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NAD+NADHAcetyl coAPyruvateFigure 2

Glucose (6 carbons)2 NAD+

2 ATP2 NADH4 ATP (net 2 ATP)2 Pyruvate (3 carbons)Figure 1

Acetyl CoA (2 carbon chain)6 carbon chainCO

2

CO2

5 carbon chain4 carbon chain4 carbon chainATP3 NADH & 2 FADH

2

Figure 3

carbon fatty acid +2 carbon chaincarbon fatty acid +2 carbon chainPDH, FADH

2

etyl CoAebsPetyl CoAcarbon fatty acid

..

Low Na+

Low soluteHigh Na+

High soluteIntracellular fluidExtracellular fluid

C ountertransport

Low Na+

High soluteHigh Na+

Low soluteIntracellular fluidExtracellular fluid

C otransport

0.5 Osm

hypertoniccell shrinksH

2O

0.3Osm

0.1 Osmhypotoniccell swells0.3 OsmH

2O

isotonic0.3 Osm

0.3Osm

Cl-

Ca2+

Na+

Na+

Na+

Na+

Na+

K+

K+

H+

H+

Amino acids

GlucoseHCO3

-

ATPATPATPADPADPADPFigure 4

E X A M 1: C h a pters 1 5

C H A P T E R 1

physiology h o w things w ork and function

B o dy O rga nization: several levels

M olecular can influence function of cell; class focus is proteins

Cellular m olecules form cellular units; different cells specialize into:1) m uscle

2) nerve

3) epithelial

4) connectivetissuecells

Tissue differentiated cells with similar properties co me together to for m tissue in four

classes:

1) m uscle aids in m o ve ment of material fro m one part of the body to another

2) nerve coordinate and control physiological function

3) epithelial for m lining and coverings

4) connectivetissue holds things together

Organs consists of several kinds of tissues; consists of subunits called functional unitsOr gan syste ms interaction of organs for an overall function

ho m eostasis hu man bo dy m aintains a relative constant internal environ ment (ex: body

te mperature; p H balance; ionic concentration)

ho m eostaticcontrol includes a range and set point

H o m eostatic M ec ha nis ms:

negative feedback requires a change in the environ ment to happen; end product of a

process inhibits an earlier step in the process regulating the a mount of product produced;

important in m aintaining ho meostasis; seen in reflex arcs

o reflex arc begins with a (1) stimulus, w hich is a change in the internal or external

environ ment; (2) a receptor detects the stimulus producing a signal that travels the (3)

afferent path way towards the (4) integrating center; the signal travels the (5) efferentpath way a way from the integrating center to the (6) effector w here a change in

activity produces the (7) response of the syste m

positive feedback requires a change in the environ ment to happen; end product of a

process that accelerates or keeps a process going (ex: contractions d uring birth; blood

clotting)

feedforward regulation anticipates a change; happens before a change (ex: going fro m a

hot building to cold outside, body begins shivering before body temperature drops;

s melling food or anticipating eating, m o uth salivates and stomach begins digestive

secretions)

adaptation change in gene frequency over time due to selection

accli matization change in physiology due to long-ter m environ mental issues (ex: low sea level

to high sea level has less oxygen)

critical period time during develop ment and m aturation w here acclimatization is per manent

no m atter w here you go (ex: children living in high sea level area have puffed out chest and stays

even w hen m o ve d to low sea level; adults acquire puffed out chest w hen living in high sea level

but goes away w he n m o ved to low sea level)

C H A P T E R 2

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C he mical B o n ds: fro m strongest to weakest

covalent shared electrons; che mical reactions m ake and break bon ds

o polar u nequal distribution of charge; hydrophilic (water soluble); lipophobic; cell

m e m brane restricts m o ve ment

o non-polar equal distribution of charge; lipophilic (lipid soluble); hydrophobic;

m o ves through cell m e m brane easilyionic attraction between cations and anions (ex: H C O 3

-; N a +; Cl-; Ca 2+)

hydrogen attraction bet ween partial charges of particles; important in determining

biological structure

V an der W a als i mportant w hen ato ms are very close together

a m p hipathicm olecule has a polar region at one end and larger non-polar region at the other

end; forms droplets or bilayer

Classes of Organic M o lecules:

Carbohydrates m a de of carbon, hydrogen, and oxygen in the for m Cn(H 2O) n; provides

cell with energy; w ater soluble; m o nosaccharide glucose (C6H 12O 6) stored in the body as

polysaccharide glycogen; glucose + fructose sucrose (table sugar; disaccharide)

