidizes malte into OAA while reducing NAD+
to NADH
● PDH Regulation
○ PDH must be functioning to provide TCA with Acetyl-CoA to initiate
the cycle so inhibition of PDH inhibits the cycle
○ Pyruvate dehydrogenase kinase Phosphorylates thus inactivating PDH
○ PDH phosphatase does the reverse
○ ATP and NADH are markers of energetic satisfaction so inhibit PDH
■ ATP/NADH as a whole suppress the TCA and ADP/NAD+ as a
whole stimulate the TCA
● TCA Control Points
○ Citrate synthase: inhibited by its products citrate and succinyl CoA
and energy products
○ Isocitrate dehydrogenase: inhibited by energy products activated by
ADP and NAD+
○ Alpha ketoglutarate dehydrogenase complex: inhibited by energy
products and succinyl CoA and activated by calcium and NAD+
Chp 10.3 Electron Transport Chain
● Final pathway which utilizes all electrons harvested from fuels to generate
proton gradient which in turn will create ATP

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● The general idea is that electron carrier like NADH and FADH2 will transfer
their electrons to proteins located along the inner mitochondrial membrane
that will eventually pass of the electrons to oxygen. All the while the energy
released from the electron transfers pumps protons into the inter membrane
space
● The pathway is exegoneric which makes sense since it power endergonic ATP
formation

● C.1 (NADH-CoQ oxioreductase): NADH + H+ + CoQ → CoQH2 + NAD+

○ Responsible for transfer of electrons from NADH to coenzyme Q
(ubiquinone)
○ The avoprotein contains FMN which oxidizes NADH so it becomes
NAD+ while FMN becomes FMNH2
○ In a different subunit iron-sulfer clusters serve of the oxidizing agents
for FMNH2 to reform FMN. the iron transfers the electrons it gained
onto CoQ reducing it to CoQH2
○ The complex pushes 4 electrons across the membrane
● C.2 (Succinate-CoQ reductase): CoQ + Succinate + 2H+ → Fumarate
+ CoQH2
○ Same mechanism as complex 1 but succinate replaces NADH, FAD
replaces FMN and no electrons are pumped
● C.3 (CoQH2-cytochrome c oxioreductase)
○ Transfers electrons from CoQH2 to cytochrome c by reducing
cytochrome’s hemegroup from Fe3+ to Fe2+
○ One electron is transfer per reaction so 1 eq of CoQH2 must react with
2 eq of cytochrome C
○ Q cycle:
■
■ 2 electrons are shuttled from ubiquinol (The CoQH2 near the

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intermembrane space) to ubiquinone (the CoQ near the matrix)

■ At the same time 2 H’s are pumped through and 2 other
electrons reduce Cytochrome C
■ Cycle happens twice once fro the complex 1 CoQH2 and once
for the Complex 2 CoQH2
■ In total 4 cytochrome c’s are reduced and 4 protons are pushed
through
● C.4 (cytochrome C oxidase): 4 Cytochrome (red.) + O2 + 4 H+ → 2
H2O + 4 Cytochrome (ox.)
○ Transfers electrons from cytochrome C to the nal electron accepter,
oxygen to produce water
○ Includes cytochrome oxidase and Cu 2+ ions
○ 2 protons are pushed up the membrane
● NADH Shuttles: NADH from glycolysis cannot cross into mito matrix so
alternate means of transport called shuttle mechanisms are taken:
○ Glycerol 3-phosphate shuttle: reliant on glycerol-3 phosphate
dehydrogenase, NADH is oxidized while FAD is reduced. FADH2
proceeds into the ETC yield only 1.5 ATP
○ Malate-Aspartate Shuttle: malate dehydrogenase is utilized to reduce
OAA to malate while Oxidizing NADH to NAD+. Then maltate crosses
the inner membrane and undergoes the reverse reaction once inside.
Mitochondrial NADH can then interact with complex 1 to yield 2.5 ATP
Chp 10.4 Oxidative Phosphorylation
● pH in the inner membrane is low since [H+] is high creating electrochemical
gradient the is the source of proton motive force
● ATP Synthase subunits:
○ F0 is a transmembrane ion channel that allows ow of protons down
electrochemical gradient
○ F1 is with the matrix and has three spinning subunits which cause
condensation of ADP and Pi
● Dissipation of proton-motive force through F0 portion of ATP synthase
complex is associated with delta G knot = -220 kj/mol powering endergonic
ATP condensation through 1 of 2 possible mechanisms
○ Chemiosmotic coupling: energy transfer is direct (more accepted
theory)
○ Conrmational coupling: energy from proton-motive force dissipation

