BIO 311C

Mechanical support, dynamic structure, and motility

Support (shape/resists compression), Movement within the cell of chromosomes and organelles, movement of the entire cell

Tubulin

Emergent properties

organize microtubule assembly

two centrioles, organizing center for spindle

one centriole, forms base of flagella or cilia

• Cilia (windpipe, fallopian tubes, protists)
• Flagella (sperm, protists)

9+2 structure (9 groups of 2 units on outside of wheel)

"walk" across the microtubule doublets to create a bending movement of the flagella or cilia

Towards the nucleus

Away from the nucleus

a circle of 9 bundles and 2 microtubules

25 nm, tubulin

7 nm, actin

support (resist pulling), changes cell shape, contractile forces (muscle, cell division furrow, cell motility [pseudopodia])

Myosin

• Cortex (outer cytoplasm): gel with actin network
• Inner cytoplasm: sol with actin subunits
• Extending pseudopodium

Kinesin

8-12 nm; keratin, lamin, and others

support (cell shape), anchorage of nucleus, nuclear lamina

Twizzlers pull and peel

Microtubules (made of tubulin subunits), Microfilaments (made of actin subunits), and Intermediate Filaments (made of keratin or lamin)

Myosin

hair cells, skin cells, nail beds (all dead)

• Selective permeability
• Separating cell from non living surroundings
• Creates unique environment within cell for specialized reactions
• Asymmetric protein distribution
• Cell communication, cell signaling

saturated fatty acid chains

• Phospholipids
• Membrane proteins (integral and peripheral)
• Membrane carbohydrates (glycoproteins, glycolipids)

embedded in the membrane spanning the entire phospholipid bilayer; they are amphipathic

on the surface of the membrane and don't span the bilayer, only interacting with the phospholipid head

a hydrophobic region

Integral membrane protein and amphipathic

• "Flags" of carbohydrates on lipid or protein
• Involved in cell-cell recognition, receptors
• Located on external side of cell membrane

• Carbohydrate attached to protein
• Protein receptors

• Attached to lipid
• Cell recognition (ex: ABO blood group)

• Transport
• Enzymatic activity
• Signal transduction
• Cell-cell recognition
• Intercellular joining
• Attachment to cytoskeleton or ECM

makes glycoproteins and glycolipids, and places them on outer portion of plasma membrane

carbohydrates attached to proteins on the outside of the cell membrane

Phospholipid bilayers

endomembrane system

freely across the membrane

are hindered by the bilayer

facilitate movement of polar substances, and are very specific for a particular solute

Channel proteins (passive transport) and carrier proteins (passive and active transport)

Diffusion and facilitated diffusion

the tendency for molecules to spread out evenly into an available space

randomly, but population of molecules can be directional

from high concentration to low concentration

diffusion of water across a selectively permeable membrane

there are more solutes in the cell than in the surrounding solution, causing the cell to fill with water and explode

there is a lower concentration of solutes in the cell than the surrounding solute causing the water to move out of the cell and cause it to shrivel

The concentration of solutes is the same inside and outside the cell

there are more solutes in the cell than in the surrounding solution, which makes the cell turgid-the normal state for a plant cell

there is a lower concentration of solutes in the cell than the surrounding solute causing the water to move out of the cell and cause it to plasmolyze

The concentration of solutes is the same inside and outside the cell with not much net movement of water causing the cell to become flaccid or wilted

transport proteins

movement of polar or charged molecules down their concentration gradient into a cell

undergo change in shape the transports the polar/charged molecule across the membrane

uses energy to move solutes

the solutes move against the concentration gradient

carrier proteins (NOT channel proteins)

Na⁺-K⁺ pump

By simple diffusion through the membrane

Skin cells become full of water because the water is hypotonic

tight junctions, desmosomes, and gap junctions

make a seal to prevent fluids from getting in between cells (like tile grout)

fasten cells together in strong sheets

intermediate filaments anchor desmosomes in cytoplasm like nails and wooden planks

communication between two cells

allows cells to exchange small molecules

Tight junctions

plasmodesmata

communication between two single cells

alpha and A

signaling by direct contact

Gap junctions, cell-to-cell communication, paracrine, and synaptic

only cells nearby will receive the signaling molecules (exocytosis)

between two nerve cells

Glycolipids

neuron communication

neurons communicate with other cells (other neurons, muscle cells) at synapses

Pre-synaptic cell releases chemical signal ("neurotransmitter") that is taken up by the post-synaptic cell, and elicits a response

