Cell Bio Chapters 7,8,9,11

prokaryote

unicellular organisms lacking nucli; members of domains Archaea or Bacteria, much smaller than eukaryotes

organelles in a prokaryote

cytoplasm, nucleoid, plasmid, cell wall, ribosomes

eukaryote

an organism belonging to domain Eukarya, whose cells contain a nucleus, organelles, and a cytoskeleton

cytosol

fluid portion of cytoplasm

organelle

discrete, usually membrane-bound compartment within a cell that has a specific form and functions

benefits of organelles

1. seperates incompatible chemical reactions

2. increased efficiency of chemical reactions because substrates and enzymes can be localized

cytoplasm

all the contents of a cell inside the cell membrane

nucleoid

region of the cell with the chromosome; circular chromosomes composed of DNA contain genetic information

plasmid

extra-chromosomal, small loops of DNA containing some genes

cell wall

rigid structure outside cell membrane; composed of peptidoglycan among bacteria and other polysaccharides among archaea

ribosomes

macromoleculat machine with a large and small subunit composed of protein and RNA, synthesis proteins (convert mRNA to protein)

nucleus

contain chromosomes and is the site of transcription

nuclear membrane

double membrane surrounding nucleus

nuclear pores

complex or proteins that extends through both nuclear membranes; allows RNA to leave nucleus and nucleotides and proteins to enter

nuclear localization signal

amino acid sequence that directs peptides to be transferred to the nucleus

mitochondria

site of cellular respiration (conversion of glucose to ATP); has 2 membranes with the inner membrane highly folded, has some unique genes coded by mitochondrial DNA

Endomembrane system

endoplasmic reticulum, Golgi apparatus, lysosomes, and peroxisomes

Rough endoplasmic reticulum

covered in ribosomes; site of synthesis of membrane-bound proteins to be contained in vesicles and transported to other organelles or released from cell

smooth endoplasmic reticulum

lacks ribosomes; site of lipid synthesis and processing, Ca2+ reservoir

golgi apparatus

protein, lipid, and carbohydrate processing; an intermediate step between RER and final destination of membrane bound proteins; consists of a series of cisternae

lysosome

catabolism and recycling of molecules

peroxisome

site or oxydation reduction reactions, isolate reactive oxygen molecules and other toxins to make them less toxic

endomembrane system pathway

1. ribosomes on RER translate mRNA into protein

2. protein exits RER in a vesicle and travels to golgi apparatus

3. protein is further modified in the golgi

4. protein exits transface of golgi

5. protein is secreted from the cell through exocytosis or trafficked to an organelle

how protein is directed to ER

1. signal sequence is synthesized in cytosol

2. signal sequence binds to a signal recognition particle (SRP)

3. SRP bind to a receptor on the rough ER

4. SRP is released and protein synthesis continues with ribosome bound to RER

protein sorting after leaving golgi

1. proteins carry unique tags that bind to unique receptors inside trans-Golgi

2. triggers release of unique vesicles from the Golgi that are transported to their destination

lysosomal recycling mechanisms

1. receptor-mediated exocytosis: macromolecules outside cells bind to receptors bound to cell membrane, thus inducing endocytosis. Resultant endosomed is acidified to mature into lysosome

2. phagocytosis: endocytosis brings small cells or particles into cell to form phagosome, which fused with a lysosome to be digested

3. autophagy: damaged organelle is enclosed within a membrane, which is delivered to a lysosome for digestion

microfilaments

composed of actin; maintain cell shape, interact with myosin to allow muscle contraction, involved in cytokinesis

intermediate filaments

composed of keratin, lamin, and other proteins; maintain cell shape, anchor nucleus and some organelles to cell membrane

microtubules

composed of alpha and beta tubulin dimers, maintain cell shape, main components of flagella and cilia

spindle fibers

move chromosomes during cell division, tracts for organelle movement

motor molecules

allow chemomechanical transduction

myosin

muscle contraction, cell movement, organelle transport

kinesin

transport toward positive end of microtubule

dynein

transport toward negative end of microtubule

entropy

(S); measure level of disorder in a system (joules/K); delta S = S(final)-S(initial)

enthalpy

(H); total energy in a molecule; includes potential energy in bonds and kinetic energy due to movement

exothermic reaction

releases heat because products have less potential energy, delta H<0

endothermic reaction

absorbs heat because products have more potential energy; delta H > 0

Gibbs free energy

energy of a reaction that is available to do work; delta G = delta H -T delta S

exergonic

spontaneous reaction, delta G < 0

endergonic

nonspontaneous reaction; delta G > 0

energetic coupling

free energy from an exergonic reaction can be used to drive an endergonic reaction

reduction-oxidation (redox) reaction

chemical reactions that involve the transfer of electrons from one molecule to another

oxidation

loss of electrons; electrons move away from an atom; loss of potential energy; exergonic half of reaction

reduction

gain of electrons; electrons move toward an atom; gain of potential energy; endergonic half of reaction

flavin adenine dinucleotide (FAD)

a cellular electron acceptor that is reduced by 2 electrons and 2 H+ to FADH2; electron donors with high potential energy at -H bond

nicatinamide adenine dinucleotide (NAD+)

a cellular electron acceptor that is reduced by 2 electrons and 1 H+ to NADH, electron donors with high potential energy at -H bond

adenine triphosphate (ATP)

short-term energy source found in all cells; three phosphates with 4 negativel charged oxygen molcules create weak bonds with high potential energy

hydrolysis of ATP

reaction with H2O that results in loss of one phosphate and release of 7.3 kcal/mol energy

phosphorylation

Pi released from ATP is bonded to another molecule; that molecule is not activated, increasing the reactants potential energy; activated molecule can now more easily form bonds with other molecules because removing the phosphate is exergonic