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creates F1 conrmational change which causes ATP condensation

● Respiratory control: Low oxygen leads to NADH build up inhibiting TCA
● Under aerobic conditions high ADP increase ETC while high ATP decrease

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Chapter 11: Lipid and Amino Acid metabolism

Chp 11.1 LIPID DIGESTION AND ABSORBTION
● First ingested fats are emulsied in the duodenum making them water
soluble increasing their surface area and in turn their rate of enzymatic
breakdown
● Pancreatic lipase, colipase, and cholesterol esterase hydrolyze lipids into free
fatty acids, 2-monoacylglycerol groups and cholesterol
● Digested lipids form micelles which are vital to digestion transport and
absorption
○ Diffusion of micelles to the brush border of the intestinal mucosal cells
allows for absorption
● In the mucosa, lipids are re-esteried into triacylglycerols and cholesteryl
esters and then they are packaged along with apoproteins, KADE vitamins,
and other lipids into chylomicrons which enter the blood stream by way of
the lymphatic system
Chp 11.2 Lipid mobilization
● Lipoprotein lipase breaks down chylomicrons and VLDLs
● Within fat tissue Hormone sensitive lipase breaks down triacylglycerols for
export as glycerol and fatty acids
○ HSL is stimulated by low insulin, high epinephrine and cortisol
Chp 11.3 Lipid Transport molecules
● Albumin binds free fatty acids to transport them through the blood stream
● Apoproteins: Associate with lipids and a receptor molecules involved in
signaling
● Lipoproteins: aggregates of apoproteins and lipids that are the structures in
which triacylglycerols and cholesterol are transported in. Classied on their
density (higher fat to protein ratio equals lower density – listed below in
order of increasing density)
○ Chylomicrons: highly soluble and are responsible for transport of
dietary triacylglycerols, cholesterol and cholesteryl esters. Assembled
in intestine
○ VLDL: Same metabolism chylomicrons but use endogenous
triacylglycerols and are assembled in the liver
○ IDL: transition particle between VLDL and LDL, VLDL loses
triacylglycerol to be IDL and IDL gains cholesterol to be LDL
○ LDL: carry the majority of cholesterol in the blood and deliver

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cholesterol to cells for biosynthetic purposes

○ HDL: synthesized in both the liver and intestines, they are protein
dense containing apoproteins which specically are used for
cholesterol clean up from excess in blood vessels. Donatatte
cholesterol to IDL causing conversion to LDL
Chp 11.4 Cholesterol Metabolism:
● Most cholesterol is ingested and delivered to cells via LDL or HDL
● De novo Cholesterol synthesis

○
○ Driven by ATP
● Lecithin-Cholesterol Acyl Transferase (LCAT) : found in blood stream and
activated by HDL apoproteins, this enzymes adds fatty acids to cholesterols
form water solluable cholesteryl ester
● Cholesteryl ester transfer protein (CETP) facilitates transfer of cholesteryl
esters to IDLs which then become LDLs

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Chp 11.5 Fatty acid metabolism

● Humans can only synthesize 1 fatty acid – palmitic acid (16:0)
● Unsaturated fatty acid double bond mutation:
○ Enoyl-CoA isomerase: converts a cis bond to a trans bond shifted one
carbon closer to the carbonyl
○ 2,4-dienoyl-CoA reductase: converts 2 conjugated double bonds to one
double bond in between where the conjugated double bonds were
●