• 1. Two neuron cells separated by a synapse
• 2. Pre-synaptic neuron releases neurotransmitters into gap
• 3. Post-synaptic neuron receptors bind neurotransmitter, opens Na⁺/K⁺ channel

Signal can be transduced along neuron (via depolarization of the membrane) and continued across many cells

endocrine cell-->blood vessel-->hormone travels in bloodstream to target cells-->target cell

• 1. Caterpillar eating plant (wounded plant and chemical in saliva)
• 2. Signal transduction pathway through leaf
• 3. Synthesis and release of airborne chemicals
• 4. Recruitment of parasitic wasps, which lay eggs in caterpillars

-Only specific target cells recognize and respond to given chemical sign

-Signal is received, transduced through the cells and elicits a response

-Cell communication and signaling is often in response to some trigger

signal molecules bind to receptor

signal is transmitted to response element

output of signal

Reception, transduction, and response

Ligand-->Receptor-->"Relay Molecules"-->Regulation of Cellular Activities

a signal is specifically recognized by target cells.

Only target cells will have the correct receptor to bind signal

Like cell phones (cells) and phone numbers (signals)

the cell and the membrane

change the shape of the receptor protein

Structure-function relationships

Membrane bound receptors and intracellular receptors

Span the membrane

Located in cytoplasm or nucleus

A membrane bound receptor

Water soluble/polar ligands and hydrophobic/very small molecular ligands

"transcription factors" which bind DNA and turn genes on or off

G-protein linked receptors, receptor tyrosine kinase, and ion channel receptors

integral membrane proteins and amphipathic

a-helix secondary structure

sensory perception (sight, smell), diseases

changes its shape, therefore changing its function

receptor and an ezyme

the receptor functions as a dimer

phosphorylates to neighboring receptor's tyrosine amino acids

Signal molecule attaches to receptor to form a dimer

Phosphorylates with another

activates cellular responses

commonly found in the nervous system, in which the signal molecule is a neurotransmitter

an ion channel receptor function in local cell-cell communication

G-protein linked receptor, receptor tyrosine kinase, ion channel receptor

multi-step pathway using molecules and proteins to transmit signal to response element

• -amplifies signal
• -but the signal itself is not transmitted

'relay molecules'

proteins that change shape as signal is 'carried' through the pathway and are phosphorylated

NOT proteins, but they broadcast the signal

cAMP and Ca²⁺

an RNA molecule

cAMP-->activates a kinase-->kinase phosphorylates to a target protein-->target protein activity changes

When scared, releases adrenaline

When your hand touches fire, Ca²⁺ is released from ER to make the microfilaments contract and pull your hand away from the fire

Cholera and Viagra

Vibrio cholerae in drinking water secretes a toxin which modifies the G-protein

This G-protein is involved in salt and water excretion

In response to the toxin, the G-protein is unable to hydrolyze GTP to GDP=ALWAYS active

G-protein permanently signals -cAMP- intestines secrete water continuously

• cGMP (like cAMP) is also a second messenger: it relaxes smooth muscle
• In this situation, cGMP is converted to inactive GMP too quickly

Viagra slows the conversion of cGMP to GMP so that the smooth muscle stays relaxed longer and more blood can enter the blood vessels

the output of signal which results in regulation of cellular activities and can occur in cytoplasm or nucleus

transient so the cell can continue to respond to new environmental cues

active state must be reset

Ex: phosphorylation-dephosphorylation; cAMP to AMP, GTP to GDP; Ca²⁺ gradients re-established

sum of all chemical reactions in a cell

catabolic and anabolic

pathways break down products to release energy

pathways synthesize products (energy can be stored in bonds between atoms)

Emergent properties

capacity to cause change

energy that matter possesses because of its location or structure

energy stored in bonds between atoms (a type of potential energy)

Convert energy from chemical --> kinetic --> potential

• 1. Energy can be transformed or transferred, it cannot be created or destroyed
• 2. During every energy transfer or transformation, some energy given off as heat contributes to the disorder of the universe

disorder

use energy to build order from disorder

spontaneous

entropy (disorder) because some energy is "lost" at each step

Sunlight --> Producers (plants and other photosynthetic organisms) --> Consumers (including animals); some is lost as heat --> lost as heat

one direction

Chemical elements that can exist is gaseous phase (C, O, N, S)

Chemical elements that exist as solids in soils (P, K, Ca)