Lipids co m posed of carbons and hydrogen; insoluble in water; provides source ofenergy

o fatty acids consists of a chain of carbon and hydrogen with carboxyl group at the

end; has even nu m ber of carbons

saturated fatty acid no double bonds between carbons in the chain

unsaturated fatty acid one or m ore double bon ds between carbons in the chain;

one double bond = m o nounsaturated; m ore than one do uble bond =

polyunsaturated

o triglyceride (fat) consists of glycerol and three fatty acids; provides energy for cell

functions; adds padding and insulation; important in endocrine syste m function

o phospholipids consists of glycerol, two fatty acids and a phosphate group;

a mphipathic m olecule; for m lipid bilayers in plas ma and intercellular me m braneo steroids consists of four carbon rings connected together that is a part of every

steroid

Proteins consists of carbon, hydrogen, oxygen, and nitrogen; co mposed of 20 different

a mino acids (subunits of proteins) bonded by a peptide bond

o peptide bond for med w hen carboxyl group of one a mino acid bonds with a mino

group of another; covalent

o polypeptide sequence of a mino acids linked by peptide bonds

all proteins are polypeptides, but all polypeptides are N O T proteins

Protein Structure:

1) primary deter mined by nu m ber and type of a mino acid in polypeptide chain

2) secondary two types: alpha helix and beta sheet; R-group of a mino acid influences

w hich type of folding will take place; four factors deter mine polypeptide folding:

hydrogenbonds

ionicbonds

attraction between non-polar (hydrophobic) regions

covalentbonds

3) tertiary interaction between a mino acid R-groups for ms 3-D shape of protein

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4) quaternary not all proteins have this level; proteins co m posed of m ore than one

polypeptide chain (ex: he m oglobin)

C H A P T E R 3

Protein Synthesis:regulated process in cytoplasm; D N A contains code for a mino acids to m ake

proteins1) D N A copies to R N A for ming primary R N A transcript

2) Splicing occurs re moving introns and keeping exons for ming m R N A

o exons part of gene that carries protein-coding information

o introns do not effect protein synthesis coding

3) m R N A m o ves out of cell and information is translated to polypeptide chain

o posttranslational m o dification occurs after polypeptide chain is assembled

splitting

m ethylation

glycosalation

covalent m o dulation

allosteric m o dulation

o protein degradation controlled process co mpletely breaking do w n proteins; used to

regulate nu m ber of proteins; irreversible; caused by inappropriate p H or te mperature

o denaturing process breaking do w n proteins tertiary structure but leaving primary

structure intact; can occur by three different m ethods:

changing ionic concentration

increasing te mperature

changing p H

Protein Binding Sites:a binding site is a location on a protein w here a ligand attaches to

influence protein functions; there m ay be several binding sites on a protein; there are four

characteristics of a protein binding site:

1) Specificity:the selectivity of a binding site to bind specific ligands based on shape; therem ay be a limited nu m ber of ligands for a particular binding site (ex: drug that is used to

control blood pressure will bind to protein controlling blood pressure, but may also bind

to other proteins unrelated to pressure)

2) Affinity:ease of ligand-protein binding and ho w likely a ligand will stay bound to a

protein binding site; charge distribution influences affinity; shape can also influence

affinity like specificity; ligand concentration affinity

3) Saturation: the a m ount of binding sites occupied at any given time; the lo wer the ligand

concentration needed to bind half the binding sites, the higher the affinity; two factors

affect percent saturation of binding sites:

o concentration of unbound ligand in the concentration

o affinity of binding site for the ligand4) C o m petition: w hen m ore than one type of ligand can bind to the sa me binding site;

increased concentration of one ligand, increases chance of it being bound and reduces the

a mount bound for the other ligand

R egulation of Binding Site C h aracteristics: two m echanis ms

Allosteric M o dulation: contains two sites where non-covalent binding of one site effects

the shape of the second binding site

o functional site carries out physiological function of protein

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o regulatory site the ligand (m odulator m olecule) binding to this site alters the shape,

thus the activity, of the functional site; considered the m olecular switch that controls

the functional site by altering its shape and/or affinity

C ovalent M o dulation: altering shape and activity of a protein by covalent bonding of

charged che mical groups

o phosphorylation che mical reaction covalently attaching a phosphate group (netnegative charge) m ediated by a protein kinase

protein kinase an enzy me that accelerates the rate of reaction for

phosphorylation

phosphatase enzy me used in dephosphorylation to re move phosphate group and

return protein to original shape by deactivating it

E nzy mes:proteins with binding sites called active sites and ligands called substrates; can

increase both forward and reverse reaction rates; lowers activation energy of reaction; two

m o dels of enzy me-substrate interaction:

