832 exam 2

architectural features common to all cells

architectural features common to all cells

• plasma membrane-most basic compartmentalization

• cytoplasm and nucleus-interior compartments

• cytoplasmic organelles surrounded by lipid membrane

glycoproteins

oligosaccharides attached to proteins through asparagine or serine bonds

glycolipids

phospholipids w a saccharide attached

glycocalyx

makes surface of cell extremely hydrophilic, restricting passage of hydrophobic molecules through plasma membrane (carbohydrates are hydrophilic)

membrane purpose

serves a protective function, creates opportunity to regulate

how is cell compartmentalization achieved

mainly by lipid membranes

plasma membrane and most other organelle membranes are

lipid bilayers, regulates movement of molecules in and out of the cells/organelles

phospholipid

hydrophilic head group and hydrophobic tail, connected by glycerol backbone, restricts movement of polar hydrophilic molecules between in and out of the cell—> repelled by tail in middle

proteins in membrane

span, embedded in one side, or attached peripherally to membrane, regulatory

integral protein

part of the membrane, span or embedded in it(ions, receptors, transporters)

carbohydrates in membrane

form glycocalyx on exterior side of membrane(contains glycoproteins and glycolipids)

passive transport

main transport for small molecules and ions

• simple diffusion-

  • high conc. to low conc.

  • move with the concentration gradient (rock downhill)

  • cross membrane freely(gases, H2O, steroids(hydrophobic/lipid soluble))

• facilitative diffusion

  • MUST bind to specific transport protein

  • exhibits saturation kinetics—> will only happen at a certain rate

  • most drugs use this transport

  • pores, gated channels, carrier proteins(drugs use)

  • gated channels require stimulus to open(chemical or voltage)

    • change in confirmation to let ions through

active transport

main transport for small molecules and ions

• REQUIRES ATP/electrochemical gradient

• movement against concentration gradient

• hydrolysis of ATP and phosphorylation causes conformation change in protein, which allows to go from low to high

  • electrochemical gradient can be used to generate ATP

  • also used to co-transport another molecule against its gradient

• one mechanism by which drug resistance occurs

  • drug pumped out of cell before can bind to target

vesicular transport

macromolecules(lipids, proteins) and complexes, movement determined by process

• endocytosis- invagination of plasma membrane, encloses them in vesicles and moves into cell

  • phagocytosis—> pathogens

  • receptor mediated endocytosis- receptor bound to ligands(insulin) and then engulfed in coated vesicle

• exocytosis- vesicle inside cell fuses with membrane and content dumped into the extracellular fluid—> vesicles come from golgi and lysosomes

  • contain molecules/proteins or cellular waster

transport cells use

cells use a combination of all of these within the cells for them to do their job, work together to maintain cellular homeostasis

lysosomes

digestive organelles, breakdown a variety macromolecules

• surrounded by lipid bilayer, lumen contains acid hydrolases(only function at low pH)

• 5.5 pH maintained by ATPases that pump H+ against gradient into lumen

• products broken down are recycled by anabolic processes or excreted as waste

• can fuse w other vesicles(ex. phagosomes fuse w lysosome and contents are degrades/injured or dead cell)

• Autophagy- forms auto phagosome to breakdown damaged organelles/debris from cytoplasm

mitochondria

energy generators of the cell, produce majority of ATP

• has inner and outer membrane (inner membrane is folded several times, highly impermeable)

• almost everything inside comes from transporters

  • houses mitochondrial matrix

  • cristae holds ETC and ATPsynthase

• enzymes are involved in fuel oxidation(TCA cycle and beta oxidation)

  • also found within matrix, DNA that encodes several ETC proteins

golgi complex

membranous organelle involved in sorting and distribution of proteins and lipids synthesized in the ER

• vesicles containing lipids or proteins from ER fuse with golgi

• the sorted and packaged into different vesicles w different fates and functions

  • lysosomes and secretory vesicles produced in golgi

• proteins post translational modified here, especially with sugars!

endoplasmic recticulum

network of membranous tubules with multiple essential cellular functions

• smooth ER-

  • contain enzymes for synthesis of lipids

  • site of drug and toxin metabolism by P450 enzymes

  • storage of glycogen

• rough ER- in muscle cells its sarcoplasmic recticulum

  • ribosomes located on outer surface

  • major sites of protein synthesis from mRNA

  • site of initial storage of newly synthesized proteins(determine where go)

