BIO 106 - The Chemistry of Life: Chapters 1-5

Exocytosis -What happens to the vesicle after?

*EXOCYTOSIS* = like endocytosis, another way to *move large molecules into cell membranes* The *reverse process of moving material into a cell*, Ex: *CO2, insulin, digestive enzymes* -Exocytosis is the opposite of the processes discussed above in that *its purpose is to EXPORT proteins/polysachs material from the cell* TO *extracellular fluid* -*Waste material is ENVELOPED IN A MEMBRANE* and *fuses w/ interior plasma membrane* -This *fusion opens* the membranous envelope *on the exterior* of the cell, and the *waste material is expelled into the extracellular space* -Other examples of cells releasing molecules via exocytosis include the *secretion of proteins of the extracellular matrix and secretion of neurotransmitters into the synaptic cleft by synaptic vesicles*

emergent properties What are they?

*New properties that arise with each step upward in the hierarchy of life*, owing to the arrangement and interactions of parts as complexity increases.

Eukaryotic Cells What philosophy is applicable here? What are the unique plant cell structures (4)? What are the unique animal cell structures (4)?

-*"Form follows function"* = *philosophy practiced in many industries* -In architecture, this means that *buildings should be constructed to support activities that will be carried out inside them* -Ex: a skyscraper should be built with several elevator banks; a hospital should be built so that its emergency room is easily accessible. -*Our natural world also utilizes this principle* of *form following function*, especially in cell biology, and this will become clear as we explore *eukaryotic cells* UNIQUE PLANT CELL STRUCTURES: have a *cell wall, a large central vacuole, chloroplasts, plasmodesmata* UNIQUE ANIMAL CELL STRUCTURES: *centrosome, lysosome, small vacuole, centrioles* -*Unlike prokaryotic cells*, *eukaryotic cells have*: 1) *Membrane-bound nucleus* 2) *Numerous membrane-bound organelles* (*endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others*) 3) *Several, rod-shaped chromosomes* because a eukaryotic cell's nucleus is surrounded by a membrane, it is often said to have a *"true nucleus"* -The word "organelle" means "little organ," and, *organelles have specialized cellular functions*, just *as the organs of your body* have specialized functions. -*Eukaryotic cells have a more complex structure than prokaryotic cells* -Organelles allow different functions to be compartmentalized in different areas of the cell. -*Two important components of the cell* besides DNA and Ribosomes: the *plasma membrane and the cytoplasm*

Active Transport/Electrochemical Gradient

-*Active transport* mechanisms *REQUIRE the use of the cell's energy*, usually *in adenosine triphosphate* (ATP) -*If a substance must move into the cell against its concentration gradient*—that is, if the concentration of the substance inside the *cell is greater* than its concentration in the extracellular fluid (and vice versa)—*the cell must use energy to move the substance* bc its going against diffusion (high to low) -Some active transport mechanisms move *small-molecular weight materials, such as ions*, through the membrane. *Other mechanisms transport much larger* molecules -We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in *living systems* = *gradients are more complex* bc *ions move in/out of cells* and *bc cells contain proteins that don't move across the membrane/mostly negatively charged* = there is *also an ELECTRICAL GRADIENT* which is *a difference of charge, across the plasma membrane* -The *interior- living cells is electrically negative* to the extracellular fluid in which they are bathed, and at the same time, *cells have MORE of potassium (K+)* and *LOWER concentrations of sodium (Na+)* than does the extracellular fluid -So in a living cell, the concentration gradient of *Na+ tends to drive it into the cell*, and the *electrical gradient of Na+ (a positive ion) drives it to the negatively charged interior* but the situation is more *complex for other elements such as potassium* -The *electrical gradient of K+*, a *positive ion*, also tends to drive it into the cell, but the concentration gradient of *K+ tends to drive K+ out of the cell*. The combined gradient of concentration and electrical charge that affects an ion is called its electrochemical gradient.

Carrier Proteins What proteins are faster - channel or carrier? What does carrier do that active transport also does? Material can do what depending on gradient?

-*Another protein in plasma membrane* = *carrier protein* -This aptly named protein *binds a substance + changes own shape moving the bound molecule from outside-inside DEPENDING on gradient* the *material may move opp* direction -*Carrier proteins* = typically *specific for a single substance* -This *selectivity adds to overall selectivity of the plasma membrane* -The *exact mechanism for the change of shape is poorly understood* + *proteins can change shape when hydrogen bonds are affected* but this may not fully explain this mechanism -Each *carrier protein is specific to 1 substance* and there are a finite number of these proteins in any membrane -This can *cause probs transporting enough material for the cell to function* -*When all proteins are bound to their ligands* = they are *saturated/rate of transport is at max* -*Incr concentration gradient* at this point *WILL NOT incr rate of transport* -Ex: of this process occurs in the *kidney* - *Glucose, water, salts, ions, amino acids* needed by the body are *filtered in one part of the kidney* which *includes glucose*, is then *reabsorbed in another part of the kidney* bc there are only a *finite number of carrier proteins for glucose*, if more glucose is present than the proteins can handle, the *excess is usually excreted from the body via urine* -In a *diabetic individual*, this is described as *"spilling glucose into the urine"* -A *diff group of carrier proteins* = *glucose transport proteins* (GLUTs) are involved in *transport glucose/hexose sugars* through plasma membranes within the body -*Channel/carrier proteins transport material* at *diff rates* + *CHANNEL proteins transport much more QUICKLY* than do carrier proteins -Channel proteins *facilitate diffusion at tens of millions of molecules per sec* whereas *carrier proteins work at thousand to a mil molecules per sec*

Carbohydrates in Plasma Membrane Form the glyco________ and glyco_______ who differentiate btwn self and non seld Carbohydrate chains consist of how many monosaccharide units? What is glycocalyx and what does it do?

-*Carbohydrates* are the *3rd major component* of plasma membranes -They are always *found on the exterior surface of cells* and are *bound to proteins (forming glycoproteins*) or to *lipids (forming glycolipids)* -These *carbohydrate chains* may consist of *2-60 monosaccharide units* (*straight or branched*) -Along *w/ peripheral proteins*, carbohydrates *form specialized sites* on the cell surface that *allow cells to recognize each other* These sites have unique patterns that allow the cell to be recognized, much the way that the facial features unique to each person allow him or her to be recognized. -This recognition function is very important to cells, as it *allows the immune system to differentiate between body cells ("self") and foreign cells or tissues ("non-self")* -Similar types of *glycoproteins and glycolipids are found on the surfaces of viruses and may change frequently*, *preventing immune cells recognition* and attacking them. These carbohydrates on the exterior surface of the cell—the carbohydrate components of both *glycoproteins and glycolipids* = *glycocalyx* (meaning "sugar coating") -The *glycocalyx is highly hydrophilic* and attracts *large amounts of water to the surface of the cell* -This aids in the *interaction of the cell w/ its watery environment* and in the *cell's ability to obtain substances dissolved in the water* -As discussed above, the *glycocalyx is also important for cell identification*, *self/non-self determination*, and *embryonic development*, and is used in *cell-cell attachments* to form tissues

Diffusion Moves from what to what When does it stop, at what state? Follows what? Is reliant on (3) factors that affect the incr/decr diffusion?

-*Diffusion* = *PASSIVE process of transport* single substance moves from *high concentration to low concentration until equal* across a space -*Materials move within the cell's cytosol by diffusion*, and certain materials move *through the plasma membrane by diffusion* -*Diffusion expends NO ENERGY* -On the contrary, *concentration gradients are potential energies* dissipated as the gradient is eliminated -Each *separate substance in a medium, such as extracellular fluid*, has its *own concentration gradient*, *independent of other concentration gradients* of other materials -In addition, *each substance will diffuse according to that gradient* -Within a system, there will be *diff rates of diffusion of the diff substances* in the medium Diffusion: *relies on surface area, temp, weight*

Endocytosis

-*Endocytosis* is a type of *active transport that moves particles*, such as *large molecules, parts of cells, whole cells into a cell* -There are *DIFF VARIATIONS OF ENDOCYTOSIS*, but all *share a common characteristic*: -*The plasma membrane* of the cell invaginates, *forming a pocket around the target particle -*The pocket pinches off*, resulting in the *particle being contained in a newly created intracellular vesicle* formed from the plasma membrane.

How Viruses Infect Specific Organs What does HIV penetrate of lymphocytes? What cells do hepatitis attack? Antibodies are made in response to what? What do surface markers do? What does pencilin destroy first in bacteria? What does a vaccine target first in bacteria?

-*Glycoprotein/glycolipid patterns* on the *surfaces of cells give many viruses infection* -*HIV/hepatitis viruses infect only specific organs or cells* in the human body -*HIV penetrates plasma membranes of lymphocytes called T-helper cells*, as well as some *monocytes and central nervous system cells* -The *hepatitis virus attacks liver cells* -These *viruses invade these cells* b/c the *cells have binding sites compatible with certain viruses* -Other *recognition sites on the virus's surface interact w/ human immune system*, *prompting antibody prod* -*Antibodies* are made in *response to the antigens/proteins of invasive pathogens/foreign cells* such as might occur with an *organ transplant* -These *same sites serve as places for antibodies to attach/inhibit virus* -Unfortunately, these *HIV recognition sites change rapidly b/c of mutations*, making the *production of vaccine against virus difficult*, as the *virus evolves and adapts* -A *person w/ HIV will quickly develop diff populations/variants of virus* that are distinguished by differences in these recognition sites -This rapid change of *surface markers decr immune system efficiency* in attacking the virus, bc the *antibodies will not recognize the new variations* of the surface patterns -In the case of HIV, the problem is compounded by the fact that the *virus specifically infects and destroys cells involved in the immune response, further incapacitating the host* Ex: HIV binds to CD4 receptor (glycoprotein on T cells)

Tonicity in Living Systems

-*HYPOTONIC* = *water enters a cell*, and the *cell swells* -*ISOTONIC* = the relative concentrations of *solute and solvent are equal on both sides of the membrane* There is *no net water movement*; therefore, there is *no change in the size* of the cell -*HYPERTONIC* = *water leaves a cell* and the *cell shrinks* If either the hypo- or hyper- condition goes to excess, the cell's functions become compromised, and the cell may be destroyed. -Ex: *A red blood cell will burst/LYSE*, when it *swells beyond the plasma membrane's capability* to expand. Remember, the *membrane resembles a mosaic*, with discrete spaces between the molecules composing it *If the cell swells* = *spaces btwn lipids/proteins become too large* + the *cell will break apart* In contrast, when *excessive amounts of water leave a red blood cell*, the cell *shrinks*, or crenates. This has the effect of *concentrating the solutes left in the cell*, making the *cytosol denser and interfering with diffusion within the cell*. The cell's ability to *functionality = compromised* and may also result in the death of the cell. -*Various living things have ways of controlling osmosis*—a mechanism = *OSMOREGULATION* -Some organisms, such as *plants, fungi, bacteria, protists*, have *cell walls that surround the plasma membrane* and *prevent cell lysis in hypotonic* solution -The *plasma membrane can only expand to the limit of the cell wall*, so the cell will not lyse. In fact, the *cytoplasm in plants is always slightly hypertonic* to the cellular environment, and water will always enter a cell if water is available -This *inflow of water produces turgor pressure*, which *stiffens the cell walls* of the plant -In *nonwoody plants* = *turgor pressure supports the plant*. Conversely, *if the plant is not watered, the extracellular fluid will become hypertonic*, causing *water to leave* the cell = cell does not shrink because the *cell wall IS NOT FLEXIBLE but cell membrane *detaches from wall + constricts the cytoplasm* = *PLASMOLYSIS* and Plants *lose turgor pressure* in this condition and wilt -*Tonicity is a concern for all living things* -Ex: *paramecia and amoebas* which are *protists that lack cell walls*, have *contractile vacuoles* + This *vesicle collects excess water* from the cell and *pumps it out preventing lysing* as it takes on water from its environment -A *paramecium's contractile vacuole* here visualized using bright field light microscopy at 480x magnification, *continuously pumps water out of the organism's body to keep it from bursting in a hypotonic medium* -Many *marine invertebrates have internal salt levels matched to their environments* making them *isotonic w/ water in which they live* -*Fish* however, *must spend approx 5% of their metabolic energy* maintaining *osmotic homeostasis* -*Freshwater fish* live in an environment that is *hypotonic* to their cells. These fish actively take in salt through their gills and excrete diluted urine to rid themselves of excess water. *Saltwater fish* live in the reverse environment, which is *hypertonic* to their cells, and they secrete salt through their gills and excrete highly concentrated urine. -In *vertebrates* = the *kidneys regulate the amount of water* in the body. Osmoreceptors are specialized cells in the brain that monitor the concentration of solutes in the blood. If the levels of solutes increase beyond a certain range, a hormone is released that retards water loss through the kidney and dilutes the blood to safer levels. *Animals also have high concentrations of albumin*, which is *produced by the liver*, in their blood. This protein is too large to pass easily through plasma membranes and is a *major factor in controlling the osmotic pressures applied to tissues*

Properties of Life (Order and Adaptation) Figure 1.10 What does properties of life mean and what are they(ORRAG RHEE)? What is the level at which the properties of life emerge? What is the order of organisms? Who does the job and makes organs? Without cells there is no_____ Single-celled organisms are complex and made up of? Multicellular organisms have cells that form what and what systems? It's beneficial for organisms to adapt bc . incr ________ and dependent on _________?