1. lock-and-keyconfiguration

2. induced fit m o del

non-specificbinding w hen a ligand binds to other receptors besides the one of interestR egulation of E nzy me-M e diated R eactions:

substrateconcentration altered by cellular reactions or factors outside the cell;

substrate concentration rate of enzy me-m ediated reaction

enzy me concentration -enzy me concentration rate of enzy me-m ediated reaction atany substrate concentration; enzy me concentration is altered by the rate of enzy me

synthesis or degradation

enzy me activity can be altered w hen allosteric or covalent m o dulation alters the

properties of the enzy mes active site

C ell Structure: two m ain parts

plas ma m e m brane boundary between extracellular and intracellular fluid

o phospholipid bilayer co m posed of phospholipids with p olar regions on the outside and

non-polar region in the middle

o proteins two classes of m e m brane proteins:

integral me m brane proteins e mbedded within the me m brane; a mphipathic; m ost are

trans me m brane proteins because they span the entire m e m brane

peripheral m e m brane proteins located at the m e m brane surface w here they are

bound to polar regions of transme m brane proteins on the inside of the cell; help with

cell shape and m otility

o cholesterol polar, flat ring shape; sits in non-polar region of plasma m e m brane; helps

m aintain cell fluidity

o glycocalyx consists of short chains of sugar attached to the outside of plas ma

m e m brane; enable cells to identify and interact with each other

cytoplas m the region inside the cell (outside the nucleus) containing cell organelles and

cytosol

o cytosol fluid portion containing w ater and other water-soluble proteins

o organelles fro m strands of proteins to co m plex structures

m e m branous

forward

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nucleus double m e m brane; m ain function is storage and trans mission of

genetic infor mation; contain nuclear pores that allow passage of large

m olecules

mitochondria double m e m brane; A T P production

endoplas mic reticulu m (E R)

o rough E R riboso mes are bound to the surface and has flattened-sac

appearance; processing proteins fro m G olgi apparatus

o s mooth E R branched, tubular structure; lipid synthesis and short-ter m

calciu m storage

G olgi apparatus flattened sacs for ming a cup-shaped structure with vesicles

that transport products out of cell (exocytosis) or provide storage; m o difies

proteins from rough E R

lysoso mes contains acidic fluid inside and are kno wn as recycling centers;

breaks do wn cell debris and dead cells; involved with apoptosis (program m ed

killing of cell)

peroxiso mes undergoes reactions rem oving hydrogen fro m lipids, alcohol,

and potentially toxic substances

non-m e m branous

riboso mes protein factories of the cell; proteins are synthesized here then

released into the cytosol or if attached to rough E R, transferred to the G olgi

apparatus then secreted from the cell or to organelles

cytoskeleton m ade of a fila mentous network that m aintains and changes the

shape of the cell and produces cell m o ve ment; three cytoskeletal fila ments:

o microfila ments co m posed of contractile protein actin and m y osin

o inter mediatefilaments provide structural support

o microtubules co m posed of the protein tubulin; m ost rigid and present in

nerve cells, centrioles and mitotic spindle (important in mitosis), cilia, and

flagella

M e tabolic P ath ways

Cellular Respiration C 6H 12O 6 + 6 O 2 + 38 A D P + 38 P i 6 C O 2 + 6 H 2O + 38 A T P ;aerobic; uses oxygen and glucose to produce A T P and carbon; yields 38 A T P fro m three

processes

o Glycolysis takes place in cytosol; can produce A T P anaerobically fro m lactate (replaces

pyruvate) Fig. 1

o Krebs C ycle takes place in inner co mpart ment of mitochondria; can only occur in

aerobic conditions; occurs twice per m olecule of glucose; acetyl coenzy me A (acetyl

C o A) begins Krebs cycle process with a linking step (Fig. 2) then continues into the

process (Fig. 3)o O xidative P hosphorylation takes place in inner mitochondrial m e m brane; requires

oxygen and cytochromes to function; yields 34 A T P; produces w ater and N A D +

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Fat and Pr otein M etabolis m