  • site of some post translational modifications—> N linked glycosylation

cellular cytoskeleton

organizes structure and shape of cell as well as arrangement of sub-cellular organelles and movement of vesicles

mictotubules

• cylindrical tubules made of tubulin subunits

• position organelles in cytoplasm

• critical for movement of cellular vesicle

• form mitotic spindle in cell division

• microtubule formation is target of several cancer drugs

actin filament

• made up of actin subunits

• control cell shape and movement

  • cell division, contraction, phagocytosis, any movement involved in normal organ function

intermediate filaments

• different types made of distinct fibrous proteins

  • lamin, vimentins, keratin

• provide structural support for plasma and nuclear membrane

• provide stability to cells under conditions of mechanical force

nucleus

houses genetic material in cell and largest of subcellular organelles

• double lipid bilayer membrane(nuclear envelope) w special pore structures for entry and exit of proteins and RNA

• ribosomes are found on outer membrane since continuous with rough ER

• nucleolus- does not have membrane, consists of an aggregation of genes encoding ribosomal RNA and proteins that regulate them

• genetic material exists in nucleus as complex of DNA and proteins called chromatin

  • heterochromation: tightly compact

  • euchromatin: loosely compact—> location of transcribed genes

• DNA divided into chromosomes besides germ cells, human cells—> 46 chromosomes

  • 2 copies each of 22 + 2 for sex

• site of DNA replication and repair as well as transcription (RNA synthesis) and splicing of RNA into mRNA

chemical messangers

carry out intercellular communication that elicits cellular responses through the process of signal transduction—> many drugs alter these pathways that are misregulated in disease

key concepts in cell signaling

• a stimulus(change in cell environment) triggers a cell to secrete a chemical messenger

• this messenger then acts on target cell by binding to specific receptor

• this biding triggers a cascade of events that elicits a response—>signal transduction

  • often transmitted to nucleus to cause changes in gene expression

• finally the signal and response are terminated

chemical messangers

often small molecules or proteins(acetylcholine, insulin)

Endocrine(hormones) Messaging

secretory cell and target cells are distant, chemical messenger must travel through the blood, often many target tissues(insulin)

Paracrine Messaging

secretory cells and target cells in close proximity, often messengers secreted by exocytosis(cytokines,acetylcholine)

Autocrine Messaging

the secretory cell is the target cell(t lymphocyte cells)

Juxtacrine Messaging

involves direct contact between cells(touching), one with ligand and the other with receptor, ligand not secreted(t cells and dendritic cells)

ligand binding

the binding of ligand to its receptor triggers a conformational change(change in shape) in the receptor that alters its function

intracellular receptors

located inside the cytoplasm or nucleus(ligands are small hydrophobic molecules readily able to cross the membrane)

plasma membrane receptors

located at cell surface and usually are transmembrane proteins(hydrophilic signaling molecules that cannot cross the membrane)

steroids/intracellular signal transduction

hydrophobic ligands that can enter cell by simple diffusion, are planar so can slide through. signal is transduced from outside the cell into the nucleus by the steroid bound to its specific receptor

• receptors are examples of ligand-activated transcription factors

• the change in shape uncovers a domain that binds specific DNA and allows dimerization of 2 identical receptors—> two receptors bind to each other

• receptors enter nucleus, binds to genes and alters the amount of transcription

plasma membrane receptor transduction

• confirmation change “activates” the intracellular domain of the protein

• this can be an opening of a channel(gated channels), activation of enzymatic activity(kinases often phosphorylate themselves other kinase nearby—> MAP) or change in activity of proteins bound to the receptor(final receptor is not a kinase—> GCPR)

• signal is transduced to the nucleus by other proteins

• proteins bound by a second messenger alter gene expression through regulation of transcription factors

signaling pathways

regulate transcription factors to alter gene expression and elicit a cellular response

• specific for each transcription factor and depends on the amino acid sequence of the DNA binding domain

• the transcription of these genes will be regulated by the transcription factor and signaling pathway that targets it

activators

increase the rate of transcription

repressor

decrease rate of transcription, turning off pathway

how signal transduction terminated

• chemical messenger ceases to be released or is degraded

• receptor levels decrease due to internalization and or degradation

• phosphatases remove activating phosphorylation from receptors

• second messengers are degraded

tyrosine kinase receptors

plasma membrane receptor example

• RTK is activated upon ligand binding and phosphorylates itself on a certain tyrosine residue(autophosporylation)

