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Major functions of the cytoskeleton
Mechanical support, dynamic structure, and motility
Microtubules provide cell with
Support (shape/resists compression), Movement within the cell of chromosomes and organelles, movement of the entire cell
What makes up microtubules?
What scientific theme do microtubules use?
organize microtubule assembly
Centrosome (in microtubules)
two centrioles, organizing center for spindle
Basal body (in microtubules)
one centriole, forms base of flagella or cilia
Common microtubule structures
- Cilia (windpipe, fallopian tubes, protists)
- Flagella (sperm, protists)
Microtubules are arranged in what kind of structure?
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
Which way to dynein motors move vesicles in the cell?
Towards the nucleus
Which way to kinesin motors move vesicles in the cell?
Away from the nucleus
What would you see in a cross section of a flagellum?
a circle of 9 bundles and 2 microtubules
Microtubules diameter and subunit
25 nm, tubulin
Microfilaments diameter and protein subunit
7 nm, actin
Microfilaments provide cell with...
support (resist pulling), changes cell shape, contractile forces (muscle, cell division furrow, cell motility [pseudopodia])
Microfilaments use what kind of motors to contract the muscle?
Parts of the microfilament involved in the amoeboid movement (changing a cell's shape)
- Cortex (outer cytoplasm): gel with actin network
- Inner cytoplasm: sol with actin subunits
- Extending pseudopodium
What motor protein is used to move vesicles from ER to the Golgi?
Intermediate Filaments diameter and protein subunit
8-12 nm; keratin, lamin, and others
Intermediate Filaments provide cell with
support (cell shape), anchorage of nucleus, nuclear lamina
Keratins look like
Twizzlers pull and peel
What are the three types of filaments?
Microtubules (made of tubulin subunits), Microfilaments (made of actin subunits), and Intermediate Filaments (made of keratin or lamin)
Which motor protein is abundant in muscle cells?
Keratins are important for making structure of...
hair cells, skin cells, nail beds (all dead)
Why are membranes important? (5)
- Selective permeability
- Separating cell from non living surroundings
- Creates unique environment within cell for specialized reactions
- Asymmetric protein distribution
- Cell communication, cell signaling
Cells enduring a very hot environment would have phospholipids with...
saturated fatty acid chains
Components of the membrane (3)
- Membrane proteins (integral and peripheral)
- Membrane carbohydrates (glycoproteins, glycolipids)
Integral membrane proteins are located
embedded in the membrane spanning the entire phospholipid bilayer; they are amphipathic
Peripheral membrane proteins are located
on the surface of the membrane and don't span the bilayer, only interacting with the phospholipid head
Peripheral proteins lack
a hydrophobic region
A protein that served as a "channel" through the membrane would likely be...
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)
Six major functions of membrane proteins
- Enzymatic activity
- Signal transduction
- Cell-cell recognition
- Intercellular joining
- Attachment to cytoskeleton or ECM
The endomembrane system
makes glycoproteins and glycolipids, and places them on outer portion of plasma membrane
carbohydrates attached to proteins on the outside of the cell membrane
Sidedness of membrane is determined by
Solute characteristics determine how the solute is transported: Nonpolar substances move
freely across the membrane
Solute characteristics determine how the solute is transported: Nonpolar substances
are hindered by the bilayer
facilitate movement of polar substances, and are very specific for a particular solute
Two kinds of transport proteins:
Channel proteins (passive transport) and carrier proteins (passive and active transport)
Examples of passive transport of solute across membrane
Diffusion and facilitated diffusion
the tendency for molecules to spread out evenly into an available space
In diffusion, each molecules moves
randomly, but population of molecules can be directional
Diffusion of solute moves in direction of
from high concentration to low concentration
diffusion of water across a selectively permeable membrane
When an animal cell is hypotonic in a solution...
there are more solutes in the cell than in the surrounding solution, causing the cell to fill with water and explode
When an animal cell is hypertonic in a solution...
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
When an animal cell is isotonic in a solution...
The concentration of solutes is the same inside and outside the cell
When a plant cell is hypotonic in a solution...
there are more solutes in the cell than in the surrounding solution, which makes the cell turgid-the normal state for a plant cell
When a plant cell is hypertonic in a solution...