Fat M etabolis m

o Beta O xidation 18 carbon chain can yield 146 A T P

Protein and A mi no A cid M etabolis m

o D ea mination an a mino group is for med into a keto acid; produces urea; necessary for

an a mino acid to be used in cellular respiration or transfor med into a carbohydrate or fat

o Transa mination a mino group is transferred fro m an a mino acid to a keto acid; cannot

produce essential a mino acids

--> we are going to cut off

half in doing so we get some NADH, NAD and such. Fat makes you lighter,

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C ha pter 4

M o ve ment of M olecules across C ell M e m bra nes

Passive transport m o ves along the gradient (fro m greater concentration to lesser

concentration); energy for m o ve ment fro m surroundings with no direct cost to cell

o Diffusion rando m m o ve ment of m olecules from one location to another; path of

m olecule is unpredictable; will go from higher concentration to lower concentration untilequilibriu m is reached

R ate of Diffusion

temperature rate

particle size rate

surface area rate

gradient rate

m olecular interaction of m ediu m (viscosity) rate

per meability rate

Per meability can be through one cell like the plas ma m e m brane or a layer of cells

like epithelial m e m brane;

o Per meability through a layer of cells can be transcellular (through the cell);paracellular (between the cell)

Transcellular transport is controlled by m e m brane proteins

Paracellular per meability is regulated by tight junctions

T y pes of Diffusion

Si mple diffusion through a lipid bilayer

N onpolar m olecules diffuse rapidly unlike polar m olecules (ex: oxygen, carbon

dioxide, fatty acids, steroid hor mones)

Si mple diffusion through channels

C hannels usually m a de of integral m e m brane proteins that for m channels allowing

ions such as N a +, Cl-, K +, Ca 2+, N a +/K- to pass through

C hannels exist in open or closed state by process kno w n as channel gating; threefactors determine channel gating, effecting ho w long or ho w often a channel opens:

1. Ligand-gated channels binding of specific m olecules to channel proteins

directly or indirectly produce allosteric or covalent change in shape

2. V oltage-gated channels changes in the m e m brane potential cause m o ve ment of

the charged regions, altering its shape

3. M e chanically-gated channels physically deforming (stretching) the m e m brane

m a y affect confor mation

Facilitated diffusion m o ves m olecules fro m higher concentration to lower concentration

without A T P; uses transporter protein with binding site for particular solute to m o ve

across m e m brane; has m axi mal flux

A ctive transport referred to as ion pu m ps or A T Pase; goes against the gradient (fro mlesser concentration to greater concentration); two types:

o Primary active transport requires cellular use of energy fro m A T P

o Secondary active transport uses electroche mical gradient across m e m brane; has

m axi mal flux; has two binding sites: one for the solute m o ving against the gradient and

one for driving the solute

M e diated transport requires specialized protein (transporter protein); can be passive or

active

semi-permeability

-sodium ion,theres more sodium outside the cell then inside

3 sodium out and two potassium in , thus there will be more sodium outside the

,it changes the shape the ATP is

Changes the shape

With a mediated transport it will use the same usage of the binding site

passive

Transport

passive

Transport

Active (

small ions, and water

can be moved through

the channels there is

no channel just for

waterb

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Fig. 4

cotransport m o ve ment of actively transported solute into the cell

countertransport m o ve ment of actively transported solute out of the cell

E n docytosis and E xocytosis doesnt require m olecules to pass through the m e m brane; m o vesm olecules by changing shape of m e m brane

Endocytosis regions of plasma m e m brane fold into the cell for ming s mall pockets that

produce intracellular, m e m brane-bound vesicles that enclose a s mall volu me of

extracellular fluid

o phagocytosis bacteria or large particles engulfed entirely by cell

Exocytosis m e m brane-bound vesicles in the cytoplas m fuse with the plas ma m e m brane

and release contents outside the cell

O s m osis diffusion of w ater fro m high concentration to low concentration or diffusion from low

concentration of solute to high concentration of solute

penetrating solute solute that goes through the m e m brane; lipid soluble; doesnt influence

w ater m o ve me ntnon-penetrating solute solute that does not readily cross m e m brane; causes water m o ve ment

but not solute m o ve ment;

os mol one os mol is equal to 1 m ol of solute particles

O s m olarity total solute concentration; does not offer information about w ater m o ve ment;

