Reductionist : studying the parts of the whole can explain the character of the whole

you can see how they are coordinated to enable cell function 

Invented by Robert Hooke and refined by Anton Leewenhoek

was a simple microscope: piece of metal with a very crude lens witha  small point that you could dial up or down

Schleiden, Schwann, and Virchow

1. All organisms are composed of 1 or more cell

2. The cell is the structural unit of life

3. Cells arise from pre existing cells by division

Life!

HeLa cells are cultured tumor cells isolated form a cancer patient (Henrietta Lacks) by George Gey in 1951

Cultured Cells are an essential tool for cell biologists: can continuously divide as long as supplied with nutrients

- Cellular processes are highly regulated

- Cells from different species share similar structure, composition and metabolic features that have been conserved throughout evolution 

- Genes encode information to build each cell and the organism 

- Genes encode infomration for cellular reproduction, activity and structure

- Central Dogma: DNA - transcription - RNA - translation - Proteins 

Mitosis: Cloning 

Meiosis: increased genetic diversity, primarily in gametes 

- Cells reproduce and each daughter cell receives a complete set of genetic instrucitons

- Photosynthesis provides fuel for all living organisms

- Animal cells derive energy from the products of photosynthesis, mainly in the form of glucose

- Cells can convert glucose in ATP - a substance with readily available energy

Cells are able to respond to stimuli

cells evovle

cells are capable of self regulation

SIZE and type of 

ORGANELLES

- Plasma membrane of similar construction

- DNA is the genetic information

- Similar transcription/translation/ribosomes

- Shared metabolic pathways

- similar conservation of energy

- similar mechanism of photosynthesis

- proteasomes of similar construction

- have exons/introns

-complex chromosomes with DNA and proteins

- larger genome

- specialized organelles for respiration

-complex flagella and cilia

- cellulose in cell walls of plants

- division of cell sinto nucleus and cytoplasm, separated by nuclear envelope

the region where there's condensed circular DNA inside the cell 

- many bacteria have cell wall in addition to cell membrane (unlike animals!)

- prokaryotes DONT have cilia

- flagella in both groups differ

- Cytoplasm: eukaryotes have membrane bound organelles and complex cytoskeletal proteins. Both have ribosomes but they differ in size

- Cellular reproduction : eukaryotes divide by mitosis; prokaryotes by simple fission

- Locomotion: eukaryotes use both cytoplasmic movement, and cilia and flagella; prokaryotes have flagella but they differ in form and mechanism

Asexual Reproduction:

Eukaryotic: Mitosis

Prokaryotic: Binary fission

Sexual Reproduction

Eukaryotic: Meiosis

Prokaryotic: Conjugation

- provide structural support

- catalyze the chemical rxn in which amino acids are covalently linked to one another

Prokaryotic: 

Methanogens: methane producing organisms

Halophiles: highly salty conditions

Acidophiles: highly acidic conditions

Thermophiles: kind you find in hot springs

live in extreme environments

Includes the smallest known cells - mycoplasma (lack cell walls, 1/few exceptions)

Includes cyanobacteria - some photosynthetic bacteria that gave rise to green plants in O2 rich enviornment

Nitrogen Fixation

- N2 not useable, certain organisms convert N2 into ammonia, nitrites, and nitrates

- large groups of different types of bacteria used in this cycle

- significance: allows N2 to be used in the synthesis of amino acids, nucleic acids

Eukaryotic Cells: Cell Specialization

Eukaryotic cells are more copmlex ( protein sorting in the E.R., cellular respiration in the mitochondria)

Unicellular: complex single celled organisms

ex) fungi, algae

Multicellular: different cell types for different functions

- Differentiation: embryonic development

-- #s and arrangments or organelles depend on fnx of cels (more Golgi and Er in secreting cells)

Despite differentiation, cells share many features in common (metabolism, DNA, self regulation, protein synthesis - ribosomes)

