biology 110

entropy

"lost", degraded (low quality) energy -energy still there, but degraded into disordered states (states that are the same as their surroundings) -it's unusable energy that can't do work

truly disordered high entropy stated

All matter would be completely mixed up and would then form a constant gray volume

free energy

Alternative principles and equations that are more easily applicable to open systems are attained by considering concept of free energy

explanation of entropy

Entropy is really a measure of possible arrangements of atoms (or energy) that would give the same overall state. More arrangements means more entropy. -When atoms are concentrated into a smaller volume or separated into distinct volumes, there are fewer possible ways to arrange them and get the same overall state, and thus entropy is reduced.

membrane is complex

real membranes are much more complex than phospholipid bilayer. Membrane structure and properties modified by integral and peripheral membrane proteins. Membrane proteins themselves are often modified chemically by carbohydrates -> glycoproteins membrane also contains other kinds of lipids: cholesterol and glycolipids

phospholipid and bilayer structure: amphipathic

remember, phospholipids are part polar (hydrophilic) and part non-polar (hydrophobic), or amphipathic

REMEMBER

deltaG = deltaH - TdeltaS

studying energy

energy is sometimes defined as "the ability to do work", but this definition quickly gets circular since work is sometimes defined as "the energy transferred from one system to another".

mitochondrial function

energy metabolism, in particular cellular respiration to provide energy. Most of the action takes place at mitochondrial membranes. So structure of membranes critical for cellular respiration

kinetic energy

energy of objects in motion

answer to question 1

energy to decrease entropy comes from outside the organism. Life extracts energy from food or sunlight, and uses it to build up ordered regions.

isolated system

equations expressing the 1st and 2nd law only apply in isolated systems. No energy or matter can enter or leave an isolated system. -Repeat, the fundamental ideas are true everywhere, but the associated precise equations only apply in isolated systems.

Keq

equilibrium constant Keq = [B]/[A]

cytoskeleton

eukaryotic cells are relatively large; they need internal supporting cytoskeleton to maintain shape and mechanisms for changing shape and moving. Less important in plants (but still present). Plant cells use cell wall and osmotic pressure from central vacuole to maintain shape. Also plant cells usually don't change shape or move. multiple types of protein fibers make cytoskeleton.

Second law of thermo

extremely fundamental principle that applies to atoms and molecules as well as energy. Can be expressed several ways: -no energy exchange completely efficient, OR, usable energy decreases & disorder (entropy) increases. (entropy is just measure of disorder) -2nd law says total entropy always increasing. Useful energy is constantly being converted to unusable entropy. You can't keep all the useful energy that you have, therefore perpetual motion is impossible. -second law says you go from low to high entropy, but not reverse. Things don't concentrate or separate by themselves.

carriers

for larger molecules carriers - saturation kinetics. Carries one molecule at a time. Carriers become saturated when trying to move more as concentration increases. Would be graphed as a curve, starting at the bottom left corner of the graph. analogy: carrier is like a small ferry boat. Cars can only cross one or a few at a time.

Channels

generally for ions and small molecules channels - linear kinetics. Channel opens path for many molecules in succession. Channels carry proportionately more as concentration increases. Would be graphed as a straight line. analogy: channels are like a bridge. More cars appear, more cross.

hypertonic solution

higher concentration of solutes than inside cell. Cell in hypertonic solution loses water. Will shrivel up

phospholipid and bilayer structure

hydrophilic head: phosphate (maybe modified) - oriented towards water hydrophobic tail - fatty acid chains - oriented away from water, oriented towards each other. the central hydrophobic part of bilayer forms major barrier between inside and outside. To be permeable substances have to cross. this region (directly through the barrier or through some "hole" in it)

types of membrane transport: simple diffusion

if membrane permeable to substance, and concentration differs across the membrane, then substance will show net movement from high to low concentration by process of simple diffusion. When concentrations differ we say there is a "concentration gradient" and natural movement is with/down the gradient. Movement down gradient continues until concentrations equalize, then no further net movement. simple diffusion is first type of membrane transport.

permeability of pure phospholipid bilayer

if the membrane were purely a phospholipid bilayer (no holes/alterations created by other components), it would be permeable to: -nonpolar molecules - very permeable -small polar molecules - somewhat permeable and it would be impermeable to: -large polar molecules - impermeable -charged molecules/ions - very impermeable

changing membrane components with temp

imagine temperature decreases. The original membrane is now less fluid. Need to restore original desired fluidity, but at lower temp. Cell makes new phospholipids with more unsaturated and shorter fatty acids. -cells can also use "desaturase" enzymes to alter the fatty acids that are already present, making double bonds in them.