• Whether they contain inorganic or organic materials
• and
• Whether they are directly available for use as nutrients or not

Living organisms, detritus

Coal, oil, peat

atmosphere, soil, water

Minerals in rocks

Carbon cycle, Nitrogen cycle, Phosphorus cycle, Water cycle

in all organic molecules

Proteins and DNA

DNA

Petroleum

Sedimentary rock

Global

Global

Local

Global

Free energy (deltaG)

Life avoids decay by virtue of metabolism--building order out of disorder -Erwin Schrodinger

energy that can perform work in the system under uniform conditions (e.g. a cell)

• For a given chemical reaction: ΔG = ΔH - TΔS
• (change in free energy = change in total energy in a close system - temp in Kelvin x change in system's enthalpy)

Decreasing entropy requires more energy

entropy

• High potential energy=low entropy
• Low potential energy=high entropy

0

If cell's reactions are at equilibrium, there is no free energy, thus no energy to do work and the CELL IS DEAD (defining feature of life that an organism is never at equilibrium)

spontaneous, does not require energy

requires energy to proceed

Exergonic and Endergonic

• "Energy outward"
• Releases energy, occurs spontaneously
• ΔG is NEGATIVE

Ex: breakdown of macromolecules, hydrolysis reactions

• "energy inward"
• absorbs energy from surroundings, requires energy to occur
• ΔG is POSITIVE

(initial free energy is lower number than the final free energy)

Ex: synthesis of macromolecules, dehydration reactions

Exergonic (breaking down individual monomers)

-increasing entropy, products have less order than reactants (atoms have less order than monomers)

Endergonic (plants use energy from the sun to do this)

-requires energy to do; decreasing entropy (products have more order than reactants)

• Mechanical
• Transport
• Chemical

using an exergonic process to drive an endergonic one

Ex: co-transport

provides the energy used by the cell to do work

(a lot of potential energy and instability, straining bonds from negative charges)

exergonic and endergonic reactions

couple the energy of ATP hydrolysis to endergonic processes to "do work"

When it lifts its leg to take a step

The motor protein is phosphorylated by ATP which changes its shape, becoming unstable

ATP phosphorylating motor proteins

ATP phosphorylating transport proteins

ATP phosphorylating key reactants (chemically unstable)

endergonic reactions in the cell

The energy doesn't go away, just stores it in the phosphate

proteins

They speed up exergonic chemical reactions

cellular environment: pH and temperature

allosteric inhibition and activation

breaking the glycosidic bond to separate two monomers

EXERGONIC and CATABOLIC (energy released through the breaking of the bonds)

pushes reaction over the barrier, so "downhill" part of reaction can occur

the activation energy

They lower the activation energy

-ase

• Allows substrate to assemble in proper orientation (adding energy by compression)
• Enzyme can stretch the bonds towards 'transition state' conformation
• Provides appropriate micro-environment for reaction to occur
• Brief covalent interaction between side chain of amino acid and substrate

Structure function relationships

the "induced fit" between enzyme and substrate...changes the shape of the protein to allow the reaction to take place

• Co-factors (inorganic metals, like Cu, Mg, Zn, Fe)
• Co-enzymes (organic molecules, like Vitamins)

Another protein or molecule that binds to the site and competes with the substrate to inhibit it from acting

• Mimics, resembles normal substrate
• Binds to the active site
• Often reversible

inhibits the reaction, but binds in other places than the active site...changes shape of the protein and active site is affected so that the substrate cannot fit into the active site

• Bind another part of the enzyme (not active site)
• Enzyme changes shape as a result
• Loses activity

Can inhibit and activate enzyme activity

A protein's function at one site is affected by a protein binding at another site

stabilizes the active form by binding to the REGULATORY site (not active site)

stabilizes the inactive form (keeps it in the OFF position)

binding of one substrate molecule to active site of one subunit locks all subunits in active conformation

Harvesting energy by breaking chemical bonds (redox reactions and electron movement)

Organic compounds (sugars, fats, proteins) + O₂ ----> CO₂ + H₂O + energy (ATP and heat)

potential energy (need to access this energy by "breaking down" the molecule)

electrons!