-*Living organisms share several key characteristics/functions*: *order, response* to the environment, *reproduction, adaptation, growth*, *regulation, homeostasis, energy processing, and evolution* When viewed together, these nine characteristics *serve to define life* •*Cells are the level* at which the properties of life emerge. Ex: A toad represents a highly organized structure consisting of *cells, tissues, organs, organ systems* -*ORDER of Organisms* = *organized, coordinated structures of 1+ cells*- defined by *cell that does the job* and *makes organs* (formed by chromosomes/ genes). Breast cancer- genetics involved. Without cells, there is no order. Inside each cell, there's atoms and atoms make molecules. *Makes everything in shape and order.* flower structure and human structure - brain is on top because it controls Leg bones - strongest and supports the body Last vertebrate - strongest Heart- pumping blood throughout the body -*Single-celled organisms* are remarkably complex: inside each *cell, atoms make up molecules*; these in turn make up *cell organelles and other cellular inclusions* -*Multicellular organisms* similar *cells form tissues which form organs which form organ systems* (body structures with a distinct function) -*Adaptation*: *Incr survival + dependent on evolution* -*More tech = more diagnosis* (Cat scan, MRI, colonscopy) *Beneficial for an organism to adapt*. Snakes have no legs but still move by slithering. Giraffes have long necks to eat and bend to drink. High altitudes- red blood cells increase.

Factors That Affect Diffusion How does the weight affect it? The temp? The density? The surface area? The solubility? The distance?

-*Molecules move randomly* at a rate *dependent on mass/environment/thermal energy* they possess, which in turn is a function of temperature -This *movement accounts for* the *diffusion of molecules thru whatever medium* in which they are localized -A *substance will move to any space* available to it *until evenly distributed* throughout it -*After diffused completely* through a space, *removing its concentration gradient*, *molecules will still move* around in the space, *but no net movement* of the number of molecules from one area to another -This *lack of a concentration gradient/no net movement* of a substance = *dynamic equilibrium* *1) Extent of the concentration gradient*: The *greater diff in concentration = more rapid diffusion* The *closer material gets to equilibrium, the slower* *2) Mass of the molecules diffusing*: *Heavier molecules move more slowly*; *3) Temperature*: *Higher temperatures incr* the energy and the movement *4) Solvent density*: As the *density of a solvent incr, the rate of diffusion decr* bc difficult time getting through the denser medium. An example of this is a person experiencing *dehydration* = as the body's cells lose water, the rate of diffusion decreases in the cytoplasm, and the cells' functions deteriorate. *Neurons tend to be very sensitive to this effect* which is why dehydration leads to unconsciousness and possibly coma because of the decrease in diffusion rate within the cells. *5) Solubility*: As discussed earlier, *nonpolar or lipid-soluble materials pass through plasma membranes more easily* than polar materials, allowing a faster rate of diffusion. *6) Surface area and thickness of the plasma membrane*: *Incr surface area incr the rate of diffusion* whereas a thicker membrane reduces it. *7) Distance travelled*: The *greater the distance that a substance must travel, the slower* the rate of diffusion. A large, spherical cell will die bc nutrients/waste cannot reach/leave the center of the cell. Therefore, cells must either be small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled eukaryotes. -A *variation of diffusion* = the process of *filtration* where *material moves according to concentration gradient* through a membrane; *sometimes diffusion is enhanced w/ pressure*, causing the substances to filter more rapidly. *the kidney* = where *blood pressure forces water/dissolved substances/solutes out of the blood* and into the renal tubules. The rate of diffusion in this instance is almost totally *dependent on pressure* + One of the effects of *high blood pressure is the appearance of protein in the urine*, which is "squeezed through" by the abnormally high pressure.

Components of Prokaryotic Cells What were the first type of cells? What do all eukaryotic and prokaryotic cells have?

-*Only the predominantly single-celled organisms* of the *domains Bacteria and Archaea* are classified as *prokaryotes* (pro- = "before"; -kary- = "nucleus") -*Cells of animals, plants, fungi, protists* are all *eukaryotes* (ceu- = "true") and are made up of *eukaryotic cells* *ALL CELLS HAVE:* 1. *Plasma Membrane* -an *outer covering that separates* the *cell's interior* from its *surrounding environment* 2. *Cytoplasm*- consisting of a *jelly-like cytosol within the cell* + *has cellular components* 3. *DNA*- the *genetic material of the cell* 4. *Ribosomes*- which *synthesize proteins* -*Prokaryote* = a *simple, mostly single-celled (unicellular) organism* that *lacks a nucleus/membrane-bound organelles* opp of eukaryotes -*NUCLEOID* = *Prokaryotic DNA* is found *in central part of the cell*. All *prokaryotes have chromosomal DNA in a nucleoid, ribosomes, a cell membrane, and a cell wall* -*Most prokaryotes* = have *a Peptidoglycan cell wall* and *polysaccharide capsule* -The *cell wall - acts as an extra layer of protection*, helps the *cell maintain its shape*, and *prevents dehydration* -The *capsule*- *allows cell to attach to surfaces* in its environment -*Some prokaryotes* = have *flagella, pili, or fimbriae* -*Flagella = locomotion* -*Pili* = *exchange genetic material in reproduction called conjugation* -*Fimbriae* = *bacteria to attach to a host cell*

Osmosis Move from ________ solute to ________ solute Passive or active? ___________ play a large role in transport?

-*Osmosis* = the *movement of water through semipermeable membrane* DEPENDING ON *concentration gradient of water* across the membrane, which is *INVERSE proportional to the concentration of solutes* + *LOW SOLUTE TO HIGH SOLUTE* -While *diffusion transports material across membranes/cells*, *osmosis transports ONLY WATER across a membrane* and the membrane *limits the diffusion of solutes* in the water -Not surprisingly, the *aquaporins that facilitate water movement* play a *large role* in osmosis, most prominently *in red blood cells/kidney tubules* -*Osmosis* is a *special case of diffusion* -*Water*, like other substances, *moves from high concentration to low concentration* -On both sides of the membrane the *water level is the same*, but there are *diff concentrations of a dissolved substance/solute* that *cannot cross*the membrane (otherwise the concentrations on each side would be balanced by the solute crossing the membrane -If the volume of the solution on both sides of the membrane is the same, but the *concentrations of solute are different*, then there are *different amounts of water*, the solvent, on either side of the membrane. -Returning to the beaker example, recall that it has a mixture of solutes on either side of the membrane. A principle of *diffusion is that the molecules move around + spread EVENLY throughout the medium* if they can -However, *only the material capable* of getting through the membrane *will diffuse* through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Thus, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero or until the hydrostatic pressure of the water balances the osmotic pressure. Osmosis proceeds constantly in living systems.

Phagocytosis

-*PHAGOCYTOSIS* (the condition of *"cell eating"*) is the process by which *large particles (cells or relatively large particles) are taken in by a cell* -Ex: when *microorganisms invade the human body*, a type of *white blood cell called a NEUTROPHIL* will *removes the invaders* through this process, *surrounding and engulfing the microorganism*, which is then *destroyed by the neutrophil* -In preparation for phagocytosis, *a portion of the interior of the plasma membrane becomes coated with a protein* = *CLATHIRIN*, which *stabilizes this section of the membrane* -The *coated portion of the membrane then extends from the body of the cell and surrounds the particle*, eventually *enclosing it* -Once the *vesicle containing the particle is enclosed within the cell*, the *clathrin disengages from the membrane* and the *vesicle merges w/ a lysosome for the breakdown of the material in the newly formed compartment (endosome)* -When accessible nutrients from the degradation of the vesicular contents have been extracted, the newly formed *endosome merges w/ the plasma membrane to release its contents into the extracellular fluid* The endosomal membrane again becomes part of the plasma membrane.

Cytotechnologist What is a pap smear test? What do cytotechs study? They notice what in cells and can help save a patients life?

-*Pap smear* = a *doctor takes a small sample of cells from the uterine cervix* of a patient and *sends it to a medical lab* where a *cytotechnologist stains the cells/examines them for any changes* that could *indicate cervical cancer/microbial infection* *Cytotechnologists* (cyto- = "cell") are professionals who *study cells via microscopic examinations/laboratory tests* -They are *trained to determine which cellular changes are normal/abnormal* -Their *focus is not limited to cervical cells*; they *study cellular specimens from all organs* -*When they notice abnormalities*, they *consult a pathologist*, who is a medical doctor who can make a *clinical diagnosis* -*Cytotechnologists play a vital role in saving people's lives*. When abnormalities are discovered early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome

Introduction of Components and Structure of Plasma Membrane What are the most basic functions of the plasma membrane? The plasma membrane is very ____________ as it allows the red/white bloods cells to do what to enter? Cell recognition is done by what on the membrane surface? Lipids are on what cell and proteins are on what? Receptors do what? What three protein types are on the membrane?

-*Plasma membrane*(cell membrane) has *many functions*, but the most basic one is to *define the borders of the cell* and keep the *cell functional* and *determines nature of its interaction w/ environment* -The plasma membrane is *selectively permeable* = *allows only some materials entrance/exit* the cell, while *other materials require the use of a specialized structure*, and *sometimes even energy* investment for crossing -*Cells exclude some substances*, *take in* others, and *excrete others*, all in *CONTROLLED quantities* -The plasma membrane *must be very flexible to allow certain cells*, such as *red blood cells and white blood cells*, to *change shape* as they pass through *narrow capillaries* -In addition, the *surface of membrane carries markers* that allow cells to *recognize one another*, which is vital for *tissue and organ formation* during early development, and which later plays a role in the *"self" versus "non-self" distinction of the immune response* -Among the most sophisticated functions of the plasma membrane is the ability to *transmit signals by complex, integral proteins*= *RECEPTORS* = *receivers of extracellular inputs* and as *activators of intracellular processes* -These membrane receptors provide *extracellular attachment sites for effectors like hormones/growth factors* and they *activate intracellular when their effectors are bound*- Occasionally, *receptors are hijacked by viruses* (HIV, human immunodeficiency virus, is one example) that use them to *gain entry into cells*, and at times, the *genes encoding receptors become mutated*, causing the process of *signal transduction malfunctions w/ consequences* 1. *transport proteins* 2. *enzymes* 3. *receptor proteins*

Selective Permeability The plasma membrane is ASYMMTERIC bc the inside does not what with the outside? What types of substances can pass through with no problem? Which ones present problems?