  • and/or to phosphorylate other associate proteins

• this phosphorylation of these amino acid residues turns them into binding sites for other proteins which in turn transduce the signal into the cell

MAP kinase example of this- kinase cascade

• binding event activates proteins in these complexes which often have enzymatic activities

• Raf—> kinase which is activated by Ras

• Ras—> signal transducer protein

• signal moves away from receptor into the cell

• may be multiple signal transducer proteins—> keep phosphorylating each other down the line til reach intracellular target

• persistent MAPK signaling causes unregulated cell proliferation

serine/threonine kinase

plasma membrane receptor example

TGF-beta signaling- assembly of transcription factor

• cytokine alters the receptor so that it can bind to a second receptor and phosphorylate it at a serine/threonine residue—> heterodimer

• second receptor then bind to a protein and phosphorylated it(R-Smad)

• this complex goes to nucleus where it binds genes and changes transcription

• R-Smad must be phosphorylated to then interact with co-Smad protein to actually then travel to nucleus

Jak-Stat signaling

• binding of cytokine(paracrine) activates receptor to dimerize

• binds Jak proteins which then phosphorylate each other and the receptor

• STAT proteins bind and then phosphorylated by Jak Proteins

  • this triggers stats to dissosiate from receptor and dimerize

  • these move to nucleus to bind to genes, alter transcription

  • assembly of transcription factor

• deals with inflammatory pathways

• THESE RECEPTORS ARE NOT KINASES

GCPRs (heptahelical or g-coupled protein receptors)

• G proteins are tethered to the membrane by lipid anchors

• binding of ligand to the receptor triggers cellular response through the change in production of a second messenger

• in absence of ligand they associate w heterotrimetic(3 subunit alpha, beta,gamma) g-proteins

• second messenger is a small diffusible signaling molecule—> production is altered in response to a stimuli

  • they bind to effector proteins within cell to exert a cellular response—> different alpha subunits regulate production of different secondary messengers

  • Galpha(s)- increases cAMP production

  • Galpha(i/o)- inhibits cAMP production

  • Galpha(q/11)- increases DAG, IP3 and calcium

• the complex breaks apart and away from receptor upon binding of ligand

• alpha subunit exchanges GDP for GTP

• the GTP bound to Galpha(s) binds to adenylate cyclase and activates it to make cAMP

• eventually Galpha(s) hydrolyzes the bound GTP to GDP, inactivates itself, and reassociates with receptor and other subunits

• once second messenger is produced (cAMP in this case) it diffuses through cytoplasm and binds to specific proteins

Example exam questions:

• 1. Signal transduction is the process by which:

  • a. chemical messengers find their target cells

  • b. second messengers are degraded

  • c. chemical messengers are secreted by cells

  • d. signals are transmitted from the plasma membrane to the nucleus

  • e. receptors are internalized in vesicles

• 2. Which of the following is TRUE about paracrine horomones?

  • a. they are secreted by one cell and act on a nearby cell

  • b. they act on the same cell from which they are secreted

  • c. they travel through the blood to reach target cells

  • d. they do not bind receptors

  • e. none of the above

• 3. Cytokines….

  • a. are lipids attached to proteins

  • b. are chemical messengers that work by the paracrine mechanism

  • c. bind intracellular receptors

  • d. are transcription factors

• 4. MAP kinase signaling……

  • a. is initiated by activation of a tyrosine kinase receptor

  • b. involves a kinase cascade

  • c. is sometimes hyperactivated in cancer cells

  • d. can induce cells to divide

  • e. all of the above

1. d

2. a

3. b

4. e

common biological energy utilizations(uses energy)

• biosynthesis

• detoxification

• muscle contraction

• active ion transport—>ATPase

• thermogenesis

common biological energy production via oxidation of:

• carbohydrates(sugars)

• lipid

• protein

O2 does not turn to CO2, reduced to H2O in mitochondria during the ETC

CO2 is from fuel decarboxylate

energy content of simple fuel molecules

carbohydrate: 4

fat: 9—> least oxidized

protein: 4

alcohol/ethanol: 7

what regulates the fed state

insulin, lowers blood sugars—> dictates movement of sugar from blood into the cells