activation energy

minimum amount of kinetic energy needed to make a reaction happen; transition state in a reaction requires the highest free energy during a reaction

enzymes

protein catalyst used to increase rate of reaction by reducing the activation energy

enzyme active site

brings reactants (substrates) together in a precise orientation to facilitate a reaction; substrate-enzyme specificity; forced orientation of reactants makes the transition state more stabel, reducing activation energy

kinase

any enzyme that puts a phosphate on another molecule (in cellular resporation, phosphate from ATP to a protein)

phosphotase

enzyme that catalyzes the hydrolysis of phosphates

dehydrogenase

enzymes that transfer the hydrogen atoms from organic compounds to electro acceptors, thereby oxidizing the organic components (NADH or FADH2) and generating energy

inputs and outputs of glycolysis

inputs: glucose, NAD+, ADP, Pi

outputs: NADH, ATP, Pyruvate

location of glycolysis

cytosol

inputs and outputs of pyruvate processing

inputs: pyruvate, NAD+

outputs: NADH, CO2, Acetyl CoA

location of pyruvate processing

matrix of the mitochondria (or cytosol in prokaryotes)

inputs and outputs of citric acid cycle

inputs: Acetyl CoA, NAD+, FAD, ADP, Pi

outputs: NADH, FADH2, ATP, CO2

location of citric acid cycle

matrix of mitochondria (or cytosol in prokaryotes)

inputs and outputs of oxidative phosphorylation and ETC

inputs: NADH, FADH2, O2, ADP, Pi

outputs: NAD+, FAD+, H2O, ATP

location of ETC and oxidative phosphorylation

inner membrane of mitochondria (or plamsa membrane of prokaryotes)

cellular respiration

complete oxidation of carbons in glucose to CO2

glycolysis

glucose (6 carbons) is oxidized to 2 pyruvates (3 carbons each); produces 2 NADH and 2 ATP

Pyruvate processing

each pyruvate (3 carbons) is oxidized to 1 CO2 and 1 molceule of acetyl-CoA; couples to produce 2 NADH per glucose

citric acid cycle

each acetyl CoA is oxidized to 2 CO2; coupled to produce 6 NADH, 2 FADH2, and 2 ATP per glucose

electron transport chain

electrons from NADH and FADH2 cycle through electron transporters to create an H+ gradient; H+ flow down concentration gradient, resulting in oxidative phosphorylation, creating about 25 ATP/glucose

energy payoff phase

exergonic reactions are used to reduce 2 NAD+ to NADH and 4 ADP to ATP

substrate-level phosphorylation

transfer of phosphate group from one substrate to ADP to produce ATP

phosphofructokinase

converts fructose-6-phosphate to fructose-1, 6-bisphosphate during step 3 of glycolysis

importance of step 3 (of 10 steps) in glycolysis

• key regulatory step, is irreversible and after this step process is committes to forming pyruvates

negative feedback in glycolysis

enzyme can be inhibited by ATP, high levels of ATP act as a negative feedback regulator of enzyme activity- if high levels are detected, then enzyme will lessen rate of glucose conversion

pyruvate dehydrogenase

key enzyme that catalyzes the oxidation of pyruvate and reduction of NAD+

chemical formula for pyruvate processing

pyruvate + NAD+ + CoA-SH —> CO2 + NADH + Acetyl CoA

citric acid cycle (simple)

acetyl-CoA is oxidized to CO2

Products of one cycle

8 carboxylic acids are produces by enzymes in a cycle

• most steps involve gradual oxidation of carbon to eventually release 2 CO2 for every acetyl group that enters the cycle

carrier molecules in citric acid cycle

• most potential energy is stored in NADH, FADH2, and ATP

• negative feedback when high lvels of ATP and NADH are present

how much energy is released by citric acid cycle?

685 kcal/mol

ubiquinone (Q)

non-protein moelcule involved in electron transport across membrane

what happens to potential energy in ETC?

potential energy is reduced with each transfer of electrons, O2 is reduced to H2) in final step; this energy is used to drive H+ into transmembrane space, creating a strong chemical gradient

chemiosmosis hypothesis

proton gradient is used to drive production of ATP, with the key pump being atp synthase

oxidative phosphorylation

production of ATP by ATP-sunthase using proton gradient created by electron-transport chain; spinning process catalyzes the production of ATP to ADP and Pi

how much ATP is produced from cellular respiration?

about 29 molecules of ATP in total; which is driven by the oxidation of NADH and FADH2

primary cell walls

fibrous composite secreted when plant cells first develop; long strands of cellulose bundled into microfibrils, cross-linked by hydrogen bonds

secondary cell walls

secreted between cell wall and cell membrane as plant cells mature; variable composition

collagen

fibrous protein wrapped into a triple helix; multiple strands bind together to form fibrils

proteoglycan

gelatinous glycoproteins that surround collagen and push it into place

desmosome

strong cell to cell attachment composed of linking proteins between cells and anchoring proteins within cells

direct signaling

intercellular communication that occurs though gap junctions

autocrine

affects same cell that secreted it

paracrine

affect neighboring cells; neuronal signaling is special case of paracrine signaling

endocrine

released into bloodstream and act on distant tissue

hormone

chemical messenger released from cells into the bloodstream to exert action on target cells some distance away

neurotransmitter

chemical messenger that acts across a neural synapse

neurohormone

chemical messenger released by a neuron into the blood stream (neuropeptide or neurosteroid)

neuromodulator

hormone or neurotransmitter that modifies synaptic function (generally paracrine)

peptide messengers

most signaling molecules are hydrophilic peptides

biogenic amines

simple molecules with an amine group (-NH2); often amino acid derivatives that are hydrophilic