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
When a plant cell is isotonic in a solution...
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
Facilitated diffusion requires...
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
Energy is needed in active transport because
the solutes move against the concentration gradient
Active transport uses
carrier proteins (NOT channel proteins)
An example of active transport
How would a steroid hormone move across the membrane into the cell?
By simple diffusion through the membrane
If you stay in a pool too long, your fingers turn wrinkly. Why?
Skin cells become full of water because the water is hypotonic
Three kinds of animal cell junctions
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
What type of animal cell junction is analogous to the seal between bathroom tiles?
Plant cell junction
communication between two single cells
Yeast mating types
alpha and A
signaling by direct contact
Examples of local communication
Gap junctions, cell-to-cell communication, paracrine, and synaptic
only cells nearby will receive the signaling molecules (exocytosis)
between two nerve cells
What type of proteins are used for cell-cell recognition?
Example of local and long distance signaling
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
Synaptic signaling summary
- 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
Hormonal long distance signaling steps
endocrine cell-->blood vessel-->hormone travels in bloodstream to target cells-->target cell
Long distance signaling in plants (4 steps)
- 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
Major themes of Cell Communication (3)
-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
Reception in signal transduction
signal molecules bind to receptor
Transduction in signal transduction
signal is transmitted to response element
Response in signal transduction
output of signal
Steps in signal transduction (3)
Reception, transduction, and response
The signal transduction pathway
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)
Receptors in signal transduction can be in
the cell and the membrane
Often, a ligand binding a receptor will
change the shape of the receptor protein
Ligand-binding receptor is an example of which theme in biology?
Two classes of receptors
Membrane bound receptors and intracellular receptors
Membrane bound receptors
Span the membrane
Located in cytoplasm or nucleus
What type of receptor would bind a polar ligand?
A membrane bound receptor
Two types of ligands
Water soluble/polar ligands and hydrophobic/very small molecular ligands
Intracellular receptors can sometimes be
"transcription factors" which bind DNA and turn genes on or off
Three major families of membrane receptors
G-protein linked receptors, receptor tyrosine kinase, and ion channel receptors
Membrane receptors are probably
integral membrane proteins and amphipathic
G-protein linked receptor structure
a-helix secondary structure
G-protein linked receptor involved in
sensory perception (sight, smell), diseases
After the G-protein linked receptor is activated, it
changes its shape, therefore changing its function
Receptor tyrosine kinase is both a
receptor and an ezyme
the receptor functions as a dimer
phosphorylates to neighboring receptor's tyrosine amino acids
Steps in activation of tyrosine kinase
Signal molecule attaches to receptor to form a dimer
Phosphorylates with another
activates cellular responses
Ion channel receptors are
commonly found in the nervous system, in which the signal molecule is a neurotransmitter
The Na+/K+ pump is
an ion channel receptor function in local cell-cell communication
Three types of membrane receptors
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
Signal is transduced by
Relay molecules are often
proteins that change shape as signal is 'carried' through the pathway and are phosphorylated
Second messengers are relay molecules which are
NOT proteins, but they broadcast the signal
Common second messengers
cAMP and Ca2+
Cyclic AMP is
an RNA molecule
Steps in cAMP
cAMP-->activates a kinase-->kinase phosphorylates to a target protein-->target protein activity changes
cAMP involved in what kind of reaction?
When scared, releases adrenaline
Ca2+ acts as a second messenger is what kind of response?
When your hand touches fire, Ca2+ is released from ER to make the microfilaments contract and pull your hand away from the fire
Case studies involving the malfunctioning of signaling molecules
Cholera and Viagra
What happens in cholera?
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
Why does erectile dysfunction happen?
- 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
Each signal or activated relay protein must be
transient so the cell can continue to respond to new environmental cues
Reversibility in signal transduction
active state must be reset
Ex: phosphorylation-dephosphorylation; cAMP to AMP, GTP to GDP; Ca2+ gradients re-established
Metabolism is the
sum of all chemical reactions in a cell
What are the two categories of chemical reactions in a cell?
catabolic and anabolic
Catabolic reactions in a cell
pathways break down products to release energy
Anabolic reactions in a cell
pathways synthesize products (energy can be stored in bonds between atoms)
Metabolism uses what theme biology?