tight junctions

impermeable connections around the outside of cells. Found in epithelial cell layers. Often separates a lumen of organ from rest of body, prevents organ contents from leaking into rest of the body

extracellular matrix

in metazoans (multicellular animals) cells often organized into tissues (groups of cells with similar function) Extracellular matrix (ECM) holds cells into tissue. -ECM consists of proteins and complex carbohydrates, made inside cells and then secreted by exocytosis. -when relatively few cells, ECM forms "connective tissue". connective tissue includes ligaments and tendons.

equilibrium with not spontaneous reactions

in not spontaneous reaction, reaction doesn't proceed (or not much), so reactants predominate, "equilibrium lies to left" -Keq < 1 (more reactant A than product B)

equilibrium with spontaneous reactions

in spontaneous reaction, reaction proceeds (wholly or mostly), so products predominate at equilibrium, "equilibrium lies to the right (or with the products)". -Keq > 1 (just a technical way of saying more product B than reactant A)

Intermediate filament structure

intermediate in thickness between microfilaments and microtubules. Made of several different kinds of fibrous protein subunits that are arranged into a cable (not hollow, thinner than a microtubule)

Endomembrane system

internal endomembrane system in eukaryotic cells (endo = inside, opposite of exo). Includes: Endoplasmic reticulum (ER) Golgi complex (or Golgi apparatus) vesicles

plastids and pigments

Plastids: general class of plant-specific organelles. Most important are chloroplasts: site for capturing light energy in photosynthesis. Plastids often contain pigments that absorb certain colors of light and make plastids appear colored. In the case of chloroplasts: green chlorophyll. Chlorophyll absorbs red and violet ends of spectrum, color you see is what's left, which is green. Carotene absorbs blue-violet, emits orange color.

primary lysosomes

Primary lysosomes derive from trans face of Golgi and fuse with vesicles derived from endocytosis.

DNA -> RNA -> protein

RE-EMPHASIZE: protein sequence determines structure determines function. The protein sequence comes from mRNA sequence, which was copied from DNA sequence.

Rough Endoplasmic Reticulum (RER)

RER has attached ribosomes -> rough, bumpy-looking surface in the electron microscope. RER structure: composed of interconnected flattened sacs (not tubules). Concentrated near nucleus in cytoplasm. Outer membrane of nuclear envelope often has ribosomes. The outer nuclear membrane is part of the RER.

electromagnetic (radiant) energy

light energy, called EM radiation (includes infrared, ultraviolet, x-rays, gamma rays)

glycolipids

lipids with carbohydrates attached.

hypotonic solution

lower concentration of solutes than inside the cell. Cell in hypotonic solution gains water. Will expand

mRNA

messenger RNA. RNA subset copied from DNA in the euchromatin whose sequence determines sequence of amino acids in polypeptides.

membrane transport

molecules can also move one at a time across membranes, called "membrane transport"

motor proteins Dynein and kinesin

motor proteins Dynein and Kinesin interact with microtubules to generate motion. Dynein and kinesis move material (vesicles) opposite directions on microtubule "railroad tracks" Cilia and flagella also use dynein to move microtubules against each other to generate whip and wave motions.

motor proteins

movement and shape changes use motor proteins to convert chemical energy to mechanical motion.

Myosin

myosin interacts with actin microfilaments. This creates amoeboid motion. Actin-myosin basis of contraction in muscle cells.

smooth endoplasmic reticulum

no ribosomes on surface of smooth endoplasmic reticulum, SER -> no bumps, looks smooth in the electron microscope. Structure: network of interconnected tubules only (not sacs). Dispersed throughout much of cytoplasm.

rRNA

rRNA catalyzes (speeds up) the dehydration synthesis reaction of covalent bonds. Unusual in that most other catalysts in the cells are proteins. rRNA speeds up a reaction that is normally very slow (has large activation energy).

transport kinetics

rate of transport vs concentration

Type 3: active transport

-Cell can concentrate a molecule by using energy to actively move molecules from low to high concentration, hence active transport. -movement from low to high concentration said to be "against/up the gradient" -requires specific transporter protein. -requires energy (usually ATP) to move against the gradient (opposite to direction of diffusion) -allows active control of cell contents by expending energy, rather than relying on the already existing gradients. -three types of transporters in active transport: uniporters, symporters, antiporters.

things needed for life

-Cells need energy to live, and they need matter, that is, atoms of the various elements to make molecules. -energy and the elements are all things that cells can't make; they must come from the outside. -while energy and the elements can't be made and must come from the outside, living things do pass them from one organism to another.