• sugar is either stored(glycogen) or metabolized to fatty acids—> shuffle from one to the other

• can build fat from sugars

• lipogenesis—>acetyl-CoA converted to fats

• high caloric intake turns into storage

glucagon(fasting state)

glycolysis is triggered by rise in glucagon

fat=triglyceride(fat storage)=esters

triglyceride- 3 ester groups

ester-fatty acid+alcohol w water elimination/condensation

• breaks down triglycerides through hydrolysis, opposite is condensation rxn

lipids

includes:

• triacylglycerides(fat and nonpolar)

• phospholipids(phosphate esters, glycerol backbone and charged)

  • phosphatidylcholine=lecithin

• Steroids(cyclic and lipophilic)

• cholesterol—> waxy fat-like substance

• fatty acids

fatty acids

triglyceride is 3 fatty acids combined

• saturated—> bent tail

• unsaturated—> unbent

• cis or trans describe the double bonds

w, triangle symbol (FA chains)

first position of double bond in relativity to omega

#of double bonds

exam question:

select the chemical term that describes this molecule appropriately:

exam quesiton:

which of these molecules depicts a fatty acid?

ketone bodies

formed in the liver during ketogenisis, liver switches to produce this for muscles and brain during starved state

ketoacidosis

pathological metabolic state marked by extreme and uncontrolled ketosis(high ketone conc.)

glycogen synthesis

• after meals, insulin acts on hepatocytes to stimulate action of enzymes such as glycogen synthase

• glucose transformed into glycogen as long as insulin and glucose remain plentiful

• Fed state- liver takes up more glucose than released

• this is an energy consuming process

glycogenolysis

• when there is a need for energy, glycogen is broken down and converted back into glucose

• glycogen phosphorylase primary enzyme for glycogen breakdown

  • enzymatic conversion of glycogen polymers to glucose monomer

  • takes place in liver and muscle tissues

  • liver can consume glucose6phosphate or remove phosphate group to release free glucose molecule into blood for other cell use

  • muscles will keep glucose they make as they cannot remove the phosphate

• during fasting state

exam question:

which of the following biomolecules does not serve as fuel for energy production?

• a. amino acids

• b. fatty acids

• c. ATP

• d. triglycerides

• e. glucose

c

leptin

• protein hormone that plays key role in regulating energy intake and energy expenditure

  • includes appetite and metabolism

  • most important adipose derived hormone—> made in fat tissue

chylomicrons

lipoproteins produced in gut(intestinal epithelial cells) after fat digestion and secreted into lymph then makes to blood—>carries fat through blood(since not water soluble)

exam question:

select the correct term that describes the transport form of dietary fat in the blood stream after systemic absorption through the intestinal epithelium?

• a. trigylceride

• b. insulin

• c. VLDL

• d. chylomicrons

• e. glycogen

d

exam question:

select the correct statement that describes a metabolic change that occurs in the fasting state:

• a. hepatic glycogenolysis generates glucose that enters the bloodstream

• b. elevation of serum insulin levels induces glycogenolysis

• c. ketone bodies are used for gluconeogenesis

• d. triglycerides serve as fuel for RBC

• e. glucose released by muscle cells is used for brain energy metabolism

a

exam question:

amino acids can serve as substrates for gluconeogenesis. Select the correct molecule that serves the purpose of urinary nitrogen excretion:

• a. ammonia

• b. glycine

• c. formaldehyde

• d. urea

• e. creatine

d

gluconeogenesis(starved state)

• protein turnover induced in muscles and amino acids travel to liver to use as precursors

• lactate produced by RBC returns to liver to be used as a substrate

  • ketogenesis here, can make out of FA from the adipose tissue

• glycerol released from adipose tissue then used by liver

  • lipolysis occurs in adipose tissues and is glucagon driven

  • stores and mobilizes when needed

glycosidic bond

sugar- sugar bond, see in glycogen production—> takes energy to produce

oxidoreductases

catalyze oxidation-reduction rxn

• ex. dehydrogenases

transferases

catalyze C,N or P group transfer rxn

• ex. kinases

hydrolases

catalyze cleavage of bonds by water(hydrolytic) rxn

• ex. proteases—> HIV and viral disease

isomerases

catalyze racemization/isomerization rxn—> rearrange/reorganize parts of molecules=isomer