includes both penetrating and non-penetrating solutes

hy poos m otic a solution containing less than 0.3 os mol/L solutes

isoos m otic a solution containing 0.3 os mol/L solutes

hy peros m otic a solution containing m ore than 0.3 os mol/L solutes

For non-penetrating solutes O N L Y

T o nicity

hypotonic concentration of non-penetrating solutes is less than 0.3 os m ol/L in cells causing

w ater to m o ve into cell allo wing it to swell

isotonic non-penetrating solutes do not leave or enter cell because of equal intra- andextracellular fluids of 0.3 os mol/L; no net m o ve ment

hypertonic concentration of non-penetrating solutes is m ore than 0.3 os mol/L in cells causing

w ater to m o ve out of cell and it shrinks

E xa m ples

1. 0.3 M glucose (non-penetrating) 0.3 os mol = isotonic, isoos motic

2. 0.3 N a Cl 0.3 M N a + and 0.3 M Cl- 0.6 os mol = hy pertonic, hyperosmotic

3. 0.3 M urea (penetrating) 0.3 os mol = hypotonic, isoos motic

do i have a net movement of

water ? or do i have a movement of water?

the water is going to move in

and the cell will swell -Hypo

water is going move out and the cell wil

which is hyper

al solute

centration

for the three Hyp,iso, and hyperosmotic it has to have a total solute concentration

what is a lipid solute?

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4. 0.3 M urea and 0.3 M glucose 0.3 os mol urea and 0.3 os mol of glucose = isotonic,

hyperosmotic

C ha pter 5

Signal Transduction binding of a m essenger to a receptor protein initiating a sequence of

events leading to the cells response to that m essenger; advantages:1. signal a mplification

2. integration and coordination of the response

lipid-soluble m essenger receptor located inside nucleus; used to regulate transcription

and the a mount of proteins in cell

w ater-soluble m essenger receptors are trans me m brane proteins; binding sites on

extracellular side of protein; four types of receptors:

1. ligand-gated ion channel receptors increases per meability

2. receptors that function as enzy mes (tyrosine kinase) phosphorylates protein inside

cell and changes its behavior

3. JA K kinases directly associated with m e m brane protein; results in ne w proteins

4. G-protein-coupled receptors G-protein bound to receptor to couple it with an ionchannel or enzy me

first m essengers che mical m essengers that bind to specific plas ma m e m brane receptors

second m essengers substances that enter or are generated in cytoplasm as a result of receptor

activation

Signal Transduction Path ways

C yclic A M P 1st m essengerbinds to receptor activates G protein

activates effector protein (adenylyl cyclase) converting A T P to c A M P (2nd

m essenger) activates c A M P-dependent protein kinase phosphorylates other

enzy mes leading to cells response; can be ter minated by enzy me

phosphodiesterase

Protein Kinase C - 1st m essengerbinds to receptor activates G protein

activates effector protein (phospholipase C) breaking do wn PIP2 to D A G and

IP3 (2nd m essengers)

1. D A G activates protein kinase C phophorylates proteins leading to cells response

2. IP3 binds to receptors in endoplasmic reticulu m opens Ca2+ channels releasing it into

cytosol produces m ore events leading the cells response

C alciu m/cal modulin as 2nd m essenger, Ca 2+ binds to the protein calmodulin

cal modulin changes shape Ca 2+-calmodulin activate or inhibit calmodulin-

dependent protein kinases calmodulin-dependent protein kinases activate or

inhibit other proteins

Eicosanoid Synthesis 1st m essengerbinds to receptoractivates

phospholipase A2 splits arachidonic acid fro m m e m brane phospholipids

m etabolized by two pathways

1. cyclooxygenase pathw ay (C O X) leads to for mation of cyclic endoperoxides,

prostaglandins (vascular actions) and thro mboxanes (blood clotting and vascular actions)

2. lipoxygenase path wa y leads to formation of leukotrienes ( mediate allergic or

inflam m atory reactions)

ll 4 of these

ip3 removes calcium

(A phosphodiesterase (PDE) is any enzyme that breaks a phosphodiester bond.)

Calmodulin - is a calcium-binding messenger protein

expressed in all eukaryotic cells. CaM is a multifunctional

intermediate messenger protein that transduces

calcium signals by binding calcium ions and then

modifying its interactions with various target proteins

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new idea

if i have a nerve cell and we move a signal along this. there are two ways

/ to use. there is a membrane that is used and a synapse on the way what we use

is a neuotransmitter more negative

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