First law of thermodynamics

-First law of thermodynamics, energy cannot be created or destroyed. Energy converts from one form to another, but total amount of energy does not change. First law is not changed by special relativity (E=mc^2). Mass and energy are "equivalent". Mass and energy are always in proportion to each other. When one increases or decreases, the other increases or decreases by the same amount. Since mass and energy are equivalent, you may have to consider mass when you evaluate the energy of an object, and consider energy when you evaluate mass, but total mass and total energy are both conserved independently. No mass is ever created or destroyed. No energy ever created or destroyed. They just change form.

interesting dietary consequence of controlling fatty acid mobility #1: fish oil pills

-If unsaturated fatty acids are healthier than saturated ones, would it be better to eat the fatty acids from warm-blooded animals growing at internal 37 deg. C or cold blooded fish swimming in cold water (5-15 deg C)? -many people even take fish oil pills, triglycerides extracted from fish living in cold arctic water containing these healthy fatty acids. -fatty acids from cold water fish are more unsaturated and generally healthier than beef or chicken.

free energy in an equilibrium

-Individual molecules: A (reactant) ---> B (product) -Groups of molecules: A (or B) ----> mix of A and B -reactions are generally reversible; go both ways. Individual molecules of A can become individual molecules of B and likewise for B becoming A

problem of thermodynamics

-Problem: cells create/maintain order (homeostasis). Doesn't this violate the 2nd law? -no, equation of the second law describes total change in isolated system. If you put insulated box around something, 2nd law has to hold inside box overall. But inside that isolated system energy can be used to create order in one part of the system (reducing entropy somewhat there) while entropy increases by a greater amount in another part, so the net is an increase in entropy over the entire isolated system.

does steam or water have more entropy?

-Steam: steam is evenly spread out over a large volume, while water is confined to a much smaller volume. -steam, like all gases, can fill the volume of a container -recall more atomic arrangements means more entropy. There are many ways atoms/molecules in steam can be arranged in that volume, thus more entropy. -on the other hand, water, like all liquids, has to stay within a "puddle". Fewer ways that water atoms/molecules can be arranged if they have to stay in the puddle, thus less entropy. -generally more disorder, more entropy, in gases, and more order, less entropy, in liquids.

active and coupled transport

-all active transporters also saturate, like carriers in facilitated diffusion. -additional possibility for transport agains gradient , coupled transport

Connections. between cells

-another function of membrane proteins - to form connections between cells. -three kinds of specialized connections: tight junctions, anchoring junctions, and communicating junctions

diffusion drives much membrane transport

-basic "force" behind single molecules crossing membranes is diffusion.

exocytosis

-bulk movement out of cell. -Vesicle fuses with cell membrane, releases contents. -Protein secretion is one example

two situations to consider

-cells change membrane components to compensate for changes in environmental temp. -cells with different natural temperatures have different natural membrane components. Goal in both: keep membrane fluidity constant.

application of free energy

-free energy predicts the outcome of reactions in any system (isolated or open). -free energy changes predict spontaneity of a reaction and thus relative amount of products at the end of a reaction.

diffusion

-like the spreading of dye in water, diffusion is movement from an area of high concentration to one of low concentration. -diffusion is energetically favorable (towards a lower energy state), creating a tendency that moves molecules from high to low concentration. -diffusion really results from the effect of entropy.

Endoplasmic Reticulum

-major component of endomembrane system -Structure: network of interconnected tubules ("little tubes") and interconnected flattened sacs. Interior called lumen. -interior of any organ or organelle is called the lumen. For example, lumen of small intestine is the central canal where food gets digested. -interconnected lumen of ER is continuous throughout cytoplasm, could travel inside the lumen throughout (like in a tiny submarine)

osmosis

-membranes are permeable to water. But not common to many common solutes (sugars, amino acids, ions, etc.). -high concentration of impermeable solutes inside cell. These don't change and can't move much. -But concentration of solutes outside cell changes. -Since solutes can't move, water responds by moving in/out of cell by osmosis.

Single molecule membrane transport

-molecules need to cross these fluid membranes. -individual (or a few) molecules can cross the membrane at a time via membrane transport. -several varieties of membrane transport, some straight through, some using membrane proteins to provide a pathway.

lowest energy state

-reactions that release free energy happen spontaneously and release energy. -reactions that don't release free energy (that require energy) simply don't happen spontaneously. -So the result is systems are always releasing free energy when the can and spontaneously heading to the lowest energy state. -if the outside environment has lost of energy (e.g. is hot), it may gain energy, but take that source of energy away and a the system will again tend to the lowest energy state.

RER function

-site for ribosomes that are synthesizing proteins for three sets of destinations in the cell: 1) proteins to be incorporated into membranes 2) proteins to be exported from cell 3) proteins destined to stay inside other organelles -during synthesis, proteins of these three types made on RER will become separated from the cytoplasm by the ER membrane. -newly synthesized proteins for membrane and export and other organelles are segregated inside the lumen. All or parts of these proteins enter the ER lumen from the cytoplasm. -chemically modifies these proteins while in lumen (especially modified by adding carbohydrates, "glycosylation") -sends vesicles (small membrane-bound sacs, approximately spherical, containing protein cargo) away from RER, beginning the protein trafficking pathway that send these proteins to correct final destinations

interesting dietary consequence #2: where do oils vs fats come from?