-*Plasma membranes* are *asymmetric*: the *interior of membrane is not identical to exterior* of the membrane -In fact, there is a considerable *diff btwn phospholipids + proteins* between the *two leaflets that form a membrane* -*On interior of membrane* = some *proteins serve to anchor the membrane to fibers of the cytoskeleton* -There are *peripheral proteins* on the exterior of the membrane that *bind elements of the extracellular matrix* -*Carbohydrates attached to lipids or proteins*, are also found on the exterior surface of the plasma membrane -These *carbohydrate complexes help the cell bind substances for extracellular fluid* = *adds selective nature* of plasma membranes -*Amphiphilic*: They have *hydrophilic and hydrophobic* regions movement of some materials through the membrane and hinders the movement of others. -*Lipid-soluble material w/ low molecular weight* can *easily slip thru hydrophobic lipid* core of the membrane -Substances such as the *fat-soluble vitamins A, D, E, K* readily *pass thru digestive tract/tissues* -*Fat-soluble drugs/hormones* also gain *easy entry into cells* and are readily *transported into the body's tissues/organs* -*Oxygen/carbon dioxide* have *no charge so pass through via simple diffusion* -*Polar substances* present *problems* for the membrane -While some polar molecules *connect easily w/ outside* of a cell, they *cannot pass the lipid core of the plasma membrane* -*Small ions could slip thru spaces in mosaic of the membrane*, their *charge prevents them* from doing so -*Ions such as sodium, potassium, calcium, and chloride* must have special means of *need to penetrate plasma membranes* -*Simple sugars/amino acids* also *need help w/ transport across plasma membranes*, achieved *by various transmembrane proteins (channels)*

Secondary Active Transport (Co-transport)

-*Secondary active transport* brings *sodium ions, and possibly other compounds, into the cell* -As *sodium ion concentrations build outside of the plasma membrane* because of the action of the primary active transport process, an *electrochemical gradient is created* -If a *channel protein exists and is open*, the *sodium ions will be in* through the membrane -This movement is *used to transport other substances that can attach themselves to the transport protein through the membrane* -Many *amino acids, as well as glucose, enter a cell this way* -This secondary process is also used to *store high-energy hydrogen ions in the mitochondria of plant and animal cells* for the production of ATP. The potential energy that accumulates in the *stored hydrogen ions is translated into kinetic energy* as the *ions surge through the channel protein ATP synthase*, and that *energy is used to convert ADP into ATP*

Hypotonic Solutions Hypertonic Solutions Isotonic Solutions

-*Three terms—hypotonic, isotonic, and hypertonic*—are used to *relate the osmolarity of a cell to the osmolarity of the extracellular fluid* that contains the cells -*HYPOTONIC* = the *extracellular fluid has lower osmolarity than the fluid inside* the cell, and *water enters the cell* (In living systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the *extracellular fluid has a higher concentration of water in the solution than does the cell* In this situation, water will follow its concentration gradient and enter the cell, *LOW SOLUTE* (*LYSED* - Animal + *PLASMOLYZED* - PLANT) -*HYPERTONIC* = As for a hypertonic solution, the prefix hyper- refers to the *extracellular fluid having a higher osmolarity than the cell's cytoplasm*; therefore, the *fluid contains less water than the cell does* Because the *cell has a relatively higher concentration of water, water will leave the cell* + *MORE SOLUTE* (*SHRIVELED - Animal + *TURGID* - Plant) -*ISOTONIC* = In an isotonic solution, the *extracellular fluid has the same osmolarity as the cell* + If the *osmolarity of the cell matches that of the extracellular fluid*, there will be *no net movement of water* into or out of the cell, *although water will still move* in and out. Blood cells and plant cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances. (*NORMAL* - *ANIMAL* + *FLACCID* - Plant)

Moving Against a Gradient

-*To move substances against a concentration/electrochemical gradient* = the cell *must use energy* -This energy is *harvested from ATP* generated through the *cell's metabolism* -*Active transport mechanisms*, collectively called *pumps*, *work against electrochemical gradients* *Small substances constantly pass through* plasma membranes -*Active transport maintains concentrations* of *IONS/other substances needed by living cells* in the face of these passive movements -Much of a *cell's supply of metabolic energy may be spent maintaining these processes* (Most of a *red blood cell's metabolic energy* is used to maintain the imbalance between *exterior and interior sodium and potassium levels* required by the cell.) -Because *active transport mechanisms DEPEND on cell's metabolism for energy* they are sensitive to many metabolic poisons that interfere with the supply of ATP. Two mechanisms exist for the transport of small-molecular weight material and small molecules -*Primary active transport moves ions across a membrane and creates a difference in charge* across that membrane, which is directly dependent on ATP -*Secondary active transport* describes the *movement of material bc electrochemical gradient established by primary active transport that does not directly require ATP*

Tonicity

-*Tonicity* = describes *how an extracellular solution can change the cell volume by affecting osmosis* or the ability of a *surrounding solution to cause a cell to gain/lose water* -A *solution's tonicity* often *directly correlates w/ osmolarity of the solution* -*Osmolarity* describes the *total solute concentration of the solution* -A *solution w/ low osmolarity* has a *greater number of water molecules relative to solute particles* = a solution with *high osmolarity has fewer water molecules w/ respect to solute particles* -In a situation in which solutions of two different osmolarities are separated by a membrane permeable to water, though not to the solute, *water will move from the side of the membrane with lower osmolarity (and more water) to the side with higher osmolarity (and less water)* This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move—*the water—moves along its own concentration gradient* -An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear, if the second solution contains more dissolved molecules than there are cells.

Receptor-mediated Endocytosis

-A *targeted VARIATION OF ENDOCYTOSIS employs RECEPTOR PROTEINS* in the plasma membrane that have a *specific binding affinity for certain substances* -In *receptor-mediated endocytosis* = uptake of *substances by the cell is targeted to a single type of substance that binds to the receptor on the external surface* of the cell membrane -In *receptor-mediated endocytosis*, as in phagocytosis, *clathrin is attached to the cytoplasmic side* of the plasma membrane -If uptake of a compound is *dependent on receptor-mediated endocytosis and the process is ineffective*, the *material will not be removed from the tissue fluids or blood but instead, it *will stay in those fluids and incr in concentration* -Some *human diseases are caused by the failure of receptor-mediated endocytosis* -Ex: form of *cholesterol termed low-density lipoprotein or LDL* (also referred to as "bad" cholesterol) is *removed from the blood* by receptor-mediated endocytosis -In the human genetic disease familial *hypercholesterolemia* = the *LDL receptors are defective or missing entirely* -*People with this condition have life-threatening levels of cholesterol* in their blood, because their *cells cannot clear LDL particles* from their blood. -Although *receptor-mediated endocytosis is designed to bring specific substances in* that are normally found in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site -*Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells*

Pinocytosis

-A *variation of endocytosis* = *PINOCYTOSIS* -This literally means *"cell drinking"* and was named at a time *when the assumption was that the cell was purposefully taking in extracellular fluid* -In reality, this is a process that *takes in molecules, including water*, which the *cell needs from the extracellular fluid* -*Pinocytosis* results in a much *smaller vesicle than does phagocytosis* and the *vesicle does not need to merge with a lysosome for breakdown* -*A further variation of pinocytosis* = *POTOCYTOSIS* -This process *uses a coating protein = CAVEOLIN* on the *cytoplasmic side of the plasma membrane, which performs a similar function to clathrin* -The *cavities in the plasma membrane that form the vacuoles* have *membrane receptors/lipid rafts in addition to caveolin* -The *vacuoles or vesicles formed in caveolae (singular caveola)* are *smaller than those in pinocytosis* -*Potocytosis = bring small molecules into the cell* and to *transport these molecules through the cell for their release on the other side* of the cell, a process = *TRANSCYTOSIS*

Carrier Proteins for Active Transport

-An important membrane adaption for *ACTIVE TRANSPORT* is the presence of *specific carrier proteins/pumps to facilitate movement*: there are three types of these proteins or transporters -*UNIPORTER* = carries *1 specific ion/molecule* -*SYNPORTER* = carries *2 diff ions/molecules both in the same direction* -*ANTIPORTER* = carries *2 diff ions/molecules in opp directions* -*All of these transporters* can also *transport small, uncharged organic molecules like glucose* -These *three types of carrier proteins* are also found *in facilitated diffusion*, but they *do not require ATP* to work in that process -Some examples of *pumps for active transport are: -Na+-K+ ATPase*, which *carries sodium and potassium ions* -*H+-K+ ATPase*, which *carries hydrogen and potassium ions* -Both of these are *antiporter carrier proteins* -Two other carrier proteins are *Ca2+ ATPase and H+ ATPase* which carry only *calcium and only hydrogen ions*, respectively. Both are pumps.

Cell Size The electron microscope can see from what micrometer range and what items? The light microscope can see from what micrometer range and what items? What can we see with the naked eye? What size is needed for cells? What kind of surface area to volume do cells need to have? As a cell grows, it become less ________? But to become more ________ the only way is to?

-At *0.1 to 5.0 μm in diameter* = *prokaryotic cells SMALLER than eukaryotic cells* which have *diameters 10-100 μm* -The *small size of prokaryotes allows ions/organic molecules that enter to quickly diffuse to parts of the cell* -Similarly, *any wastes produced within a prokaryotic cell can quickly diffuse out* -This is *not the case in eukaryotic cells* which have developed different structural adaptations to *enhance intracellular transport* -*Electron Microscope (0.1 to 50nm)* = *atom, lipids, protein, flu virus, mitochondria, bacteria, animal/plant cell* -*Light Microscope (100nm to 1mm)* = *flu virus, mitochondria, bacteria, animal/plant cell, human/frog cell* -*Naked eye (100nm to 100m)*: *human/frog/chicken/ostrich egg, adult female* -*SMALL size* is *NECESSARY for all cells* (prokaryotic or eukaryotic) -First, we'll *consider the area/volume of a typical cell* -*Not all cells are spherical* in shape, but most *tend to approximate* a sphere You may remember from your high school geometry course that the formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3 -Thus, *as the radius of a cell incr*, its *surface area incr as the square of its radius*, but *its volume incr as the cube of its radius* (much more rapidly) -Therefore, *as a cell incr in size*, its *surface area-to-volume ratio decreases* -*This same principle would apply if the cell had the shape of a cube* -If the *cell grows too large* = the *plasma membrane will not have sufficient surface area to support the rate of diffusion* required for the increased volume -*CELL SIZE* should be: *large enough to house DNA, proteins, structures needed to survive/reproduce*, but *small enough to allow for surface-to-volume ratio that will allow adequate exchange* with the environment. -In other words, *as a cell grows, it becomes less efficient* -*To become more efficient is to divide*; another way is to *develop organelles that perform specific tasks*. These adaptations lead to the development of more *sophisticated cells called eukaryotic cells*

Facilitated transport What types of proteins help this? Does it require energy - passive or active?

-In *facilitated transport* (facilitated diffusion) = *materials diffuse across the plasma membrane* *via* the help of *membrane proteins* -*A concentration gradient exists* that would *allow these materials to diffuse* into the cell *w/o expending cellular energy* -However, these *materials are ions/polar molecules* that are *repelled by the hydrophobic parts* of the cell membrane -*Facilitated transport proteins shield these materials* from the repulsive force of the membrane, allowing them to diffuse into the cell. -The *material being transported* is first *attached to glycoprotein receptors* on the exterior surface of the plasma membrane -This *allows the material needed by the cell* to be *removed from the extracellular fluid* -The *substances are passed to specific integral proteins* that *facilitate their passage* -*Some integral proteins* are collections of *beta-pleated sheets* that form a *pore/channel thru the phospholipid bilayer* -*Others are carrier proteins* which *bind w/ substance and aid its diffusion* through the membrane

Bulk Transport

-In addition to *moving small ions/molecules through the membrane*, *cells also need to remove/take in larger molecules and particles* -*Some cells are even capable of ENGULFING ENTIRE UNICELLULAR MICROORGANISMS* -You might have correctly hypothesized that the *uptake and release of large particles by the cell requires energy* -But *A LARGE PARTICLE*, however, *cannot pass through* the membrane, *even with energy* supplied by the cell.

Geneticist

-Many *diseases arise from genetic mutations* that *prevent protein synthesis* of critical proteins -Ex: *Lowe disease* (also called oculocerebrorenal syndrome, because it *affects the eyes, brain, kidneys*) -In Lowe disease, there is a *deficiency in an enzyme in Golgi apparatus* -Children with Lowe disease are *born with cataracts*, typically develop *kidney disease* after the first year of life, and may have *impaired mental abilities* -Lowe disease is a *genetic disease caused by a mutation on the X chromosome* -The X chromosome is one of the two human sex chromosome, as these chromosomes *determine a person's sex* -*Females possess two X chromosomes* while *males possess one X and one Y chromosome* -In females, the *genes on only one of the two X chromosomes are expressed* -Therefore, *females have a 50/50 chance* of having the disease -However, *males only have one X chromosome* and the genes on this chromosome are always expressed so *males will always have Lowe disease if their X chromosome carries* the Lowe disease gene. The location of the mutated gene, as well as the locations of many other mutations that cause genetic diseases, has now been identified -Through *prenatal testing*, a woman can *find out if the fetus is afflicted* with one of several genetic diseases. Geneticists analyze the results of prenatal genetic tests and may counsel pregnant women on available options. They may also *conduct genetic research that leads to new drugs or foods*, or perform DNA analyses that are used in forensic investigations.

Extracellular Matrix of Animal Cells Most animal cells do what to the extracellular space? What is the extracellular matrix? What happens when a molecule in the matrix binds to a receptor?