● Following feeding acetyl-CoA builds up in the mitochondria as a byproduct of

the TCA so it must be moved to the cytoplasm for fatty acid synthesis
○ Citrate (acetyl-CoA) shuttle: accumulated acetyl CoA is converted to
citrate by binding OAA with the help of citrate synthase. Citrate can
diffuse across membrane at which point citrate lyase separates out the
acetyl CoA from the OAA. OAA returns to matrix to shuttle more
acetyl-CoA
■ Acetyl CoA is activated for fatty acid synthesis by acetyl
carboxylase in the rate limiting step of the process to make
malonyl-CoA
● This enzyme is promoted by insulin and citrate
○ Fatty acid synthesis: catalyzed by fatty acid synthase in a repetitive 5

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step process
■

■ Activation (A/B) - attachment of an acyl carrier protein activates

the growing chain and the malonyl respectively
■ Condensation ( C) - bond forms and CO2 is lost
■ Reduction (D) - a carbonyl is reduced to an alcohol
■ Dehydration (E) - water is lost replacing hydroxyl with double
bond
■ 2nd reduction (F) - double bond is reduced to form a saturated
fatty acid chain
● Fatty acid Oxidation
○ Most occurs in mitochondria
○ Reverse of synthesis
○ A oxidation : break down of branched fatty acids
○ W oxidation : occurs in ER produces carboxylic acid
● B-oxidation: after entry and activation has 4 repetitive steps breaking of an
Acetyl-CoA with each cycle
○ Occurs in mitochondria
○ Mitochondrial entry: long chain fatty acids require transport via
carnatine shuttle which is catalyzed by carnatine transferase 1 in the
rate limiting step of breakdown where as shorter chain can just diffuse
into the matrix
○ Activation: fatty-acycl-CoA synthetase activates fatty acid for
degradation by binding a CoA

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○ B-oxidation cycle

○
■ 1. Oxidation of fatty acid forms double bond
■ 2. Hydration of double bond forms hydroxyl
■ 3. Oxidation of hydroxyl group forms carbonyl
■ 4. Thiolysis rxn splits chain b keto acid into acetyl CoA and an
acyl Coa thats now 2 carbons shorter
● If chain is an odd number of carbons on the nal thyolosis
a 3 carbon acyl will be left behind. propionyl-CoA
carboxylase will convert it to a methylmalonyl-CoA which
then will be converted to succinyl-CoA (which can enter
the citric acid cycle) by methylmalonyl-CoA mutase
Chp 11.6 Ketone Bodies

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● Produced by liver at the same rate as metabolized by muscle/renal cortex in

times of fasting due to acetyl CoA build up

●
● Ketogenesis: occurs in mitochondria of the liver. HMG synthase converts
Acetyl-CoA to HMG-CoA then HMG-CoA lyase converts that to aceoacetate
(a ketone body) which can then be reduced into 3-hydroxybutyrate (Another
ketone body)
● Ketolysis: Thiophorase (also called succinyl-CoA acetoacetyl-CoAtransferase)
catalyzes oxidation of acetoacetate to acetoacetyl-CoA
● Under starving conditions glycolysis, glucose uptake and pyruvate
dehydrogenase are prevented in the brain and instead ketone bodies are
used as fuel. This switch is important because it spares proteins from being
catabolized
Chp 11.7 Protein catabolism
● Proteolysis of your food beings in stomach with pepsin, continues as it
passes pancreas with the secretion of trypsin, chymotrypsin and

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carboxypeptidase a and b, and is nished by intestinal brush border enzymes

dipeptidase and aminopeptidase
● End products of protein digestion are tri/dipeptides and aminos
● Aminos will normally be stored for future protein building but can be
catabolized for energy by removing the nitrogen and breaking down the
carbon skeleton
● Nitrogen is removed from proteins through transamination or deamination a
pushed into the urea cycle to remove it from your body

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Chapter 12: metabolism: bioenergetics/regulation