-solid fats from warm-blooded (37 deg C) animals -oils from plants generally growing at lower temp than 37 deg C -but not all plants are equal. More unsaturated oils come from temperate plants. Warmer tropical plants have less unsaturated (more saturated) oils. Compare the less healthy palm oil (50% sat) grown in the tropics versus healthier canola (7% sat) and corn oil (13% sat) gown in the temperate climate around here

Golgi complex/Golgi apparatus structure

-stack of flattened sacs, generally near nucleus, one to several per cell. -Cis face: side towards nucleus, receives transport vesicles from ER, entrance door -Trans face: side away from nucleus, sends vesicles away from Golgi exit door. -Remember, in the cis face, out the trans face

overview of thermodynamics

-thermodynamics predicts the future. It specifies which events (or reactions or processes) will happen and which will not. -1st and 2nd laws can be used to predict the future in isolated systems. -1st law: any reaction in isolated system that gains or loses energy won't happen. -2nd law: any reaction in isolated system that loses entropy won't happen. -combined: any reaction in an isolated system that conserves energy and gains entropy will happen. -1st law regulates the amount of energy (its always the same). 2nd law regulates the distribution (arrangements ) of energy (and mass).

Quantitation of free energy

-total internal energy = enthalpy = H -useful energy = free energy = G Unusable energy is a function of Entropy (= S) and temperature (=T) -total energy = usable + unusable --> H = G + TS -but since we can only measure changes, it would be: delta H + delta G + delta TS -Rearrange and consider when T is constant: delta G = delta H - T delta S -delta = end - beginning. If quantity goes up, delta is positive. If quantity goes down, delta is negative.

osmosis

-water moving in/out of cell -solutes can't cross membrane, so water will move, in the opposite direction. For example, rather than losing solutes to equalize concentrations, cells gain water to dilute the solutes and equalize concentrations.

type 2: facilitated diffusion

-what about charged or large polar molecules? pure lipid bilayers are not permeable to them. -these can cross membrane using a carrier protein or a channel protein, each type of carrier or channel is specific for a particular type of molecule. Carriers/channels are two different kinds of integral membrane proteins with different properties. -transporting molecules that cannot cross membrane by themselves down their concentration gradient is called facilitated diffusion. that is, diffusion facilitated by carrier/channel. Also called passive transport (passive, since no energy is required). -unlike simple diffusion where whatever is permeable crosses the membrane, cells can control what crosses the membrane in facilitated diffusion.

exergonic reactions

-when delta G is less than 0, it is a spontaneous reaction, exergonic. -Spontaneous reactions happen "spontaneously", which really means without any additional input of energy. Products form. End of reaction contains lots of products. -deltaG is negative in exergonic reactions (G, or free energy, at end is less than G at beginning)

if life is compatible with the 2nd law, then there are three follow up questions:

1) where does the energy that life uses to oppose entropy come from? 2) what is the system that we can have an isolation box around to show that we follow the 2nd law inside it? 3) where does the disorder decrease in that box and where does it increase? -but these are all easily answered, so the 2nd law of thermodynamics is no reason to reject Nat. Selection

order of events in protein synthesis

1. mRNA transcribed in nucleus (euchromatin) 2. mRNA exits via nuclear pores 3. mRNA meets small subunits in cytoplasm 4. mRNA - small subunit joined by large subunits 5. mRNA is translated into protein

Reversible reactions

A and B can go forward and back, but do this at different rates, so any starting mixture of A and B will come to an equilibrium, with a set mixture of A and B. -amount of A and B in the mixture determined by the relative rate of forward and back, which is also determined by the free energy difference between A and B. -Recall equilibrium is the dynamic endpoint of a reaction, the place where a reaction ends up where individual A becomes B and B becomes A, but no net change in the mixture. -After equilibrium is reached, there also isn't any change in free energy, deltaG = 0. No net change in the molecules, so no change in the total energy or entropy. -However, approaching equilibrium from any other state releases free energy.

a major distinction between chloroplasts and mitochondria

Chloroplasts are larger and have a more extensively folded innermost membrane, the thylakoid. all mitochondria in living eukaryotes are alike. Chloroplasts are distinct with somewhat different chlorophylls and somewhat different structures.

Dynamic functions of the cytoskeleton: shape

Cytoskeleton confers shape and organization to cell, but its a dynamic (not a static) shape Changes in cytoskeleton allow changes in shape and movement. Some examples: -actin filaments move against each other -microtubules will lengthen and shorten -microtubules completely rearrange for cell division. Old structures disassemble, and spindles form from chromosomes to separate during mitosis.