-Most *animal cells release proteins/materials into extracellular space* -The primary components of these materials are *proteins (collagen = fibers interwoven w/ carbohydrate-containing protein molecules called PROTEOGLYCANS* -Collectively, *these materials are called the extracellular matrix* -Not only does the extracellular matrix *hold the cells together to form a tissue*, but it also *allows the cells to communicate w/ each other*. How can this happen? -*Cells have protein receptors* on the extracellular surfaces of their *plasma membranes* -When a *molecule within the matrix binds to the receptor*, it *changes the molecular structure* of the receptor -The *receptor changes the conformation of the microfilaments* positioned just inside the plasma membrane -These conformational *changes induce chemical signals to nucleus* and *turn "on"/"off" transcription of specific DNA*, which affects the production of associated proteins, thus *changing the activities* within the cell -*Blood clotting* provides an example of the role of the extracellular matrix in cell communication. *When the cells lining a blood vessel are damaged*, they display a *protein receptor called tissue factor* binds with another factor in the extracellular matrix, it *causes platelets to adhere to the wall of the damaged blood vessel*, stimulates the adjacent smooth *muscle cells in the blood vessel contract* (thus constricting the blood vessel), and initiates a series of steps that *stimulate the platelets to produce clotting factors*

Passive Transport What is it and what does it depend on and what direction does it move from? What processes follow passive transport (3)? Difference btwn diffusion and facilitated diffusion?

-Plasma membranes must *allow certain substances to enter/leave a cell* and *prevent harmful materials from entering* and some *essential materials from leaving* = *selectively permeable*—they allow some substances to pass through, but not others -*If they were to lose this selectivity*, the *cell would no longer sustain itself* and it *would be destroyed* -*Some cells require larger amounts of specific substances* than do other cells; they must *have a way of obtaining these materials* from extracellular fluids -This *may happen passively*, as certain *materials move back and forth*, or the cell may have special mechanisms that *facilitate transport* -*Some materials are so important* to a cell that it *spends energy, hydrolyzing adenosine triphosphate (ATP)*, to *obtain them* Ex: *Red blood cells* use some of their energy doing just that -All cells *spend energy to maintain an imbalance of sodium and potassium ions* between the interior and exterior of the cell. -The *most direct form* of membrane transport are *passive* -*Passive transport* = a *naturally occurring* phenomenon and needs *no energy* to accomplish the movement -In passive transport, *substances move from higher concentration to lower concentration* - A physical space in which there is a *range of concentrations of a single substance* is said to have a *concentration gradient*

Integral and Peripheral Proteins What integrates the cytoskeleton and microfilaments? Integral proteins transport ___________ molecules into the membrane? Peripheral proteins also do what like the glycoproteins? What do they different?

-Proteins make up the *2nd major component of plasma membranes* -*Integral proteins* ( *integrins- span the membrane and attach on the other side* to proteins connected to microfilaments of the cytoskeleton.) are, as their name suggests, *integrated completely into the membrane structure*, and their *hydrophobic* membrane- spanning regions interact with the hydrophobic region of the the phospholipid bilayer -*Single-pass integral membrane proteins* usually have a *hydrophobic transmembrane of 20-25 amino acids* -Some span only part of the membrane—associating with a single layer—while others stretch from one side of the membrane to the other, and are exposed on either side -Some *complex proteins are composed of up to 12 segments of a single protein*, which are extensively *folded/embedded in the membrane* = *hydrophilic region* or regions, and one or several mildly hydrophobic regions -This arrangement of regions of the protein tends to *orient the protein alongside phospholipids*, *w/ hydrophobic region of the protein* adjacent to the tails of the phospholipids and the hydrophilic region or regions of the protein protruding *from the membrane in contact w/ the cytosol* or extracellular fluid. -*Integral membranes proteins* may have *one or more alpha-helices* that *span the membrane* or they may have *beta-sheets that span the membrane* -*Peripheral proteins* are found on the *exterior/interior surfaces* of membranes, *attached to integral proteins/phospholipids* -*Peripheral proteins, + integral proteins* = may serve as *enzymes/structural attachments for the fibers* of the cytoskeleton, or as part of the *cell's recognition sites* = These are sometimes referred to as *"cell-specific" proteins* also when attached to -The body *recognizes its own proteins and attacks foreign proteins of invasive pathogens*

Channels What proteins help in faciitated transport? What proteins open/close like gates?

-The *integral proteins involved in facilitated transport* = *transport proteins*, and they function as either *channels for material/carriers* -In both cases, they are *transmembrane proteins* Negative charged cant pass through *POTASSIUM AND SODIUM can't pass* + *HYDROGEN/CARBON DIOXIDE CAN PASS* THROUGH -*Channels are specific for the transported substance* -*Channel proteins have hydrophilic domains* exposed to the *intracellular and extracellular fluids*; they additionally have a *hydrophilic channel through their core* that provides a *hydrated opening through the membrane layers* -*Passage through the channel allows ions/charged/polar compounds* to *AVOID nonpolar central layer* of the plasma membrane that would otherwise *slow or prevent entry* into the cell -*Dr. Peter Agre* received the 2003 Nobel Prize in Chemistry *researched Rh proteins* + founded *Aquaporins* = *channel proteins allow water to pass through the membrane QUICKLY* -*Facilitated transport* moves *substances down their concentration gradients* + they *may cross the membrane w/ channel proteins* -*Channel proteins* are *either open/"gated"* which *controls channel opening* -The *attachment of a particular ion to the channel protein* may *CONTROL the opening* or other mechanisms or substances may be involved -In some *tissues* = *sodium/chloride ions pass freely thru open channels* + whereas *in other tissues a gate must be opened to allow passage* -Ex: this *occurs in the kidney* where *both forms of channels are in diff parts of renal tubules* -*Cells involved in transmission of electrical impulses* (*nerve and muscle* cells) have *gated channels for sodium, potassium, calcium* in their membranes -*Opening/closing these channels changes the concentrations on opp sides of the membrane* of these ions = resulting in the *facilitation of electrical transmission along membranes* (*nerve cells*) or in *muscle contraction* (*muscle cells*)

Membrane Fluidity The membrane is fairly rigid and can what if penetrated? Unsaturated fatty acids don't have a max number of ________ but have carbon atoms bending? Saturated fatty acids in a cold environment would make a membrane less ______

-The *mosaic characteristic of the membrane* in *fluid mosaic model*, helps to *illustrate its nature* -The *integral proteins/lipids exist in the membrane* as *separate* but *loosely attached molecules* -These resemble the *separate, multicolored tiles* of a mosaic picture, and they *float, moving w/ respect to one another* -The membrane is not like a balloon, however, that can expand and contract; rather, it is *fairly rigid and can burst if penetrated* or if a *cell takes in too much water* but w/ mosaic nature, a *very fine needle can easily penetrate a plasma membrane w/o causing it to burst* -The *mosaic characteristics explain some but not all of its fluidity* -There are *two factors *that help maintain this fluid characteristic = one factor is the nature of the *phospholipids* themselves -*In saturated form*, the *fatty acids in phospholipid tails are SATURATED w/ bound hydrogen atoms* -There are *no double bonds btwn carbon atoms* -This results in *tails are relatively straight* -In contrast, *unsaturated fatty acids don't have maximal number of hydrogen atoms*, but they do *contain some double bonds btwn carbon atoms* - a double bond results in a *bend in the string of carbons of approximately 30 degrees* -If *saturated fatty acids*, with their straight tails, are *compressed by decr temps*, they *press in on each other, making a dense/rigid membrane* -If *unsaturated fatty acids are compressed*, the *"kinks" in their tails elbow adjacent phospholipid molecules* away, maintaining some space between the phospholipid molecules This *"elbow room" helps to keep fluidity in the membrane at temps saturated fatty acid tails in their phospholipids would "freeze"* or solidify -The *relative fluidity of the membrane is important in a cold environment* -A *cold environment compresses membranes of saturated fatty acids*, making them *less fluid and more susceptible to rupturing* -Many *organisms (fish) are capable of adapting to cold environments* by *changing proportion of unsaturated fatty acids in response to low temps* -*Animals have an additional membrane* constituent that assists in *maintaining fluidity* -*Cholesterol*, which lies alongside the phospholipids in the membrane, tends to *dampen temp effects* on the membrane -Thus, this *lipid functions as a buffer*, *prevents lower temps from inhibiting fluidity + incr temps from incr fluidity* too much -Thus, *cholesterol extends*, in both directions, the range of temperature in which the *membrane is appr fluid* and *consequently functional* -*Cholesterol* = *btwn phospholipids + 2 phospholipid layers* also serves other functions, such as *organizing transmembrane proteins into lipid rafts*

Microbiologist What do they study? They can also identify what?

-The *most effective action to prevent the spread of contagious illnesses is to wash your hands.* Why? *Bc microbes* (organisms so tiny that they can only be seen with microscopes) *are ubiquitous on doorknobs, money, your hands*, and many other surfaces. -However, *not all microbes* (also called microorganisms) *cause disease*; *most are actually beneficial* like *microbes in your gut that make vitamin K* + *others ferment beer/wine* -*Microbiologists* = scientists who *study microbes* -Microbiologists can pursue a number of careers. Not only do *they work in the food industry*, they are also *employed in the veterinary/medical fields/pharmaceutical sector* serving key roles in research and development by *identifying new sources of antibiotics* that could be used to treat bacterial infections. -*Environmental microbiologists* may look for *new ways to use genetically engineered microbes* for the *removal of pollutants* from soil or groundwater, as well as hazardous elements from contaminated sites -These *uses of microbes* = *bioremediation technologies* -*Microbiologists* can also *work in the field of bioinformatics*, providing specialized knowledge and insight for the design, *development, and specificity of computer models* of, for example, bacterial epidemics.

Primary Active Transport

-The *primary active transport* that functions *w/ active transport of sodium/potassium allows secondary active transport to occur* -The *second transport method* is still considered *active bc it depends on the use of energy* as does primary transport -*Primary active transport* = *moves ions across a membrane*, creating an *electrochemical gradient (electrogenic transport)* -*One of the most important* pumps in *ANIMAL cells* is the *sodium-potassium pump (Na+-K+ ATPase)*, which *maintains the electrochemical gradient* (and the correct concentrations of Na+ and K+) in living cells The sodium-potassium pump *moves K+ into the cell* while *moving Na+ out* at the same time, at a ratio of *3 Na+ for every 2 K+ ions in* -The *Na+- K+ ATPase exists in 2 forms* depending on its orientation to the interior or exterior of the cell and its *affinity for either sodium or potassium ions*. The process consists of the following six steps. *1) With the *enzyme TOWARDS INTERIOR of the cell* = the *carrier has a high affinity for sodium ions* + *Three ions bind to the protein* *2) *ATP is hydrolyzed by the protein carrier* and a *low-energy phosphate group attaches* to it. *3) As a result, the *carrier changes shape and re-orients itself towards the exterior* of the membrane. The *protein's affinity for sodium decr* and the *3 sodium ions leave* the carrier. *4) The *shape change incr the carrier's affinity for potassium ions*, and *2 such ions attach to the protein* Subsequently, the *low-energy phosphate group detaches* from the carrier. *5) With the *phosphate group removed and potassium ions attached*, the *carrier protein repositions itself towards the interior* of the cell. *6) The *carrier protein, in its new configuration, has a decr affinity for potassium*, and the *2 ions are released into the cytoplasm*. The *protein now has a higher affinity for sodium ions*, and the process starts again. Several things have happened as a result of this process. At this point, there are more sodium ions outside of the cell than inside and more potassium ions inside than out. For every three ions of sodium that move out, two ions of potassium move in. This results in the *interior being slightly more negative relative to the exterior* This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential.

Immunologist

-The *variations in peripheral proteins/carbohydrates*that *affect cell's recognition sites* are of prime *interest in immunology* -These *changes are taken into consideration in vaccine development* -Many infectious diseases, such as *smallpox, polio, diphtheria, tetanus, were conquered by vaccines* -*Immunologists* = the physicians and *scientists who research/develop vaccines*, as well as *treat/study allergies* or other immune problems. -*Some study/treat autoimmune problems* (diseases in which a *person's immune system attacks own cells or tissues, such as lupus*) and immunodeficiencies, whether acquired (such as acquired *immunodeficiency syndrome, or AIDS*) or hereditary (such as severe combined immunodeficiency, or SCID) -*Immunologists* are called in to help *treat organ transplantation patients*, who must have their *immune systems suppressed so bodies will not reject a transplanted organ* -Some *understand natural immunity/effects of a person's environment* on it -Others work on questions about how the immune system affects diseases such as cancer. In the past, the importance of having a healthy immune system in preventing cancer was not at all understood. -To work as an immunologist, a *PhD or MD* is required. In addition, immunologists undertake at least *2-3 years of training in an accredited program* and must pass an *examination given by the American Board of Allergy and Immunology* -Immunologists must *possess knowledge of the functions of the human body as they relate to issues beyond immunization*, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures.