Energy is the
capacity to cause change
Potential energy is
energy that matter possesses because of its location or structure
Chemical energy is
energy stored in bonds between atoms (a type of potential energy)
How are organisms energy transformers?
Convert energy from chemical --> kinetic --> potential
The two "rules" of Thermodynamics
- 1. Energy can be transformed or transferred, it cannot be created or destroyed2. During every energy transfer or transformation, some energy given off as heat contributes to the disorder of the universe
Entropy is a measure of
To reduce entropy, we must
use energy to build order from disorder
A process that occurs without energy input is
The process of transferring or transforming energy contributes to the overall
entropy (disorder) because some energy is "lost" at each step
The flow of energy in an ecosystem
Sunlight --> Producers (plants and other photosynthetic organisms) --> Consumers (including animals); some is lost as heat --> lost as heat
Chemicals cycle, while energy flows in
Global cycling in Biogeochemical cycles
Chemical elements that can exist is gaseous phase (C, O, N, S)
Local cycling in Biogeochemical cycles
Chemical elements that exist as solids in soils (P, K, Ca)
The four main reservoirs that nutrients cycle through are defined by
- Whether they contain inorganic or organic materials
- Whether they are directly available for use as nutrients or not
In Biogeochemical cycles, organic materials available as nutrients (Reservoir A) are
Living organisms, detritus
In Biogeochemical cycles, organic materials unavailable as nutrients (Reservoir B) are
Coal, oil, peat
In Biogeochemical cycles, inorganic materials available as nutrients (Reservoir C) are
atmosphere, soil, water
In Biogeochemical cycles, inorganic materials unavailable as nutrients (Reservoir D) are
Minerals in rocks
The four important cycles
Carbon cycle, Nitrogen cycle, Phosphorus cycle, Water cycle
Where is carbon found in our bodies?
in all organic molecules
Where is nitrogen found in our bodies?
Proteins and DNA
Where is phosphorus found in our bodies?
Where is water found in our bodies?
Where are the major reservoirs where carbon is found?
Where are the major reservoirs where nitrogen is found?
Where are the major reservoirs where phosphorus is found?
Where are the major reservoirs where water is found?
What are the general features of the carbon cycle? (how is it obtained, global or local?)
What are the general features of the nitrogen cycle? (how is it obtained, global or local?)
What are the general features of the phosphorus cycle? (how is it obtained, global or local?)
What are the general features of the water cycle? (how is it obtained, global or local?)
Measuring the energy that can perform work in the cell is determined by the change in
Free energy (deltaG)
What is life?
Life avoids decay by virtue of metabolism--building order out of disorder -Erwin Schrodinger
Gibbs Free Energy (G)
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
Water moving from a high potential energy to low potential energy contributes to
- High potential energy=low entropy
- Low potential energy=high entropy
Reactions at equilibrium have a ΔG=
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)
ΔG<0, the process is....
spontaneous, does not require energy
ΔG>0, the process....
requires energy to proceed
Two types of reactions in metabolism
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
What type of reaction is breaking down glucose?
C6H12O6 + 6O2 ---> 6CO2 + 6H2O
Exergonic (breaking down individual monomers)
-increasing entropy, products have less order than reactants (atoms have less order than monomers)
What type of reaction is creation of glucose?
6CO2 + 6H2O ----> C6H12O6 + 6O2
Endergonic (plants use energy from the sun to do this)
-requires energy to do; decreasing entropy (products have more order than reactants)
Cells do three kinds of work
Cell does work by energy coupling...
using an exergonic process to drive an endergonic one
provides the energy used by the cell to do work
(a lot of potential energy and instability, straining bonds from negative charges)
ATP can be used to couple...
exergonic and endergonic reactions
couple the energy of ATP hydrolysis to endergonic processes to "do work"
When is a motor protein unstable?