Experimental evidence of membrane fluidity

Frye and Edidin. did experiment to confirm and measure membrane fluidity. -label membrane proteins in two different cells: human cell with red label, mouse cell with green label. -fuse cells and observe over time. If they saw that the red and green stay separate, then the membrane is static. But if they see that the red and green mix, then the membrane is fluid. -Result: red and green mixed, so they found that the membrane is fluid.

open systems

Hard to apply these equations to biological systems, which are inherently open systems. Matter and energy enter and leave.

Free energy determines whether energy is released.

If products have less free energy, then free energy is released (spontaneous reaction). On the other hand, if products have more free energy, then free energy must be supplied if you want to force the reaction to happen (won't happen spontaneously). -look at graphs on slides

chloroplast function continued

In most common form of photosynthesis, CO2 is reduced using electrons from water (water is oxidized). When water is oxidized, O2 is released, the source of all O2 in our atmosphere. like mitochondria, chloroplasts are also dynamic. They especially move/change in response to light. Chloroplasts have a number of other functions, including synthesizing monomers. membrane structure also critical for photosynthesis.

Ribosome structure

Large complex of noncovalently associated ribosomal RNA (rRNA) and protein assembled in nucleolus, found in cytoplasm. Some ribosomes attached to membranes, some are free in cytosol 5 rRNA components and >50 protein components molecular weight of 2-3 million Daltons large and small subunits Euk. ribosomes are larger, but similar to prok.

Lysosomal recycling

Lysosomes are used to recycle "old" organelles. In this case, primary lysosome fuses with a special double-membraned vesicle built around an "old" organelle, called the autophagosome. After fusion, the contents are degraded, allowing the products to be recycled and reused by the cell. Recent evidence suggests this recycling increases with exercise, may prove part of the benefits of exercise. Experimentally extending life span (which can be done in lab animals, by greatly restricting calories in diet) also enhances recycling. Both exercise and extending life span somehow "keep cells young", by enhancing recycling.

how lysosomes are formed

Lysosomes formed from combining two directions. in the outbound direction, primary lysosomes bud off from trans Golgi, like secretory vesicles, but primary lysosomes don't fuse with plasma membrane, instead take a different path. in the inbound direction, vesicles from endocytosis engulf ingested material; this material accumulates in endosomes. Fusion of inbound endosomes with outbound primary lysosomes yields secondary lysosomes, which break down ingested material. Degraded contents (including monomers from hydrolyzed macromolecules) can then be used by the cell. This is how cells take in/digest (some of) their food. (review picture on slide 7 of second set of notes)

Mitochondria

Mitochondria are power plant of cell.

Mitochondrial evolutionary history

Mitochondria original free-living bacteria, entered early photo-eukaryotic cells (became endosymbionts) they eventually lost ability to live independently and lost most of their DNA. Retained some DNA involved in ribosomes and translation and the key energy metabolism function. Reflecting free-living bacterial past, mitochondria only arise fro preexisting mitochondria. They are self-replicating inside the cell. the cell can't make more. Since they're part of the cytoplasm, mitochondria inherited only through the egg (mother) not the sperm (father). Egg has cytoplasm, with mitochondria, whereas part of the sperm that enters egg on fertilization is nucleus, with nuclear DNA, but no cytoplasm and no mitochondria.

Basal lamina

Special ECM organized into thin sheets forms basal lamina (or basement "membrane", NOT a lipid bilayer) Basal lamina separates epithelial cells (cells that form layers, often surrounding internal cavities) from rest of body. Basal lamina secreted from basal surface (surface opposite of lumen) Basal lamina determines orientation of epithelial cells, making them polar. Basal surface is usually different from apical surface (surface next to the lumen)

SER Function

Specialized function: site of phospholipid and thus membrane synthesis. Site of cholesterol and other steroid synthesis. Site of detoxification (especially in the liver of animals). Modify and break down foreign substances (toxins, drugs). Activity of many drugs is limited by being broken down in SER, a good and bad thing.

membran fluidity

Thus membrane at physiological temp is fluid and dynamic. -since phospholipids and triglycerides both made mostly of fatty acids, there is a natural comparison between fluidity of the membrane and fluidity of triglycerides. -natural membrane fluidity more like room temperature oil than a room temperature fat -just like how butter would melt at higher T and harden at lower T, membranes are the same; they become more fluid at higher T and less fluid at lower T.

Entropy and time

Time only goes in the direction that increases entropy, and entropy only increases in the same direction as time.

First and second law are ...