Fluid Mosaic Model The model was identified in the _______ and its principal components were what (2)? The first model was made when and by which people and how? In 1950, what mistake was fixed from the first model? In what year did the fluid mosaic model finally come out? Unlike triglycerides, phospholipids are made of what? Cholesterol has how many carbon fused rings? Proteins: __% Lipids: __% Carbs: ___%

-The existence of the *plasma membrane identified in the 1890s*, and *its chemical components were identified in 1915* -The *principal components were* = *lipids and proteins* -The *first model* of the plasma membrane's structure was proposed *in 1935 by Hugh Davson and James Danielli* it was based on the *"railroad track" appearance* of the plasma membrane in early electron micrographs -They theorized that the structure of the *plasma membrane resembles a sandwich*, with *protein = bread*, and *lipids = filling* -In the *1950s*, advances in *microscopy, notably transmission electron microscopy (TEM)*, allowed researchers to see that the *core consisted of a DOUBLE, rather than a single, layer* -A *new model *that better explains both the microscopic observations and the function of that plasma membrane was *proposed by S.J. Singer and Garth L. Nicolson in 1972* -*The explanation proposed by Singer and Nicolson* is called the *FLUID MOSAIC MODEL* the model has evolved somewhat over time, but it still best accounts for the structure and functions of the plasma membrane as we now understand them -The fluid mosaic model *describes the structure of the plasma membrane as a mosaic* of components—including UNSATURATED FATS *phospholipids, cholesterol, proteins, carbohydrates*—that gives the *membrane a fluid character* -Plasma membranes range from *5 to 10 nm in thickness* -For comparison, *human red blood cells, visible via light microscopy*, are approximately *8 μm* wide, or approximately *1,000 times wider than a plasma membrane* -The *principal components* of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and *have carbohydrates attached to some of the lipids/proteins* -A *phospholipid* is a molecule *consisting of glycerol*, *2 fatty acids*, and *a phosphate-linked head group* -*Cholesterol*, another lipid composed of *4 fused carbon rings* is *found in phospholipids* in the core of the membrane -The *proportions of proteins, lipids, carbohydrates* in the plasma membrane *vary by cell type*, but for a typical *human cell*, *protein = 50%* of the composition by mass, *lipids = 40%* of the composition by mass, with the remaining *carbohydrates = 10%* -Ex: *myelin* = an *outgrowth of the membrane* of *specialized cells insulating axons of peripheral nerves*, (*18% protein* and *76% lipid*) -The *mitochondrial inner membrane* contains *76% protein and only *24% lipid* -The plasma membrane of *human red blood cells* is *30% lipid* -*Carbohydrates* are present only on the *exterior surface of the plasma membrane* and are attached to *proteins = glycoproteins*, or attached to *lipids = glycolipids*

Reporting Scientific Work Difference between scientific writing and creative writing. What 3 things are important for scientific research? What 2 ways can scientists share results? What's a grant proposal? What is the format of a scientific paper?

-Whether basic science or applied science, *scientists must share their findings for other researchers to expand upon their discoveries*. *Planning, conducting, analyzing results are all important for scientific research*. -*Scientists can share results* = *scientific meeting* or conference, but most use *peer-reviewed manuscripts that are published in scientific journals*. *Peer-reviewed manuscripts are scientific papers that are reviewed by a scientist's colleagues/peers*judge whether or not the scientist's work is suitable for publication. -*Grant proposals*= *requests for research funding subject to peer review*. *Scientists publish their work for reproduction of experiments to expand on the findings* and *scientific paper diff than creative writing*. -*There are fixed guidelines in scientific results*: *brief, concise, accurate* and *allow peers to reproduce experiments*. -The scientific paper has *introduction, materials and methods, results, and discussion* (*"IMRaD" format*) Sometimes *reference sections as well as an abstract* (a concise summary) at the beginning of the paper.

EUKARYOTIC (Animal, Plant, Fungi, Protist) Cell Organelles What organelles are involved with genetic control(2-3)? Where does the rRNA reside? What are the 2 types of ribosomes? What organelles are involved with manufacturing, distributing, breakdown (6)? Difference between the two ERs. What is made by the Rough ER and processed by the golgi apparatus? What do vesicles do that vacuoles dont? Glyoxomes use what organelle to convert fat to sugar? What organelles process energy (2)? Which membrane of the mitochondria makes the ATP? What are the chromosomes like? What organelles are used for structural support/movement and communication (12)? What in the cytoskeleton is made up of actin and keratin? What has 9 triplets of microtubules?

1) GENETIC CONTROL -*Nucleus*: *DNA/synthesis of ribosomes and proteins*, stores *chromatin- dna/protein + ribo synthesis*, *membrane 2 phospholipid bilayers*, linear 46 chromosomes, *nucleolus- rRNA* -*Ribosomes*: (Like prokaryotes) *large/small subunits protein and RNA*, membrane/er/outer nuclear env, receive *orders from nucleus for protein synthesis where DNA->mRNA*, mRNA comes to *ribosomes translation to bases to amino acids*, found in pancreas for digestive enzymes •*Free ribosomes in the cytosol* •*Bound ribosomes are attached to the outside of the endoplasmic reticulum* or nuclear envelope. 2)MANUFACTURING, DISTRIBUTING, BREAKDOWN -*Rough ER*: *ribosomes attached to its cytoplasmic surface* give it a studded appearance, *modifies proteins*, *makes phospholipids* -*Smooth ER*: few-no ribosomes, *synthesis of carbohydrates/lipids/hormones*, *detoxifies medication/poisons*, *storage of calcium ions*, *makes vesicles*, adds short chains/sugar, comes in cis leaves trans -*Golgi Apparatus*: Sorting, tagging, *packaging/distribution of lipids and proteins*, *synthesize polysachs* -*Lysosomes*: •*made by rough ER* and processed in the *Golgi apparatus* garbage, *food vacuoles/enzymes breakdown macromolecules* proteins, polysaccharides, lipids, nucleic acids, microphages, *low pH*, *destroy bacteria by white blood cells*, *fuse with other vesicles* -*Vesicles/Vacuoles*: *storage/transport*, vesicles fuse membranes, vacuoles don't, plant vacuoles breakdown macromolecules -*Peroxisomes*: small round, *oxidation reactions breakdown fatty/amino acids*, *detoxify poisons*, *glyoxysomes in plants convert fats to sugars* 3)ENERGY PROCESSING -*Mitochondria*: *oval double phospholipid membrane*, own *ribo/DNA*, powerhouse bc *makes ATP w/ glucose via cell respiration*, *uses O2*, *produces CO2*,•Folds of the inner mitochondrial membrane, called *cristae, increase the membrane's surface area,* enhancing the mitochondrion's ability to produce ATP. -*Chloroplasts*: *photosynthesis, *stack of fluid-filled sacs (thylakoids) = grana*, light harvesting reactions, synthesis of sugar in stroma, own genome- circular chromosome 4)STRUCTURAL SUPPORT, MOVEMENT, COMMUNICATION -*Cytoskeleton*: *ions/organic molecules*, *shape/movement*, protein fibers-*microfilaments* (globular protein- *actin uses ATP*, *7nm*), *intermediate filaments* (*8-10nm, structural, keratin/epidermis*), *microtubules*(two globular a and b tubulins, 25nm*, resist compression) -*Centrosome*: *microtubule-org center w/ 2 centrioles- 9 triplets of microtubules*, where microtubules originate, *replicates before cell division* -*Cytoplasm*: organelles in *gel-like cytosol, *75% water*, *solid consistency from proteins*, *sugars, polysaccharides, amino/nucleic/fatty acids, glycerol*, dissolved *sodium potassium, calcium* -*Plasma Membrane*: (like prokaryotes) *phospholipid bilayer w/ embedded proteins* - tunnels/pumps (*channels shielding hydrophilic ions thru hydrophobic center* + *use ATP to actively transport molecules in/out*), *phospholipid (lipid w/ 2 fatty acid chains + phosphate group)*, controls the *passage of organic molecules, ions, water, oxygen, wastes Some membranes *absorb* + *folded into microvilli* found in *small intesine* - *damaged by celiac disease and bad response to gluten* (CO2/NH3)* -*Extracellular Matrix* -*Plasmodesmata*: *plant transfer water* from its roots, through its stems, and to its leaves uses the *vascular tissues (xylem and phloem)* -*Desmosomes*: *cadherins connect intermediate filaments*, *skin, heart, muscle cells* -*Cell Junctions* *Tight Junction*: cells are held tightly against each other *by proteins (claudins and occludins)* -*Gap Junction*: *6 connexins arrange themselves in a connexon*, *cardiac muscle* -*Cell Walls*: *protects/supports/shapes*, fungi/protists have, peptidoglycan- prokaryotic, plants- cellulose -*Flagella*: move by *bending motor proteins called dynein feet* -*Cillia*: *exchange genetic info*, *9 + 2 microtubule* move by *bending motor proteins called dynein feet*

Parts of Prokaryotic Cell (rod-shaped bacterium)

1. Plasma Membrane 2. Cell Wall 3. Capsule 4. Nucleoid 5. Ribosomes 6. Fimbriae 7. Flagella BACTERIA ATTACHES ITSELF W FIMBRIAE AND MOVES W FLAGELLA TO INFECTCAPSULE CAUSES DISEASE - pathogenicity PENICILLIN DESTROYS/LYSES CELL WALLS OF BACTERIA VACCINE MADE BY CAPSULE

Four levels of protein structure

1. Primary: *unique sequence of amino acids in a polypeptide chain* 2. Secondary: *local folding of the polypeptide*. The most common are the *α-helix and β-pleated sheet held in shape by hydrogen bonds* The hydrogen bonds form *btwn oxygen atom in the carbonyl group* in one amino acid and *another amino acid that is 4 amino acids farther* along the chain -*β-pleated sheet* are formed by *hydrogen bonding btwn atoms on backbone of polypeptide chain* -*R groups are attached to carbons and extend above/below folds of the pleat* -The *pleated segments align parallel/antiparallel to each other*, and *hydrogen bonds form btwn the partially posi nitrogen atom in the amino group* + *partially negative oxygen atom in the carbonyl group* -The α-helix and β-pleated sheet structures are found in *most globular and fibrous proteins* and they play an important structural role. 3. Tertiary: *Unique 3D structure of polypeptide* due to *chemical interactions at work on the polypeptide chain* -*Interactions among R groups creates the complex 3D tertiary structure of a protein* -*R groups found in the amino acids counteract hydrogen bonds* described for standard secondary structures -*R groups w/ like charges are repelled* by each other and *those w/ unlike charges are attracted to each other (ionic bonds)* -*Hydrophobic R groups of nonpolar amino acids lay inside the protein* whereas the *hydrophilic R groups lay outside* known as hydrophobic interactions -*Interaction btwn cysteine side chains* = *disulfide linkages w/ oxygen* the *only covalent bond* forming during protein folding. 4. Quaternary: More than 1 amino acide chain *proteins are formed from several polypeptides* from subunits, and the *interaction of these subunits forms quaternary structure* -*Weak interactions btwn subunits help stabilize overall structure* Ex: *insulin (a globular protein)* has a combination of *hydrogen bonds/disulfide bonds mostly clumped into a ball shape* b/c it *started as single polypeptide* and *loses some internal sequences via post-translational modification* after the formation of the disulfide linkages that hold the remaining chains together. *Silk (a fibrous protein) has a β-pleated sheet structure from hydrogen bonding* between different chains.

The Scientific Method Figure 1.5 Biologists study the world with what? Who made the scientific method and when and how?

Biologists *study the living world w/ questions* and *seeking science-based responses* -The *scientific method was first documented by England's Sir Francis Bacon* in *1620* who set up *inductive methods for scientific inquiry* and can be applied to almost all fields of study as a logical, rational problem-solving method The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let's think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: "Why is the classroom so warm?"

Intercellular Junctions and Endomembrane System

Cells can also communicate with each other via direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata are junctions between plant cells, whereas animal cell contacts include tight junctions, gap junctions, and desmosomes.•The endomembrane system includes the •nuclear envelope, •endoplasmic reticulum (ER), •Golgi apparatus, •lysosomes, •vacuoles, and •plasma membrane.

Homeostasis Figure 1.13 How do polar bears maintain homeostasis in cold environments? How do dogs and humans in hot environments? To functions, cells need _____, _____, ________ _________? These change but organisms maintain internal conditions via ________. What is thermoregulation?

Figure 1.13 *Polar bears* (Ursus maritimus) and other mammals *living in ice-covered regions* maintain their body temperature by *generating heat and reducing heat loss w/ FUR, feathers, blubber, fat* -Dogs pant, humans perspire in hot conditions -To function: *cells need proper temp, pH, chemical concentration* -These *conditions may change* from one moment to the next but *organisms are able to MAINTAIN INTERNAL CONDITIONS via homeostasis* (literally, *"steady state"*) -*Thermoregulation* = *organism* needs to *regulate body temp*

Cytochrome C Involved in what? Where and when is it released?

Involved in energy transfer, it is a protein released from mitochondria when cell is stressed.