Multicellular eukaryotes have different cell types for different functions 

Cell research focuses on 6 organisms: E. Coli, yeast: Saccharomyces, mustard plant Arabidopsis, nematode Caenorhabditis elegans, the fruit fly Drosophila, and the mouse Mus Musculuns

Cells are measured in µm and nanometers 

Cell size is limited:

- by the volume of cytoplasm that can be supported by the genes in the nucleus, by the volume of cytoplasm that can be supported by the exchange of nutrients, and by the distance over which substances can efficiently travel through the cytoplasm via diffusio

Proks have a faster rate of diffusion/effusion

Euks surface to volume ratio is reduced (much LARGER volume)

- concentrating components that you need for specific activities and by shuttling mechanisms

ex) a lot of enzymes needed for cellular respiration are in the mitochondria

don't depend on shared electrons but on attractive forces between atoms having an opposite charge

Individual noncovalent bonds are weak 

1. Water is highly asymmetric

2. Each of the two covalent bonds in the molecule is highly polarized

3. All three atoms in a water molecule are adept at forming hydrogen bonds

Ester = carboxylic acid + alcohol

Amide = carboxylic acid + amine

Primarily stores of chemical energy

Durable building materials for biological construction

C-O-C

between sugars

disaccharides serve as energy ready stores

oligosaccharides are important on the glycolipids and glycoproteins

Glycogen: most highly branched,energy storage

Starch: helical, energy storage

Cellulose: unbranched, highly extended, structural role

Nonpolar

dissolve in organic solvents

Fats, Steroids, and Phospholipids

chemically reducing the double bonds with hydrogen bonds

(can convert cis to trans) 

very rich in chemical energy

extremely insoluble in water

fatty acids arent always identical (mixed or identical)

the study of the various types of energy transformations that occur in living organisms

sun is the ultimate source of energy (producers take CO2 and use sun energy to form glucose, humans are heterotrophs and obtain our food from organic molecules)

Energy: capacity to do work, or the capacity to change or move something

Thermodynamics: the study of the changes in energy that accompany events in the universe

the law of conservation of energy, energy is neither created/destroyed (doesnt predict ΔH)

Transduction: conversion of energy from one form to another (ex plugging in a clock, sunlight)

universe can be divided into system and surroundings (system has internal energy in some state of flux)

reactions that lose heat lose internal energy (exothermic)

events in the universe tned to proceed from a state of higher energy to a state of lower energy

-- such events are called spontaneous (without the input of external energy)

--LOSS OF AVAILABLE ENERGY DURING A PROCESS IS THE RESULT OF A TENDENCY FOR RANDOMNESS TO INCREASE WHENEVER THERE'S A TRANSFER OF ENERGY

the energy available to do work

spontaneous if G > 0 (exergonic)

spontaneity depends on both enthalpy and entropy

all chemical reactions are theoretically reversible

all chemical reactions spontaneously proceed toward equilibrium

the rates of chemical reactions are proportional to the concentration of reactants

at perfect equilibrium, G = 0 (forward/reverse energies are essentially going to be the same)

The Standard G are described under standard conditions 

They're not representative of cellular conditions but are useful to make comparisons

standard g = -RTlnKeq

Gprevailing conditions may cause ΔG negative even when standard is positive

Making G negative may involve coupling endergonic and exergonic reactions in a sequence

simultaneously coupled reactions have a common intermediate

ATP hydrolysis is often coupled to endergnoic rxns in cells

instead of simply releasing the phosphate group, there's a phosphoral TRANSFER reaction; that phosphate is transferred to something else such as an organic molecule, an enzyme, etc. 