Universal; their principles apply everywhere. They are also very powerful; they predict the future. Tells what will and won't happen.

golgi complex function

_further modify proteins synthesized on RER -Sort proteins by eventual destination, send them away in vesicles: membrane destination versus export versus other organelles -in particular, proteins for export (secretion) are packed into secretory vesicles. -Thus golgi serves as the sorting and logistics center of the cell. -If the ER is the protein and lipid factory of the cell, the Golgi is the warehouse.

how do we know membranes are bilayers?

a classic experiment: -take a sample of red blood cells. Easy to estimate surface area, no internal membranes. -Count RBCs and compute their total surface area. -isolate phospholipids from the cells. -experimentally create a monolayer (a layer one molecule thick) with these P-lipids. -measure area of monolayer. -compare areas, and find that area of phospholipid monolayer is twice surface area of starting cells. -conclusion: phospholipids in the cell from a layer two molecules thick, a bilayer. -Results: monolayer = 2 times RBC surface area -> membrane in cells was bilayer. If monolayer had been 3 times RBC surface, then membrane would be trilayer.

heat energy

a special form of kinetic energy in the random motion and vibration of atoms and molecules. We feel this random motion of small particles as heat.

granum

a stack of thylakoid

cholesterol

a steroid lipid with four carbon rings

coupled transport

active transport creates one gradient; that gradient used to move another molecule. Transport is "coupled". -Example: Na out, K in antiporter energized by ATP creates Na gradient (greater outside), used by symporter that moves glucose in driven by movement of Na in down its gradient

Mitochondria and human history

all your mitochondria are from your mom and her mom, and her mom, etc. If a mom has no daughters her mitochondria are lost to future generations, so only one or a few mitochondrial DNA types survive by chance. Tracing this back leads to a "mitochondrial Eve", source of all human mitochondria, likely a woman living in East Africa 200 thousand years ago.

Fiber

any long, thin molecule and object. Fibril and filament are other names for fiber. -Microtubules -Microfilaments (actin fiber) -intermediate filaments

Bulk movement

as part of secretion and other activities cells carry out bulk movement across plasma membrane (many molecules moved at once)

Endocytosis

bulk movement into cell. Inward folding ("invagination") of membrane gets larger and then pinches off completely, creates membrane-bound vesicle in cytoplasm. Similar to a reverse of exocytosis. three types of endocytosis: -phagocytosis (cell eating) - solid particles -pinocytosis (cell drinking) - liquid droplets -receptor-mediated endocytosis

mitochondria structure

bullet-shaped organelle with two membranes. Two bilayers, but very different from nuclear envelope. Outer membrane forms a smooth cover over the entire organelle. Inner membrane has extensive infoldings (invaginations) called cristae. These infoldings increase its surface area greatly. Soluble compartments inside inner membrane is called the matrix. Compartments between two membranes is called the inter membrane space

how to create coarse control in facilitated diffusion

cell can make carrier/channel protein for a molecule or not, creates coarse control

control of membrane fluidity

cells can maintain desired fluidity of their membranes by changing fatty acids in P-lipids. -unsaturated fatty acids increase fluidity -saturated fatty acids decrease fluidity -shorter chains increase fluidity -longer chains decrease fluidity.

different natural components in different organisms at different natural temp

cells naturally at high temp have more saturated, longer. Cells naturally at low temp have more unsaturated, shorter. Membrane stay equally fluid despite different temperatures.

aquaporins

channels that enhance the small permeability of water of the pure lipid bilayer

anchoring junctions

close connections between two cells, provide mechanical strength, permeable. -desmosomes: connect cytoskeleton of two cells -hemidesmosomes: connect cytoskeleton of cell to ECM.

fluid mosaic model

complete membrane described by fluid mosaic model -it is conceptual (a set of ideas that approximates a complex phenomenon). -states that membrane lipids not fixed, can move laterally (in the plane of the membrane). -membrane proteins also not fixed, can move laterally. -integral membrane proteins float freely, although partially submerged, in thin sea of lipid. -peripheral membrane proteins float freely on the surface (either extra or intracellular)

pathway for exported (secreted) proteins

complete set of steps for exported (secreted) proteins, proteins that will leave cell: 1) inside RER 2) inside transport vesicles 3) inside sacs of cis Golgi 4) inside sacs of trans Golgi 5) inside secretory vesicles 6) secretory vesicles fuse with plasma membrane (called exocytosis). this releases the vesicles' contents into extracellular space (space outside of a cell, could be blood, digestive tract, etc.) where they diffuse away, completing secretion of the proteins.

communicating junctions

connections allowing molecules and signals to move between cells. -gap junctions in animals -plasmodesmata in plants, particularly important to provide communication in plants which have few other means of communication

example of energy and mass conservation

nuclear reactor: mass and energy in the fuel nuclei in the reactor core are converted into mass and energy in energetic particles. The fuel nuclei lose mass (and thus the equivalent energy), but the particles released gain the same amount of energy (and thus the equivalent mass). -Lots of conversion between different forms of energy in this nuclear reactor example, but energy is exactly conserved (energy before = energy after) and separate from mass. And mass is exactly conserved separate from energy.