Chp 12.1 thermodynaics
● While whole organisms are considered open systems since they exchange
energy and matter with the environment rxns on subcellular levels are
considered closed
● Modied standard state conditions give us delta G knot prime which is used
to measure energy of biological reaction
○ Same as standard state but includes requirement for pH of 7
● In general delta G for reactions that create more product than reactants
(breaking bonds) tend to be negative while those that start with greater
number of reactants than products (forming bonds it positive)
Chp 12.2 ATP
● Fuels in our body are converted to energy molecules like ATP
○ Combustion of fats yield 9 kcal/g compared to other energy sources
like carbs, ketones and proteins which average around 4 kcal/ g. This
property is called being energy dense and it is the reason fats are used
for long term energy storage
● ATP is a mid level energy carrier (unlike cAMP which is high) with its
hydrolysis yielding about 30 kJ/mol. This is advantageous since ATP is often
coupled to make other rxns proceed. Whatever energy is not consumed by
the coupled rxn would be lost to heat leading to inefciency
● ATP cleavage is the transfer of a high energy phosphate to another molecule
○ This of activates/inactivates the target molecule
● Energy is carrier in the phosphate bonds that hold together 2 repulsive
negative atoms
Chp 12.3 Biological redox
● Electron Carries: high energy molecules which are ubiquitous in the cell and
can serve as electron donors and receptors in many important biological
processes
○ Most are solluable like NADH, FADH2, NADPH, ubiquinone,
cytochrome, glutathione
○ FMN is a membrane bound electron carrier while some proteins with
iron clusters can also act as electron carriers
● Flavoproteins: nucleic acid derivatives which contain riboavin a modied B2
vitamin
○ FMN and FAD are the most common

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○ Function as coenzymes in glutathione reduction, fatty acid oxidation

and decarboxylation of pyruvate.
Chp 12.4 Metabolic states
● Compounds are maintained at homeostatic levels as opposed to equilibrium
levels in the body which allows us to store potential energy in our bodies
● Regulation of the compounds vary depending on the state of our body:
● Postprandial state: the absorptive state that occurs after being well fed
○

○ Blood glucose levels rise and stimulate insulin release which targets
three major tissues: muscle liver and fat
○ Insulin promotes glycogen synthesis in the liver and muscle cells
○ After glycogen stores are lled the liver will start producing fatty acids
and triacylglycerols instead
○ Insulin promotes synthesis of triacylglycerols in adipose tissues
○ Insulin promotes synthesis of protein in muscles

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○ Insulin promotes glucose entry into muscles and fat

● Postabsorptive State: the short term fasting state

○

○ Counterregulatory hormones like glucagon, cortisol, epinephrine,

growth hormone and norepinephrine induce actions opposite to
insulin’s effects
○ Glucose is released into the blood from tissues like the liver
undergoing glycogen degradation which happens quickly
○ The liver also undergoes gluconeogenesis but that doesn’t reach its
max until 12 hours in
○ Stimulated by the decrease in insulin and increase in epinephrine
skeletal muscle releases aminos while fatty acids are released from
adipose tissue

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● Prolonged fasting state: aka starving

○ Sets in around 24+ hours without eating
○ Glucagon and epinephrine are highly upregulated
○ Gluconeogenesis becomes the predominant source of glucose for the
body
○ Lipolysis is used to creates ketone bodies which the brain uses for two
thirds of its energy (glucose from degradation of proteins and
remaining fatty acids as the rest)
○ Muscle tissues will use fatty acids for energy
Chp 12.5 hormone Regulation
● Major divisions in hormones are their solubility: water soluble proteins have
fast, sharp reactions often causing signal cascades while fat soluble proteins
enact slower, long range, longer lasting effects often through translational
regulation
● Insuline: water soluble peptide hormone secreted by islet of langerhan beta
cells that is triggered by increase of blood glucose
○ Regulates sugar uptake of fat, liver and muscle cells but does not
regulate glucose intake of nervous, kidney, mucosa, pancreatic, or red
blood cells
○ Insulin release is directly proportional to blood glucose level above
threshold of 100 mg/dl or 5.6mM
○ Insulin increaseS:
■ Glucose and triacylglycerol uptake by fat cells
■ Lipoprotein lipase activity which clears VLDL and chylomicrons
from the blood
■ Lipogenesis in adipose and liver
○ Insulin Decreases:
■ Lipolysis in fat cells
■ And ketogenesis in liver
● Glucagon: water soluble peptide hormone that is secreted by alpha islet of
langerhan cells in response to low blood glucose
○ Also stimulated by excess amino acids, especially the positively
charged aminos like arginine lysine and histidine
○ The hormone’s primary target is hepatocytes and not adipose tissues
so is not considered major fat mobilizing enzyme like insulin
○ enacts its effects through secondary messengers