The Scientific Method Steps Figure 1.6 If hypothesis is incorrect, what can you do?

The *scientific method consists of a series of well-defined steps*. If a *hypothesis is not supported by experimental data, a new hypothesis can be proposed.* In the example below, the scientific method is used to solve an everyday problem. Order the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses. 1. Observation 2. Question 3. Hypothesis (answer) 4. Prediction 5. Experiment 6. Result

Evolution connection- humans What is artificial selection? What do humans produce and what do they accidentally cause?

•Evolution is a core theme of biology. •*Humans selectively breed plants and animals* in the process of *artificial selection* to produce •*move prod crops*, •*better livestock*, and •a *great variety of pets that bear little resemblance to their wild ancestors*. •Humans also unintentionally cause •the *evolution of antibiotic-resistant bacteria*, •the *evolution of pesticide-resistant pests*, and •the *loss of species through habitat loss* and *global climate change*

endosymbiotic theory

•The endosymbiont theory states that •mitochondria and chloroplasts - own dna/ribo were formerly small prokaryotes and •they began living within larger cells.

Biological Study: Neurobiology, paleontogoly, zoology, botany

- Another field of biological study, *neurobiology* = studies the *biology of the nervous system*, considered a branch of biology, it is also *recognized as an interdisciplinary field of study-neuroscience* -Because of its interdisciplinary nature, this subdiscipline studies *diff functions of the nervous system using molecular, cellular, developmental, medical, computational approaches* -*Paleontology* = another branch of biology, *uses fossils to study life's history*. *Zoology and botany are the study of animals and plants*, respectively. Biologists can also specialize as *biotechnologists, ecologists, or physiologists*, to name just a few areas. This is just a small sample of the many fields that biologists can pursue.

Biology is the study of _______ Biologist study from _______ level to ______ level to _______ level Researchers are committed to 1. 2. 3. Figure 1.3

-*Biology is the study of living organisms and their interactions with one another and their environments* (broad definition b/c the scope of biology is vast) -*Biologists may study* from the *microscopic or submicroscopic view of a cell* to *ecosystems* and the *whole living planet* -Daily news: *Escherichia coli (norm residents of digestive tract aid in absorption of Vitamin K) outbreaks in spinach* and *Salmonella contamination in peanut butter* + *cure for AIDS, Alzheimer's disease, and cancer* -Researchers are committed to *finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change*

Isomers What are isomers? What do structural isomers differ in? What about geometric isomers (opp of structural)? What is a cis configuration? What is a trans configuration? Which one has a bend? What are enantiomers?

-*3D placement of atoms and chemical bonds* within *organic molecules central to understanding chemistry* -*Molecules that share the same chemical formula differ in the placement (structure)* of their atoms and/or chemical bonds are known as isomers -*Structural isomers* (like butane and isobutene) *differ in the placement of their covalent bonds: both molecules have 4 carbons and 10 hydrogens (C4H10)* but the *diff arrangement of the atoms* within the molecules *leads to differences in their chemical properties* -Ex: due to *their diff chemical properties*, butane is suited for use as a fuel for cigarette lighters and torches, whereas isobutene is suited for use as a refrigerant and a propellant in spray cans. -*Geometric isomers, on the other hand, have similar placements of their covalent bonds but differ in DOUBLE bonds PLACEMENT are made to the surrounding atoms*, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule. -*When the carbons are bound on the same side of the double bond* = this is the *cis* configuration; if they are on *opp sides of the double bond* = it is a *trans* configuration where *carbons form a more linear structure*, whereas the carbons in the *cis configuration make a bend (change in direction)* of the carbon backbone. -*Molecules that have the same number/type of atoms arranged differently* are called *ISOMERS* (a) *Structural isomers have a diff covalent arrangement of atoms*. (b) *Geometric isomers have a diff arrangement of atoms around a double bond*. (c) -*Enantiomers* = *mirror images of each other*

Scientific Reasoning Figure 1.7 What do all forms of science have (goal)? What are the 2 driving forces for development of science? What 2 methods of logical thinking do scientists use to understand the world? A gentleman in ____ discovered what and how? The scientific method may seem too rigid and structured but there is ____________.

-*All forms of science*: an ultimate *goal "to know"* -*Curiosity/inquiry* are the *driving forces for development of science* -*Scientists* seek to *understand the world/how it operates* w/ *2 methods of logical thinking: inductive reasoning and deductive reasoning* -*Inductive reasoning* = *logical thinking using related careful specific observations to arrive at a general conclusion* (descriptive science). A *life scientist/ biologist makes observations* (qualitative or quantitative), and the raw data w/ drawings, pictures, photos, or videos -*Deductive reasoning*(hypothesis-based science) = *thinking moves opp to inductive reasoning*, *general principle/law to forecast specific results* -Scientist can extrapolate/predict specific results valid as long as the general principles are valid. -Ex: climate change studies -Scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change. -The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. •In the 1940s, biochemists first isolated and identified the proteins actin and myosin from muscle cells. •In 1954, scientists, using newly developed techniques of microscopy, established how filaments of actin and myosin interact in muscle contraction. •In the next decade, researchers identified actin filaments in all types of cells. •In the 1970s, scientists were able to visualize actin filaments using fluorescent tags and in living cells. •In the 1980s, biologists were able to record the changing architecture of the cytoskeleton. For example, *a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog's fur* had a tiny hook structure. On closer inspection, he discovered that the burrs' gripping device was more reliable than a zipper. He eventually developed a company and produced the hook-and-loop fastener popularly known today as *Velcro*. *Descriptive science* and hypothesis-based science are in continuous dialogue. -The *scientific method may seem too rigid and structured* but *there is flexibility*. Sometimes an *experiment leads to conclusions* that favor a change in approach; often, *an experiment brings new scientific questions to the puzzle*. Scientific reasoning is more complex than the scientific method alone suggests. Notice, too, that the scientific method can be applied to solving problems that aren't necessarily scientific in nature.

Covalent Bonds and Other Bonds and Interactions What is another way the octet rule can be satisfied besides ionic bonds? What is a covalent bond? Which is stronger: ionic or covalent? The more covalent bonds between atoms, the ________. Why do organisms have difficulty acquiring nitrogen for molecules?

-*Another way the octet rule can be satisfied* = *unpaired electron in outer shell share a pair of electrons* = *covalent bonds*. These *bonds are stronger and common than ionic bonds in the molecules* of living organisms. -*Covalent bonds are commonly found in carbon-based organic molecules*, such as our *DNA/proteins* -*Covalent bonds* are also found in *inorganic molecules like H2O, CO2, and O2* -*The more covalent bonds btwn two atoms, the stronger* their connection (triple bonds- strongest) -*The strength of different levels of covalent bonding* is why *living organisms have a difficulty acquiring nitrogen for their molecules*, even though *molecular nitrogen, N2, is the most abundant gas in the atmosphere* -Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, the sharing of these three pairs of electrons between the two nitrogen atoms allows for the filling of their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA. -*The formation of water molecules provides an example of covalent bonding*. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. *The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atoms and the incomplete outer shell of the oxygen atoms.* To completely fill the outer shell of oxygen, which has six electrons in its outer shell but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence the well-known formula H2O. The electrons are shared between the two elements to fill the outer shell of each, making both elements more stable.

Atomic Number and Mass What do the number of protons tell us? What are isotopes? What is the atomic mass in relation to isotopes?

-*Atoms of each element* = *characteristic number of protons/electrons* -The number of *protons determines an element's ATOMIC NUMBER* and is used to distinguish one element from another -The number of *neutrons is variable*, *resulting in isotopes*, which are *diff forms of the same atom that vary only in the number of neutrons* they possess -Together, the number of *protons and neutrons determine an element's mass number* -*Element's isotopes* = *same protons, diff neutrons*, *scientists also determine the atomic mass*, which is the calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons).

Carl Woese and the Phylogenetic Tree What are the 5 kingdoms of life and what where they organized by? When did Carl Woese make this and what 3 domains showed? What is bacteria known as and what is archaea known as? Taxonomic tree has GFO CPK To construct his tree, Woese used ________ _________ rather than similarities based on morphology (shape). He used comparative sequencing of genes and compares ___/___ sequences.

-*Biologists grouped living organisms into 5 kingdoms: animals, plants, fungi, protists, and bacteria*. The organizational scheme was *based mainly on physical features*, as opposed to physiology, biochemistry, or molecular biology, all of which are *used by modern systematics*. -*American microbiologist Carl Woese* in the early *1970s has shown life on Earth has evolved along 3 lineages Bacteria (diverse prokaryotes), Archaea (extreme prokaryotes), and Eukarya* -The *first two are prokaryotic cells* -The *third domain contains the eukaryotes* and *includes unicellular microorganisms* together w/ *four original kingdoms* (excluding bacteria) -*Woese defined Archaea as a new domain*, and this resulted in a *new taxonomic tree- names species/classifies them into a hierarchy of *genus, family, order, class, phylum, kingdom*. Many organisms belonging to the Archaea domain *live under extreme conditions and are called extremophiles* -To construct his tree, Woese *used genetic relationships rather than similarities* based on morphology (shape). He used *comparative sequencing of genes universally distributed* + *compared homologous DNA/RNA sequences provided Woese w/ variability of prokaryotes*

The Process of Science What is biology - knowledge that covers ______ and can be tested by?

-*Biology is a science* (Latin scientia, meaning "knowledge") can be defined as *knowledge that covers general truths/laws, when acquired/tested by the scientific method* -It becomes clear that *the application of the scientific method plays a major role in science*. The *scientific method* = a *method of research w/ defined steps of experiments and careful observation*

The Diversity of Life Biology is so _______ bc of evolution. Evolution is? What are plants, animals/humans, fungus in ecosystems? What is a phylogenetic tree and who made it and how?

-*Biology* = has such a *broad scope w/ tremendous diversity of life* on earth -The *source of this diversity* is *EVOLUTION*, = *gradual change of new species arising from older species* -*Evolutionary biologists study microscopic world to ecosystems*- *PLANTS = producers*, *ANIMALS/HUMANS = consumers*, *FUNGI/MICROORGS = decomposers* -*Evolution of various life forms on Earth* = can be summarized in a *PHYLOGENETIC TREE (Carl Woese obtaining from ribosomal RNA genes)* = showing the *evolutionary relationships of species based on similarities and differences in genetic/physical traits* -A phylogenetic tree is *composed of nodes and branches*. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch is proportional to the time elapsed since the split

Introduction of Themes and Concepts of Biology Biology is the science that studies ____? Example of a branch of biology? Some biologists study what bc events that preceded life are not considered? Biology has wrestled w 3 questions: 1. 2. 3.

-*Biology* = is the *science that studies life* -For example, a branch of biology called *virology studies viruses*. It turns out that although *viruses can attack living organisms, cause diseases, reproduce* -Some biologists study the early molecular evolution that gave rise to life; since the *events that preceded life are not biological events*, these scientists are also excluded from biology in the strict sense of the term -*From its earliest beginnings, biology has wrestled with*: *what shared properties make something "alive"*? And *once we know something is alive, how do we find meaningful levels of organization* in its structure? And, finally, when faced with the remarkable diversity of life, *how do we org the diff kinds of organisms*? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.

Electron Orbitals What did the Bohr Model forget to show? Mathematical equations can predict what? Susbshells are designated by _, _, _, _ The s subshell is shaped and can hold how many? The p subshell is shaped? What about 3n and 4n? Moving away from the nucleus, the energy levels do what?

-*Bohr model of the atom doesn't reflect how electrons are spatially distributed* surrounding the nucleus. *They don't circle the nucleus like the earth orbits the sun*, but are *found in electron orbitals*. These relatively *complex shapes result from the fact that electrons behave not just like particles, but also like waves*. -*Mathematical equations* from quantum mechanics known as *wave functions can predict within a certain level of probability where an electron might be* at any given time. *The area where an electron is most likely to be found* = *ORBITAL* -*Subshells are designated by the letter s, p, d, and f* -The *s subshell* = *spherical in shape* and has *1 orbital* (can hold 2 electrons) -*Principal shell 2n has 1 s and 1 p subshell* (can hold 8 electrons) -The *p subshell* = *3 dumbbell-shaped orbitals* -*Subshells d and f have more complex shapes and contain five and seven orbitals* -Principal *shell 3n has s, p, and d subshells and can hold 18 electrons* -Principal *shell 4n has s, p, d and f orbitals and can hold 32 electrons* -*Moving away from the nucleus*, the number of *electrons and orbitals found in the energy levels incr* -*Closest orbital to the nucleus (filled first) = 1s orbital* can hold up to *two electrons* -This *orbital is equivalent to the innermost electron shell of the Bohr model* of the atom. - Ex: Hydrogen has one electron; therefore, it has only one spot within the 1s orbital occupied. This is designated as 1s1, where the superscripted 1 refers to the one electron within the 1s orbital. Helium has two electrons; therefore, it can completely fill the 1s orbital with its two electrons. This is designated as 1s2, referring to the two electrons of helium in the 1s orbital. Hydrogen and helium are the only two elements that have the 1s and no other electron orbitals in the electrically neutral state.