peripheral membrane proteins

on only one surface of membrane. More loosely bound to membrane. peripheral proteins are on just one side. This one is only extracellular. It ionically and noncovalently bonds to membrane or integral membrane proteins.

dynamic functions continued

other cells move using microfilaments to change shape Amoeba lacks cilia and flagella. Instead, actin filaments create amoeboid movement, sending pseudopods out and pulling them in to crawl along a surface REMINDER: no cells use intermediate filaments to move. Fibers can't move by themselves, need special proteins, motor proteins

Plasma membrane

outer plasma membrane covers the cell. Common to all cells, prokaryotic and eukaryotic. Plasma membrane is barrier and selective "door". Cells, like a factory, need to move stuff in and out the doors to keep production going. Barrier separates external (extracellular) from internal (cytoplasm) compartments As a "door", regulates cell contents. Some things allowed to pass through, others not. Thus, this is called a semipermeable barrier.

Cellular respiration

oxidation of reduced organic compounds to provide energy for the cell. oxidation removes electrons from these organic compounds. O2 is used to accept the electrons (that is, O2 becomes reduced).

membrane pathways happen simultaneously

pathway also similar for proteins destined for organelles except that vesicles leaving trans Golgi either: 1) become organelles themselves or 2) fuse with existing organelles to deliver their protein cargo to it. Note that these pathways are just a few of many pathways for macromolecules all going on inside a cell at the same time. Some are "outbound", from center to outside, some are "inbound", from outside to center.

membrane protein pathway

pathway similar for membrane proteins, except they are only partly in lumen and partly in cytoplasm. They remain buried in the membrane in step #6, exocytosis, rather than released into extracellular space.

pure bilayer is altered by proteins

proteins in membrane modify its properties proteins have to modify lipid bilayer, to allow needed things to enter/exit cell. Glucose, for example, is absolutely needed by the cell, but doesn't cross a pure phospholipid bilayer. two kinds of membrane proteins: integral membrane proteins peripheral membrane proteins

Ribosome function

ribosomes are a universal organelle, found in all cells it is the site where mRNA directs protein synthesis Covalent bonds that link amino acids are made at the ribosome.

isotonic solution

same concentration of solutes as inside cell. Cell does not gain or lose water. -example: hospital IV solution to be injected into veins and will surround blood and body cells. it is an isotonic solution of glucose and salts.

intermediate filament function

shape and structural support, more static element. Forms nuclear lamina (protein network immediately inside the nuclear envelope). No role in movement or motion. Note that the other two cytoskeletal elements do have roles in cell motion and movement

fundamental thermodynamics

since energy and matter are equivalent by E=mc^2, its good to think of energy, along with matter, as simply part of the fundamental existence of everything. Energy is just what it is. -We can still consider E separately from mass to create a study of energy. -the study of energy is called thermodynamics.

chloroplast function

site of photosynthesis. Sun provides earth with energy. Sun is greatest energy source. Chloroplast converts light energy to chemical energy through photosynthesis. Light energy used to reduce CO2 to make reduced carbon compounds. Reduced carbon compounds have lots of H's, few O's, include plant carbohydrates, proteins, and oils. We then eat these reduced carbon compounds and re-oxidize them to make energy for our lives.

vesicles

small membrane-bound sacs for transport between compartments. Contains proteins and other molecules. "Bud off" ER or Golgi, go to another compartment. Different names (transport, secretory, lysosomal) depending on origin and destination of the vesicle.

stroma

soluble material inside the inner membrane and outside the grana

dynamic functions of the cytoskeleton: movement

some cells move using protruding cilia and flagella (made of microtubules) -cilia and flagella same structures, but different length and motions -Kinetoplastid trypanosome, with a single long flagellum, whip-like motion -sperm of many animal species rely on flagellum -ciliate paramecium with many cilia, wave-like motion

how to create very fine and rapid control in facilitated diffusion

some channels are "gated", rapidly open and close in response to voltage changes across the membrane or presence of another molecule. These gated channels are critical for nervous system, for nerves controlling, muscles, and for muscles themselves.

integral membrane proteins

span (completely cross) membrane. Very tightly bound to membrane. usually divided into three domains -Intercellular domain: inside the cell -transmembrane domain: across the membrane. Transmembrane domains have many non polar amino acids that interact with non polar tails of phospholipids. That strongly attaches to protein membrane. -extracellular domain: outside the cell

lysosomes

specialized vesicles that digest material either inside or brought from outside of the cell contain hydrolytic enzymes (protein catalysts) that will accelerate degradation of macromolecules by hydrolysis (hydrolysis -> hydrolytic enzymes). Danger for all other macromolecules! these enzymes must be segregated from cytoplasm. these enzymes function best at acidic pH maintained inside lysosome (also not good for rest of the cell). Lysosomes and hydrolytic enzymes clearly show value of specialized membrane-bound compartments. These enzymes are proteins for an organelle, made on RER and pass through vesicles and Golgi.