--allows for energy release that can drive an endergonic reaction

Catalyzed by Pyruvate kinase

reaction followed by spontaneous tautomerization of this product

The products of hydrolysis are stabilized relative to the reaction 

SUBSTRATE LEVEL PHOSPHORYLATION

Direct product is 3-phosphoglyceric acid, with an undissociated carboxylic acid group

--Dissociation occurs immediately, this ionization and resonance structure make it possiblet o stabilize the product relative to the reactants

- Resonance stabilizaiton of Pi further contributes to the free energy change

- Acetyl CoA is a thioester with a large, negative, standard free energy of hydrolysis

- Thioesters contain a sulfur atom in the position occupied by an oxygen atom in oxygen esters

ATP is the chemical link between anabolic and catabolic pathways

Hydrolysis of ATP is coupled to many endergonic reactions

Direct hydrolysis of ATP provides energy for conformational changes in proteins (i.e., muscle contraction) but is not themeans by which energy release is coupled to endergonic processes

Coupling to endergonic reactions involves transer of phosphate group from ATP to a substrate (high energy intermediate) or enzyme

Such group transfer reactions provides energy for anabolic reactions, transport of molecules across membranes against concentration & electrical potential gradients 

Cells contain many metabolites with large, negative free energy values including PEP, 1,3-BPG, phosphocreatine, as well ast thioesters (acetyl-CoA)

Inorganic polyphosphate, present in all cells, may serve as a reservoir of phosphoryl groups with high group transfer potential

Nonequilibrium (not going to be perfect state)

steady state: maintenance of concentrations of prod/react but not at equilibrium

steady state requires an input of Energy

Cellular metabolism exists as a steady state

- new substrates enter and products are removed

catalysts that speed up chemical reactions

almost always proteins

may be conjugated with nonprotein components

cofactors: inorganic enzyme conjugates

coenzymes: organic enzyme conjugates

increase rate without altering equilibria

accelerate rxns through stabilization of transition states (accelerates both forward and reverse rxns and will do so proportionally)

transition state: highest energy barrier you have to overcome (reduces Ea)

Enzyme substrate complex: first step

Enzyme active site is where the substrate binds (3D entity that allows for stabilization of transition state)

are present in cells in small amounts

are not permanently altered during the course of a reaction

cannot affect the thermodynamics

are highly specific for their particular reactants called substrates

can be regulated

A small energy input, the activation energy, is required for any chemical transformation

- The Ea barrier slows the progress of thermodynamically unstable reactants

- Reactnat molecules that reach the peak of the EA barrier are in the transition state

without an enzyme, only a few substrate molecules reach the transition state

with a catalyst, a large proportion of substrate molecules can reach the transition state

reaction equilibria are linked to the standard free energy change, whereas reaction rates are linked to Ea

ES complex (roughly complementary)

Privileged microenvironment:

proteins live in a largely aqueous environment but the protein core is nonpolar

Polar amino acids within an overall nonpolar enviornment: allows certain amino acids to assume catalytic properties

acidic or basic R groups on the enzyme may chane ph of the substrate, charged R groups may attract the substrate

cofactors of the enzyme increase the reactivity of the substrate by removing or donating electrons

shifts in the conformation after binding cause an INDUCED FIT between enzyme and the substrate

^allows for better accomodation for the transition state to reduce Ea

Covalent bonds of the substrate are strained

study of rates of enzymatic reactions under various experimental conditions

- rates of enzymatic reactions increase with increasing substrate concentrations until the enzyme is saturated

-- at saturation, every enzyme is working at maximum capacity

-- the velocity at saturation is called Vmax

Km: substrate concentration at 1/2 V max

units are concentration units

Km may reflect the affinity of the enzyme for substrate (smallers Kms have higher affinity)

1/v vs. 1/substrate = Burk plot

slope = Km/vmax

y int = 1/vmax

x int = 1/km

pH

temp may denature, or disrupt noncovalent interactions (H bonding, electrostatic rxns, etc.) that're important for stabilization of structure

sequences of chemical reactions

- each reaction in the sequence is catalyzed by a specific enzyme

- pathways are usually confined to specific locations

- pathways convert substrates into end produts via a series of metabolic intermediates

(overaccumulation is toxic)

break down complex substrates into simple end products

(provide raw mat for cells, and chemical energy)

degradative

oxidative

incremental release of E

syntheize complex end products from simple substrates

- require energy

- reductive

- use ATP and NADPH from catabolic pathways

NADPH is an electron carrier for bond formation and synthesis rxns provides source of e-