When it lifts its leg to take a step
The motor protein is phosphorylated by ATP which changes its shape, becoming unstable
Example of cell doing mechanical work with ATP
ATP phosphorylating motor proteins
Example of cell doing transport work with ATP
ATP phosphorylating transport proteins
Example of cell doing chemical work with ATP
ATP phosphorylating key reactants (chemically unstable)
Energy released from exergonic reactions is used for...
endergonic reactions in the cell
The energy doesn't go away, just stores it in the phosphate
They speed up exergonic chemical reactions
Enzyme activity is affected by
cellular environment: pH and temperature
Regulation of enzyme activity
allosteric inhibition and activation
breaking the glycosidic bond to separate two monomers
EXERGONIC and CATABOLIC (energy released through the breaking of the bonds)
Activation Energy (EA)
pushes reaction over the barrier, so "downhill" part of reaction can occur
Exergonic reactions happen at one point, the rate at which they happen depends on
the activation energy
How do enzymes speed up chemical reactions to occur spontaneously?
They lower the activation energy
The suffix of enzymes
Enzyme mechanisms for lowering EA
- 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
Enzymes are an example of what biological theme?
Structure function relationships
What is "the handshake" when referring to enzymes?
the "induced fit" between enzyme and substrate...changes the shape of the protein to allow the reaction to take place
Enzymes have non-protein 'helpers' that promote enzyme function
- Co-factors (inorganic metals, like Cu, Mg, Zn, Fe)
- Co-enzymes (organic molecules, like Vitamins)
Competitive inhibitors of enzymes
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
Noncompetitive inhibitors of enzymes
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)
Cellular respiration: the bottom line (formula)
Organic compounds (sugars, fats, proteins) + O2 ----> CO2 + H2O + energy (ATP and heat)
Chemical energy is a type of
potential energy (need to access this energy by "breaking down" the molecule)
Energy comes from movement of...
- 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
Reduction-Oxidation (redox) reactions
Transfer electrons during chemical reactions
gaining an electron
losing an electron
When electrons move from less electronegative atoms to a stronger electronegative atom, the process is
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)
Solar energy converted to chemical energy by....
During cellular respiration, electrons
lose potential energy and energy is released
- Enzymes facilitate this reaction
- Enzymes can be regulated
- Energy is released in discreet steps
Why do we need food?
- Food donates electrons in the form of H atom
- Electrons are first harvested by NAD+ (electron acceptor)
Where does glycolysis happen?
Where does the citric acid cycle happen?
Break down glucose to pyruvate, get electrons (occurs in cytosol)
Citric Acid cycle
break down pyruvate to CO2 (occurs in mitochondria)
use energy collected in NADH to phosphorylate ADP--making ATP! (occurs in mitochondria)
Glycolysis and citric acid cycle yield some ATP, but mostly yield
The two phases of glycolysis
- Phase 1: Energy investment (use 2 ATP)
- Phase 2: Energy pay off (get 4 ATP, 2 NADH)
Total yield= 2 ATP and 2 NADH
Steps in Phase I of glycolysis (investment phase)
- 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)
Steps in Phase II of glycolysis (pay off phase)
- 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
Net gain in glycolysis
- 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
Citric Acid cycle steps
- 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
Net gain in glycolysis and citric acid cycle
6 CO2, 10 NADH, 2 FADH2, 4 ATP
CoA and phosphate groups...
Bind molecules and make them highly unstable
Citric Acid cycle net gain
3 CO2, 4 NADH, FADH2, ATP per glucose molecule (multiply times two)
Oxidative phosphorylation steps
- Moving electrons down ETC, to generate a Proton Motive Force
- Using PMF to produce ATP
Electron Transport Chain
- 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
The movement of electrons down the ETC
- Pumps H+ into the inner membrane space
- Creates a proton gradient across the inner membrane of the mitochondrion
ATP synthase uses proton gradient to
uses potential energy of proton gradient across membrane to do work
The pH and number of protons is ____ proportional
In oxidative phosphorylation, electrons from ____ and ___ are used to create a ____
NADH, FADH2, proton gradient
How many ATP are generated in oxidative phosphorylation?
34 per glucose molecule
Co-enzymes in respiration
- 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
Efficiency of Fermentation vs Respiration
- 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
Two stages of photosynthesis
- Light reactions-harvest energy
- Calvin cycle-fix CO2 into sugar
Is photosynthesis endergonic or exergonic? anabolic or catabolic?
Endergonic; anabolic; ΔG+
Photosynthesis occurs in
Phase I of photosynthesis
- 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)
Light reaction in three acts
- 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)
Photosystem II in photosynthesis light reaction
Harvests light energy using antenna
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