potential energy

stored energy that can be released/recovered. -Example: rock on a hill, energy stored vs gravity, released as kinetic energy when rock rolls down. -potential energy can be stored against any of the four fundamental forces.

microtubule function

structural support for cell moves material within cells - railroad tracks of cell. Moves vesicles with aid of motor proteins. Forms spindles that moves chromosomes when cells divide during mitosis and meiosis. Cell movement, microtubules are major components of cilia and flagella.

Microfilament function

structural support, form stress fibers, (bundles of microfilaments) at points of attachment to surfaces and other cells. Cell movement and shape changes Major participant in muscle contractions in specialized muscle cells

Chloroplast structure

structure somewhat resembles mitochondria, but it is bigger. similar bullet shape, multiple membranes: -outer membrane smoothly covers entire organelle. -inner membrane also covers entire organelle smoothly -third membrane (unlike mitochondria) = thylakoid membrane. Single disk = thylakoid membrane. Like mitochondria, formerly free-living, then endosymbionts, then can't live independently.

polychromatic

sunlight (and many other sources of light) is polychromatic, which means it contains many colors. Sunlight is a spectrum of red, orange, yellow, green, blue, indigo, violet. Remember ROY G. BIV.

ecosystems

systems of living and nonliving acting together to support life.

biosphere

systems of organisms and their surrounding environment

answer to question 3

the entropy increase comes from the sun, equivalent to a "power plant" for life.

answer to question 2

the system that we can build an imaginary isolation box around, where the 2nd law must hold, is our entire solar system

Although triglycerides and phospholipids have major differences...

they both interact with other triglycerides/phospholipids via fatty acids. So in that sense they're similar and the properties of the fatty acids determine how P-lipids move and thus membrane fluidity.

Microtubule structure

thickest fiber hollow tubes made of tubulin protein subunits. Tubulin is actually a heterodimer of two slightly different polypeptides. Two polypeptides are noncovalently associated into the heterodimer, and then heterodimers are noncovalently associated into the fiber. Fiber has opposite ends (called plus and minus ends) where microtubules can assemble (grow) at the plus end and disassemble (shrink) at the minus end.

plasma membrane surface

thin covering over the entire surface of the cell. Less than 10nm thick. A thin covering over a large volume. Flexible covering. Lipids in membrane have no rigid connections. They move against each other, make a flexible covering, like a floppy soap bubble. Membrane based on a phospholipid bilayer with nonpolar tails on the inside. Also contains cholesterol, (glyco)proteins, and glycolipids

microfilament (actin fiber) structure

thinnest fiber of the three types Long, thin fibers of actin protein subunits. Again, non covalent association. Two helical strands of actin wrapped around each other.

Argument: the order found in cells and in life violates the 2nd law.

this is false. A local decrease in entropy combined with a larger increase elsewhere inside an isolated system is perfectly possible, because the net effect of a local decrease and a larger increase elsewhere is an increase in entropy over an entire isolated system. -the argument that life violates the 2nd law is still made by those who reject natural selection

uniporters

transport single molecular species in one direction.

antiporters

transport two molecular species in opposite directions.

symporters

transport two molecular species in the same direction.

receptor-mediated endocytosis

uptake of specific particles containing molecules recognized by receptor proteins. Important example, LDL receptor for LDL lipoprotein particles that carry cholesterol and other lipids in the blood (non polar lipids won't dissolve). Endocytosis mediated by LDL receptor removes LDL from blood, keeping blood lipids low. Unfortunately, many people have defects in this system that keep them from bringing LDL particles into the cells. These people accumulate lipids in there arteries, blocking blood flow to the heart leading some to have heart attacks in teens and twenties.

free energy

useful (high quality) energy -energy retained in ordered states (states that are distinct from their surroundings) -usable energy that is available to do work

osmosis review

water can cross the phospholipid bilayer directly and through special pores, aquaporins. There are many solutes dissolved in water that can't cross the membrane, though. When the concentrations of the solutes change, water must cross membranes to compensate (since the solutes can't). When solutes can't cross membrane in one direction, water crosses membrane in the opposite direction until equilibrium is reached. Water movement effectively "dilutes" concentrated solutes, and "concentrates" diluted ones.

Endergonic reaction

when delta G is greater than 0, it is not a spontaneous reaction, endergonic. -Products don't form (or not much). At end, reaction contains few products, lots of reactants. -deltaG positive (G at end is greater than G at beginning)