Carbon Dating Carbon is found where and in what form? What is Carbon-14? How is it created? It's a __________ process so more ____ is always being created. When an organism dies, what happens to 14C what process is it? Approx how many years does it take for half of 14C to convert to 14N. What is half-life?

-*Carbon is present in the atmosphere* in the *form of gaseous compounds like carbon dioxide and methane* -*Carbon-14* (14C) is a *naturally occurring radioisotope that is created in the atmosphere from atmospheric 14N* (nitrogen) by the *addition of a neutron and the loss of a proton* because of cosmic rays. *PHOTOSYNTHESIS* -This is a *continuous process, so more 14C is always being created*. As a living organism incorporates 14C initially as carbon dioxide fixed in the process of photosynthesis, *the relative amount of 14C in its body is equal to the concentration of 14C in the atmosphere* -*When an organism dies* = no longer ingesting 14C, so the *ratio btwn 14C and 12C will decline as 14C decays gradually to 14N* by a process called *beta decay*—the *emission of electrons/positrons* in a slow process -After approx 5,730 years, half of the starting concentration of 14C will have been converted back to 14N. The *time it takes for half of the orig concentration of an isotope to decay back to its more stable form* is called its *HALF-LIFE* Because the half-life of 14C is long, it is used to date formerly living objects such as old bones or wood. Comparing the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. On the basis of this amount, the age of the material, such as the pygmy mammoth can be calculated with accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, 40K (potassium-40) has a half-life of 1.25 billion years, and 235U (Uranium 235) has a half-life of about 700 million years. Through the use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms to understand how organisms have evolved from earlier species.

Microscopy Why do we use microscopes - 2 reasons? What are pictures taken w/ microscopes called? Microscope lenses do what?

-*Cells vary in size* -With few exceptions, *individual cells cannot be seen w/ naked eye*, so scientists *use microscopes* (micro- = "small"; -scope = "to look at") to study them -*Microscope* = an *instrument that magnifies an object* -Most *photographs of cells are taken by microscope* and these images can also be = *micrographs* -The optics of a *microscope's lenses change the orientation of the image* that the user sees -*A specimen that is right-side up and facing right* on the microscope slide will appear *upside-down and facing left* when viewed through a microscope, and vice versa. If the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up -This occurs because *microscopes use 2 sets of lenses to magnify the image* bc of how *light travels through the lenses*, this system of two lenses *produces an inverted image* (*binocular/dissecting microscopes*, work in a similar manner, but *include an additional magnification system that makes the final image upright*)

Introduction of Carbon What are the macromolecules of a cell? What is the fundamental component for them? Carbon has unique properties (4)

-*Cells* = are made of *many complex molecules called macromolecules*, such as *proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids* -The *macromolecules are a subset of organic molecules* (any carbon-containing liquid, solid, or gas) that are especially important for life -The *fundamental component* for all of these macromolecules is *carbon* -The *carbon atom has unique properties* that allow it to *1. form covalent bonds* to as many as four different atoms IN *2. LINEAR, ARMS, RINGS* or *"backbone," of the macromolecules* -Individual *3. carbon atoms have an incomplete outermost electron shell* With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. -*4. carbon atoms can form up to 4 covalent bonds to satisfy the octet rule* -Ex: Methane has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.

The Structure of the Atom Chemicals make up what? And what (2) do they do? An atom has the same chemical properties as ________. An atom has 2 regions? What subatomic particles make up an atom? What element has no neutrons? How much does an electron weigh and how much do protons/neutrons weigh? How to calculate atom's mass? What do protons tell us (2)? What do neutrons tell us (2)? What do electrons tell us (2)?

-*Chemicals* = *make up organisms' bodies* + the *environment* + *preserve, make nutritious food* -*How elements come together* = *smallest component/building block of an element* is the *atom* -*Atom* = the *smallest unit of matter w/ all the chemical properties of an element* For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold. -*An atom has 2 regions*: the *NUCLEUS* = *in the center of the atom* + *protons and neutrons*, and the *outermost region has electrons in orbit* around the nucleus -*Atoms = protons, electrons, neutrons, among other subatomic particles*. The only *exception is hydrogen (H) = 1 proton + 1 electron w/ no neutrons* -*Protons and neutrons have approx the same mass* = ab *1.67 × 10^-24 g* -*protons and neutrons* = *similiar in mass but differ in electric charge* -A *proton is positively charged* whereas a *neutron is uncharged* -*Electron weighs only 9.11 × 10-28 g* -*Atom's mass* = *protons + neutrons* -*PROTONS* = *atomic number, number of shells* -*NEUTRONS*= *mass*, *isotopes* -*ELECTRONS* = *atom's charge/(in valence) chemical activity*, as each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge. -Solid objects don't pass through one another b/c electrons surrounding atoms repel each other

Disaccharides formed by what? what's a glycosidic bond? Common disaccharides: Fructose is _____ than glucose so in HFCS____% Fructose and ____% Glucose.

-*Disaccharides* (di- = "two") form when *2 monosaccharides undergo dehydration reaction* -During this process, the *HYDROXYL group of 1 monosaccharide combines w/ HYDROGEN of another monosaccharide*, *releasing water forming a covalent bond -glycosidic* -*Covalent bond formed btwn a carbohydrate molecule/another molecule* (in this case, between two monosaccharides) is a *glycosidic bond* -Glycosidic bonds (also called glycosidic linkages) *can be alpha or beta* type -*Sucrose* = formed when a *monomer of glucose + monomer of fructose* are joined in a *dehydration reaction to form a glycosidic bond* -In the process, a *water molecule is lost*, the *carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group* -*SUCROSE* = a glycosidic *linkage btwn carbon 1 in glucose and carbon 2 in fructose* -*Common disaccharides are lactose, maltose, and sucrose* -*Lactose* = a disaccharide from *monomers glucose and galactose*( milk) -*Maltose* or malt sugar = a disaccharide by a dehydration reaction btwn *2 glucose molecules* -The *most common disaccharide is sucrose* = or table sugar composed of the monomers *glucose and fructose* •*Fructose = sweeter than glucose* •To make *HFCS (55% fructose 45% glucose)= glucose atoms rearranged to make the glucose isomer fructose*

Octet Rule and Valence Shell How do electrons fill orbitals? The electrons in what energy level determines stability? What is the max number of electrons in the first shell? What is the max number of electrons in the other shells? What does the outermost shell determine (2)?

-*Electrons fill orbitals in a consistent order*: they *first fill the orbitals closest to the nucleus*, then they continue to *fill orbitals of incr energy further from the nucleus* -If there are *multiple orbitals of equal energy*, *they will be filled w/ one electron in each energy level before a second electron is added*. The electrons of the *outermost energy level* = determine the *energetic stability of the atom* and its tendency to form chemical bonds. -Under standard conditions, *atoms fill the inner shells first resulting in a variable number of electrons in the outermost shell*. The *innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons* = OCTET RULE *atoms are more stable energetically w/ eight electrons in their valence (outermost) shell* - *determines chemical properties of the atom* -EX: helium has a complete outer electron shell, with two electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell containing eight electrons. In contrast, chlorine and sodium have seven and one in their outer shells, respectively, but theoretically they would be more energetically stable if they followed the octet rule and had eight

Enantiomers They are the what of eachother w/ the same ______/_____ but differ placement in 3D placement of atoms. There are two structures that are ________________. L forms do what? D forms are where? D and L are _________.

-*Enantiomers* = are *molecules that share the same chemical structure/chemical bonds* but *differ in 3D placement of atoms so that they are mirror images* -*An amino acid alanine* = *two structures are non-superimposable* -In nature, only the *L-forms of amino acids are used to make proteins* -Some *D forms of amino acids are seen in the cell walls of bacteria*, *glucose is the main product of photosynthesis* and the L-form of the molecule is rarely seen in nature. -D-alanine and L-alanine are examples of enantiomers or mirror images. Only the L-forms of amino acids are used to make proteins.

Protein Structure examples Enzyme binds where? If this is altered what happens?

-*Enzyme can bind to a specific substrate* at *active site* -If this active site is altered in overall protein structure, the *enzyme may be unable to bind to the substrate* -Primary: *unique sequence of amino acids in a polypeptide chain* -Ex: *Pancreatic hormone insulin has 2 polypeptide chains, A and B, (unique to insulin) linked by disulfide bonds* *N terminal amino acid of the A chain is glycine*, *C terminal amino acid is asparagine* Ex: *Bovine serum insulin = protein hormone made of two peptide chains* A (21 amino acids long) and B (30 amino acids long). The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide (S-S) bond. Two disulfide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulfide bonds are the same length, but are drawn different sizes for clarity. -*In sickle cell anemia* = the *hemoglobin β chain* has a *single amino acid substitution*, causing a *change in protein structure/function* Specifically, the amino acid *glutamic acid is substituted by valine in the β chain* - *Hemoglobin molecule* is *made up of 2 alpha chains + 2 beta chains* that each *consist of 150 amino acids* + has 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule is a single amino acid of the 600. What is even more remarkable is that those 600 amino acids are encoded by three nucleotides each, and the mutation is caused by a single base change (point mutation), 1 in 1800 bases. -Beta chain of hemoglobin is 147 residues in length, yet a single amino acid substitution leads to sickle cell anemia. In normal hemoglobin, the amino acid at position seven is glutamate. In sickle cell hemoglobin, this glutamate is replaced by a valine -Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and assume a crescent or "sickle" shape, which clogs arteries (Figure 3.27). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease. Sickle cells are crescent shaped, while normal cells are disc-shaped.

Types and Functions of Proteins They act as what in biochemical reactions because they lower the what energy? The enzyme is specific to the substrate and helps w what 3 things? Difference bwteen anabolic and catabolic reactions. What are the 8 functions and give some examples for each?

-*Enzymes* produced by *living cells* are *catalysts in biochemical reactions* (digestion) and *usually complex/conjugated proteins* -*Enzyme is specific for the substrate* (a reactant that binds to an enzyme) it acts on. The enzyme may help in *breakdown, rearrangement, or synthesis* reactions -*Enzymes that BREAK DOWN* their substrates are *CATABOLIC enzymes* that *BUILD MORE* complex molecules from their substrates are *ANABOLIC* enzymes, and *enzymes affect RATE OF REACTION* = *catalytic* enzymes Ex: *salivary amylase* which *hydrolyzes its substrate amylose* (starch) -*Hormones are chemical-signaling* = *small proteins/steroids* secreted by endocrine cells that act to control or regulate specific physiological processes, including *growth, development, metabolism, reproduction* -Ex: *insulin is a protein hormone* that helps to *regulate the blood glucose level* The primary types and functions of proteins 1. *Digestive Enzymes* (*Amylase, lipase, pepsin, trypsin*) Help in *digestion of food by catabolizing nutrients* into monomeric units 2. *Transport in cell membrane*(*Hemoglobin, albumin*) Carry *sugar molecules in the blood/lymph through the body* 3. *Structural* (*Actin, tubulin, keratin*, collagen) *Construct diff structures*, like the *cytoskeleton* 4. *Hormones* (*Insulin, thyroxine) Coordinate the (activity of diff body systems* 5. *Defense* (*Immunoglobulins*) *Protect the body* from foreign pathogens 6. *Contractile in muscle cells* (*Actin, myosin*) Effect *muscle contraction* 7. *Storage* (*Legume storage proteins*, egg white (*albumin*)) *develop embryo/seedling* 8. *Receptor in cell membranes* receive and transmit signals into your cells,

Omega Fatty Acids + Waxes These essential fatty acids are ______ by humans and are attained by ______. What are the effects of omega 3? They serve as ______ and ________

-*Essential fatty acids are fatty acids required* but *NOT MADE by the human body* supplemented through *ingestion via diet* -*Omega-3 fatty acids* fall into this category and are one of *only 2 known for humans (the other being omega-6 fatty acid)* -These are (more than 2 double bonds) *polyunsaturated fatty acids* + called omega-3 bc *3rd carbon from the end of the hydrocarbon chain is connected to its neighboring carbon* by a double bond -*Farthest carbon from carboxyl group* = *omega (ω) carbon* and if the *double bond is btwn 3rd/4th carbon* = *omega-3 fatty acid* -Nutritionally important because the *body does not make them*, omega-3 fatty acids include *alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA)*, all of which are *polyunsaturated*. Ex: *Salmon, trout, and tuna* Research indicates that omega-3 fatty acids *reduce the risk of sudden death from heart attacks*, *reduce triglycerides in blood*, *lower blood pressure*, and *prevent thrombosis by inhibiting blood clotting*, *reduce inflammation*, and may help reduce the risk of some cancers in animals. Like carbohydrates, fats have received a lot of bad publicity -*Many vitamins are fat soluble*, and fats serve as a *long-term storage form of fatty acids*: a source of *energy* + *insulation* -Therefore, "healthy" fats in moderate amounts should be consumed on a regular basis -*Wax* = *covers the feathers* of some aquatic birds and the *leaf surfaces* of some plants. Because of the *hydrophobic nature* of waxes, they *prevent water from sticking* on the surface. Waxes are made up of *long fatty acid chains esterified to long-chain alcohols*

Forensic Scientist What do they answer questions related to? What do they do? The development of what (2) has expanded work that forensic scientists can do? What does their work involve analyzing?