• Chemical reactions transfer electrons from one reactant to another
• In exergonic reactions, electrons will move from a higher energy level to a lower energy level
• Releasing energy

Transfer electrons during chemical reactions

gaining an electron

losing an electron

EXERGONIC (energy released)

lose potential energy (need to add energy to get them away from the stronger atom, so that is the lower potential energy)

photosynthesis

lose potential energy and energy is released

• Enzymes facilitate this reaction
• Enzymes can be regulated
• Energy is released in discreet steps

• Food donates electrons in the form of H atom
• Electrons are first harvested by NAD+ (electron acceptor)

-ose

Cytosol

Mitochondria

Break down glucose to pyruvate, get electrons (occurs in cytosol)

break down pyruvate to CO₂ (occurs in mitochondria)

use energy collected in NADH to phosphorylate ADP--making ATP! (occurs in mitochondria)

NADH

• Phase 1: Energy investment (use 2 ATP)
• Phase 2: Energy pay off (get 4 ATP, 2 NADH)

Total yield= 2 ATP and 2 NADH

• 1. Glucose is phosphorylated
• 2. Glucose is rearranged
• 3. Glucose is phosphorylated again
• 4. 6C sugar is split into two 3C sugars (isomers)
• 5. Isomerase converst one isomer into the other isomer (G3P)

• 1. 3C sugar is oxidized (loses e- to NAD+ to form NADH) and phosphorylated
• 2. Phosphates used to make ATP from ADP
• 3. Reposition remaining phosphate
• 4. PEP is formed from repositioning of P, very unstable
• 5. P is transferred to make ATP from ADP
• ...if O₂ go to Citric acid cycle, if NO O₂ go to fermentation

• Glucose --> 2 pyruvate + 2 H₂O
• 4 ATP formed - 2 ATP used --> 2 ATP
• 2 NAD⁺ + 4 e^- + 4 H⁺ --> 2 NADH + 2 H⁺

Pyruvate enters into mitochondrion and becomes Acetyl CoA

• 1. Acetyl CoA is attached to oxaloacetate
• 2. CoA is lost and acetyl is joined to oxaloacetate to form citrate
• 3. CO₂ is removed
• 4. ATP made from energy released from loss of CoA (substrate level phosphorylation)
• 5. NADH, and FADH₂ are formed

6 CO₂, 10 NADH, 2 FADH₂, 4 ATP

Bind molecules and make them highly unstable

3 CO₂, 4 NADH, FADH₂, ATP per glucose molecule (multiply times two)

• Moving electrons down ETC, to generate a Proton Motive Force
• Using PMF to produce ATP

• Four large multiprotein complexes
• Located in mitochondria inner membrane
• Electrons move down chain loses energy at every step
• ETC carriers undergo series of redox reactions

• Pumps H+ into the inner membrane space
• Creates a proton gradient across the inner membrane of the mitochondrion

phosphorylate ADP

uses potential energy of proton gradient across membrane to do work

inversely

NADH, FADH₂, proton gradient

34 per glucose molecule

• Vitamin B1 (thiamine): helps remove CO₂ from various organic compounds
• Vitamin B2 (riboflavin): component of FAD and FADH₂
• Vitamin B3 (niacin): component of NAD+ and NADH

• Glycolysis with Fermentation: 2 ATP; uses NADH as oxidizing agent; final electron acceptor=pyruvate or acetylaldehyde (to form lactic acid or alcohol)
• Glycolysis with Respiration: 36-38 ATP; uses NADH as oxidizing agent; final electron acceptor=O₂

• Electron transport chain inhibitor: Binds Fe group in Cytochrome a3
• Prevents the transport of electrons
• Disrupts respiration
• Causes free radicals

• Uncoupling agent: "unhooks" ETC from chemiosmosis
• Shuttles H+ across membrane down H+ gradient
• Eliminates proton motive force, no ATP made

• Light reactions-harvest energy
• Calvin cycle-fix CO₂ into sugar

Endergonic; anabolic; ΔG+

chloroplast

• the light reactions gather energy and transfer it to electron carriers (eg NADPH) or use energy to make ATP
• 1. electrons in chlorophyll are excited by light energy
• 2. The splitting of H2O recovers electron lost in chlorophyll, releases O2 (source of oxygen we are now breathing)
• 3. The electron is passed down ETC and energy is harvested by NADP+ (to form NADPH)
• 4. A H+ gradient established by ETC and splitting of water leads to synthesis of ATP (just like in respiration)

• 1. Energy is captured in Photosystem II-H2O is split into oxygen and hydrogen
• 2. Energy is transferred through Electron Transport Chain (ETC) to Photosystem I
• 3. Photosystem I transfers electrons, reduces NADP+ to NADPH (electron carrier)

Harvests light energy using antenna