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○ Increases liver glycogenolysis by inactivating glycogen synthase and

activating glycogen phosphorylase
○ Increases liver gluconeogenesis and ketogenesis as well
○ Decreases lipogenesis while increasing lipolysis in the liver by
activating hormone sensitive lipase
● Glucocorticoids: a secretion of the adrenal cortex which are a major part of
the ght or ight stress response
○ Cortisol: promotes mobilization of energy stores through increased
lipolysis and degradation/delivery of amino acids
■ First it inhibits glucose uptake in normal tissues while
increasing liver gluconeogenesis and output
■ Next it enhances activity of glucagon epinephrine and other
catecholamines
● Catecholamines: secreted by the adrenal medulla, the major proteins in this
class are epinephrine and norepinephrine
○ Promote glycogenolysis in the liver and muscles and lipolysis in fat
○ Increase the basal metabolic rate throughout the sympathetic nervous
system with the help of thyroid hormones
● Thyroid hormones: consist of T3 and T4 and primary function is increasing
metabolic rate
○ Activity is largely permissive meaning it kept more or less constant
○ T4 is T3 precursor and conversion is catalyzed by deionases which
remove 1 iodine
○ T4 has latency but eneacts longer lasting effects while t3 has more
rapid and short lived response
○ Together they accelerate cholesterol clearance from the blood and
increase glucose absorption in small intestine
Chp 12.6 Metabolic states in different tissues
● Liver: major roles are maintaining blood glucose and synthesizing ketones
○ In well fed state:
■ liver gets energy from oxidation of excess aminos
■ Glucose is extracted for glycogen storage and once stores are
lled glucose will go to fatty acid synthesis
○ In fasting state:
■ Liver release glucose
● Adipose tissue: metabolism is regulated primarily by insulin

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○ In fed state:
■ Insulin induces lipoprotein lipase which breaks down lipids in
blood for uptake by fat cells
■ Insulin also represses release of fatty acids from adipose cells
○ In fasted state:
■ Low insulin and high epinephrine activate hormone sensitive
lipase releasing fatty acids
● Skeletal muscle:
● When Resting-
○ In fed state: Oxidize excess glucose and amino acids for energy
○ In fasting state: Use fatty acids from blood stream
○ In prolonged fasting state: ketone bodies begin to be used
● When active-
○ Very short energy burst comes from creatine phosphate which can
directly convert ADP to ATP
○ Quick high intensity exercise uses anaerobic glycolysis
○ Moderate intensity, endurance exercise will start to use fatty acid
store for glycolysis once glycogen is consumed
● Brain: primary fuel is glucose but in prolonged fasting will use upto 66%
ketone bodies
○ When in hypoglycemic conditions (<70mg/dl) triggers release of
glucagon and epinephrine
● Cardiac muscle: prefer fatty acids always but under prolonged fasting will use
ketone bodies
Chp 12.7 whole body metabolism
● Calorimeters measure BMR based off of environmental heat exchange
● Blood levels of glucose, metabolic regulatory hormones, CO2, and oxygen can
all serve as indicators of metabolic function
● Respitory Quotient: measured in the practice of reperiometry as a readout
for metabolic rate
○ RQ=CO2 produced/O2 consumed
○ Normal rate is around .8 which lies between RQ for solely fatty acid
consumption of 0.7 ans solely carbohydrate consumption of 1.0
○ Exercise increases RQ since more energy is produced anaerobically
● Ghrelin: is a hunger hormone release in response to sensory signals of a meal
● Orexin: involved in alertness and the sleep wake cycle this increases hunger

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and is secreted in hypoglycemic conditions

● Leptin: causes fullness by inhibiting orexin
● BMI=mass (kg)/height(meters)^2
○ 18<normal<25, 25<over weight<30, 30<obese

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