• ex. triose phosphate isomerase

isozymes

enzymes that differ in amino acid sequence but catalyze the same rxn

• they will have different Km s that help regulate/fine tuning of metabolism

• ex. hexokinase(low Km) and glucokinase(high Km) with glucose storage

enzyme action as biocatalyst

• does not change the delta G

• lowers the energy barrier of the reaction to make it more favorable

• catalytic enzyme will not be consumed in the rxn

substrate

what is transformed in enzymatic rxn

cofactor

other ions that assist in enzymatic rxn

• Zn in angiotensin conversion(ACE)

coenzyme

cofactors that take part in the transformation(participate in catalysis by rpoviding functional groups , often derived from vitamins

• ex. NAD+—> vitamin derivative

active site

where substrate binds and transformation occurs on a enzyme

transition state

the energy barrier of a reaction

this is what is effected by enzymes

Km value

describes the affinity of the enzyme for the substrate

high Km value—> low affinity—> need more to efficiently bind

low Km value—> high affinity—> need less to efficiently bind

competitive inhibition

binding of active site of enzyme is competed for against substrate and inhibitor(drug)

• mimics substrate—> substrate analog

• if increase amount of substrate can out compete the inhibitor

• increase the Km, does not change Vmax

• inhibitors can stay bound to active site for a while or outcompete the substrate

• inhibitor can have a higher affinity to enzyme than substrate

• ex. ACE inhibitors, block action of enzyme by not allowing it to convert Angt 1 to angt 2—> binds better than the substrate itself

irreversible(covalent) inhibition

• organophosphate group adducts with active site forming a covalent bond

• this cannot be reversed and causes enzyme to be inactivated

• adduction of enzyme—> suicide of enzyme

• penicillin is good drug example of this—> adducts the enzyme

enzyme cascade

highly regulated—> all need to be activated and giving each other feedback whole time

• ex. blood coagulation
  (clotting)

allosteric modulation

inhibitor binds at a non active site(allosteric) which then does not allow enzyme to change confirmation to do enzymatic activity

• inhibitor does not mimic the substrate

• reversible, cannot be outcompeted by increase in substrate since it is non competitive

• ex. non-nucleoside reverse transcriptase inhibitors(NNRTIs)

• allosteric activation(effectors)—> enhance proteins/enzymes activity, decrease Km

• allosteric inhibition—> decrease activity, increase Km

• enzyme regulation—> modulators at allosteric sites tune enzyme activity to determine how active things are

use of ATP

• mechanical work- actin/myosin movement in muscles relies on ATP

  • hydrolysis(water molecule attacks gamma P in ATP) of ATP by myosin head(ATPase)—> breakage of high energy bond allows mechanical movement

• ion gradients

  • enzymes use ATP as cofactor to help push things against concentration gradient

• biosynthesis(glycogen ex.)

  • ATP is cofactor for hexokinase in turning glucose into glucose 6-P

delta G, gibbs free energy

energy released or used up during a reaction, tells you how favorable a reaction is, can couple these together to make unfavorable rxn more favorable, use of ATP as cofactor example of this

• enzymes DO NOT change delta G, make the transition state different by lowering energy barriers

ATP hydrolysis- 2 high energy bonds—> delta g of ATP is -7.3 for breaking one of these bonds

exam question:

allosteric activation is an import enzyme regulation. select correct statement:

a. allosteric effector molecules bind to the proteins allosteric site

b. allosteric effector molecules bind to the active site of the target enzyme

c.allosteric activator molecules interfere with enzyme degradation

d. allosteric activators attenuate enzymatic activity

e. allosteric activators are drug molecules that increase cellular enzyme content

a

phosphoester

phosphoric acid+alcohol

anhydride

acid+acid—> double phosphoric acid bond

cAMP metabolizing enzyme

cAMP phosphodiesterase—> hydrolysis to break

exam question

exam question

ATP energy content

-7.3 kcal/mol= delta G

this is release to drive future rxns

purines

• bicyclic bases

• adenine

• guanine

pyrimidines

• monocyclic bases

• cytosine

• thymine

• uracil

nucleosides

• base with a pentose(sugar)

• adenosine

• thymidine

• guanosine

• cytidine

• w OH is ribose

• w H is deoxyribose

nucleotide

• base+sugar+phosphate group/s

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