-*Forensic science* = the *application of science to answer questions related to the law* -*Biologists, chemists, biochemists* can be forensic scientists. Forensic scientists provide *scientific evidence for use in courts* + *examine trace materials associated w/ crimes* -*Interest in forensic science* has *increased* Tin the last few years b/c *popular TV shows feature forensic scientists* on the job. Also, the development of *molecular techniques + establishment of DNA databases* have *expanded types of work that forensic scientists can do*. Their *job activities are primarily related to crimes against people such as murder, rape, and assault*. Their work involves *analyzing samples of hair, blood, body fluids, processing DNA* found in many diff environments/materials. -*Forensic scientists also analyze other biological evidence left at crime scenes*, such as insect larvae or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take *chemistry and biology courses as well as some intensive math* courses.

Functional Groups They are groups of atoms with ? How is a carbon backbone formed by/ EACH ______________ has their own set of functional groups that contribute to what properties? Name the 8 functional groups and what is special about the last one? What does the carboxyl group do? What else does a hydrogen bond do besides water properties?

-*Functional groups* = *groups of atoms within molecules* and *confer specific chemical properties to those molecules*+ *found along the "carbon backbone" of macromolecules* -This *carbon backbone is formed by chains and/or rings of carbon atoms* w/ *substitution of an element such as nitrogen or oxygen* -*Molecules w/ other elements in their carbon backbone* are *substituted hydrocarbons* -The *functional groups* in a macromolecule are usually *attached to the carbon backbone* at one or several different places along its chain and/or ring structure -*Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids*—has its own characteristic *set of functional groups* that *contribute greatly to its differing chemical properties* and its *function in living organisms* -A *functional group can participate in specific chemical reactions* -they include: *hydroxyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl* *METHYL - NONPOLAR HYDROPHOBIC* -These groups play an *important role in the formation of molecules like DNA, proteins, carbohydrates, lipids* -Classified as *hydrophobic or hydrophilic depending on their charge or polarity characteristics* -Ex: *hydrophobic group is the non-polar methane molecule* -Among the *hydrophilic functional groups is the carboxyl group* found in amino acids, *some amino acid side chains/fatty acids form triglycerides and phospholipids* -This *carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the neg charged COO- group*; this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the *carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules*, again making the molecule more *hydrophilic* -*Hydrogen bonds btwn functional groups *(within the same molecule or between different molecules) are important to the *function of many macromolecules and help them to fold properly* into and *maintain the appropriate shape for functioning* -*Hydrogen bonds* are also *involved in various recognition processes*, such as *DNA complementary base pairing* and the *binding of an enzyme to its substrate* -*Hydrogen bonds* *connect two strands of DNA together* to create the *double-helix structure*

Hydrocarbon Chains These chains are formed by what and can look like? The geometry is determined by how many ________ there are. Single bond: eth___ + ____ along axis of bond Double bond: eth___ leads to a ______ configuration Triple bond: eth___ leads to a ______ configuration.

-*Hydrocarbon chains* = formed by *successive bonds btwn carbon atoms* and may be *branched or unbranched* -Furthermore, the overall *geometry of the molecule is altered by the diff geometries of single, double, and triple covalent bonds* -The *hydrocarbons ethane, ethene, and ethyne* = how different *carbon-to-carbon bonds affect the geometry* of the molecule. The names of all three molecules start with the prefix "eth-," which is the prefix for two carbon hydrocarbons -*The suffixes "-ane," "-ene," and "-yne" refer to the presence of single, double, or triple carbon-carbon bonds*, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butane, and butyne for four carbon molecules, and so on -*Double/triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond*, whereas *double bonds lead to a planar* configuration and *triple bonds to a linear one* -These *geometries impact shape a particular molecule can assume* -When *carbon forms single bonds w/ other atoms, the shape is tetrahedral* -When two carbon atoms form a *double bond, the shape is planar, or flat* *Single bonds are able to rotate* -*Double bonds (ethene) cannot rotate* so the atoms on either side are locked in place

Hydrocarbon Rings _______ hydrocarbons consist of linear carbon atoms. _________ hydrocarbons consist of closed rings which have _________ bonds. Benzene ring includes 3 diff molecules.

-*Hydrocarbons have been aliphatic hydrocarbons* which consist of *linear chains of carbon atoms* -*Hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms* -*Ring structures* are found in hydrocarbons, sometimes with the *presence of double bonds*, which can be seen by comparing the structure of cyclohexane to benzene -*Benzene ring include some amino acids and cholesterol* and its derivatives, including the *hormones estrogen and testosterone* -The *benzene ring is also found in the herbicide 2,4-D*. Benzene is a natural component of crude oil and has been classified as a carcinogen. *Some hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an example of such a hydrocarbon*

Hydrocarbons What are they? Many of these hydrocarbons have what bonds that store a lot of energy and release it when they are burned? What is the simplest hydrocarbon molecule? What shape does it form and how many degrees is it spaced apart? The number of C2C bonds affects what of the macromolecule?

-*Hydrocarbons* = *organic molecules* consisting entirely of *carbon and hydrogen* such as methane (CH4) described above. We often use *hydrocarbons in our daily lives as fuels*—like the *propane in a gas grill or the butane in a lighter* -Many *covalent bonds btwn the atoms in hydrocarbons store a great amount of energy* which is *released when these molecules are burned (oxidized)* -*Methane*, an excellent fuel, is the *simplest hydrocarbon molecule*, with a central carbon atom bonded to four different hydrogen atoms -The geometry of the *methane molecule, where the atoms reside in three dimensions*, is determined by the shape of its electron orbitals. *The carbons and the four hydrogen atoms form a shape known as a tetrahedron spaced 108.5 degrees apart*, with four triangular faces; for this reason, methane is described as having tetrahedral geometry -As the backbone, *hydrocarbons may exist as linear carbon chains, carbon rings, or both* -*Carbon-to-carbon bonds may be single, double, or triple covalent bonds* and each type of bond affects the geometry of the molecule in a specific way. This three-dimensional *shape or conformation of the large molecules of life (macromolecules)* is critical to *how they function*

Isotopes What is an isotope? What are 3 examples? Some isotopes emit what for a stable configuration? Radioisotopes have more what than what? Radioactive decay does what (4) What is radioactivity? What is it useful for?

-*ISOTOPES* = *diff forms of an element* that have the *same number of protons* but *diff number of neutrons*. Some elements—such as *carbon, potassium, uranium—have naturally occurring isotopes* Ex: Carbon-12 contains *six protons, six neutrons* and six electrons; therefore, it has a *mass number of 12* (six protons and six neutrons). Carbon-14 contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). -These two alternate forms of carbon are isotopes -*Some isotopes may emit neutrons, protons, and electrons* for a *more stable atomic configuration* (lower level of potential energy); *these are radioactive isotopes*, or *RADIOISOTOPES* = *more neutrons than protons* Radioactive decay - *decays white blood cells* and *releases energy*, *damages DNA* and *prevents cell division* (carbon-14 losing neutrons to eventually become carbon-12) describes *the energy loss that occurs when an unstable atom's nucleus releases radiation* •radioactive compounds in metabolic processes can *act as tracers* used in *med diagnosis*. Sophisticated imaging instruments are used to detect them: •An *imaging instrument uses positron-emission tomography (PET)* detects the *location of injected radioactive materials* •PET is *useful for diagnosing heart disorders* and *cancer* and in brain research. •*Uncontrolled exposure can damage molecules in a living cell*, especially *DNA*. •*Chemical bonds are broken* by the *emitted energy*, which causes abnormal bonds to form.

Natural Sciences Figure 1.4 8 fields of science What do experts consider natural science? Difference between physical science and natural science and their datas.

-*In a museum of natural sciences*: *frogs, plants, dinosaur skeletons, exhibits of brain functions, planetarium, gems and minerals* -*Science* includes *astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics* -*Fields of science related to physical world and processes* are considered *natural sciences* -*Some experts say* natural sciences are *astronomy, biology, chemistry, earth science, physics* -*Other scholars* divide natural sciences into *life sciences* = *study living things like biology*, *physical sciences* = *study nonliving matter like astronomy, geology, physics, and chemistry* -*Biophysics and biochemistry build on both life and physical sciences* -*Natural sciences are "hard science"* b/c use of *quantitative data* -*Social sciences study society/human behavior* b/c use *qualitative assessments for investigations/findings* -Cell biologists- study the structure/function of a cell -Biologists study anatomy/structure of an entire organism -Physiology biologists study internal functions -Zoologists study animals

Reporting Scientific Work (Introduction, Materials/Methods, Results, Discussion, Conclusion, Review articles) Where do you need to quantify and state calculations and raw data? Where in the paper does it state where the hypothesis or research question driving the research will be presented? Where does it need citations (2)? What sections are usually combined? A well done scientific paper does what?

-*Introduction* = *brief, broad, background information about the field*, rationale of the work; it justifies the work carried out and also briefly mentions the end of the paper, where the hypothesis or research question driving the research will be presented. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is considered *plagiarism* -*Materials/methods* = complete and *accurate description of the substances used*, and the method/*techniques used by the researchers to gather data*. The description should be *thorough enough to repeat the experiment but concise*, how *measurements, calculations, statistical analyses to examine raw data* -Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not combine both sections, the results section simply narrates the findings w/o any further interpretation. (tables or graphs) -Proper citations are included in this section as well. -*Conclusion* = importance of the *experimental findings*. While the *scientific paper almost certainly answered one or more scientific questions that were stated* -*A well-done scientific paper leaves doors open for the researcher* and others to *continue the findings* -*REVIEW ARTICLES follow IMRAD format* + *don't present orig scientific findings/primary lit*; *instead, they summarize and comment on findings*

Hydrogen Bonds and Van Der Waals Interactions What do ionic and covalent bonds need in order to break? What does hydrogen bonding do (3)? When polar covalent bonds contain hydrogen, how does a weak attraction occur? This bond is common between_____ ______ molecules and are easily _________ When do Van der Waals attractions occur and between what? What is required of these molecules?

-*Ionic and covalent bonds require energy to break* -However, not all bonds are ionic or covalent bonds -*Weaker bonds can also form btwn molecules* *Two weak bonds* = *hydrogen bonds and van der Waals interactions* -W/o these, *life as we know it would not exist* -*Hydrogen bonds provide many of the critical: 1) life-sustaining properties of water* 2) *stabilize the structures of proteins/DNA/building block of cells* 3) responsible for *zipping together the DNA double helix* -*When polar covalent bonds containing hydrogen form*, the *hydrogen in that bond has a slightly positive charge* and will be attracted to neighboring negative charges. *When this happens, a weak interaction occurs* between the δ+of the hydrogen from one molecule and the δ- charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This interaction is called a *HYDROGEN BOND*. This type of bond is *common between water molecules* -*Individual hydrogen bonds are weak and easily broken*; however, they occur in *very large numbers in water and in organic polymers*, creating a major force in combination -*Like hydrogen bonds*, *van der Waals interactions are weak attractions or interactions between molecules* -Van der Waals attractions *can occur between any 2+ molecules/dependent on slight fluctuations of electron densities*, which are not always symmetrical around an atom -*The molecules need to be very close to one another* These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the three-dimensional structure of the proteins in our cells that is *necessary for their proper function*.

Matter and Elements Table 2.1 What is life made up of? And what is matter? How many elements are essential for life? What do trace elements do? The atmosphere has what two elements and in what %? What element is in life, atmosphere and earth's crust? IN life what are the percentages? The earth's crust has what two elements and what %?

-*Life is made up of matter*. *MATTER* = is *any substance occupying space and has mass* -*ELEMENTS* = *unique forms of matter w/ chemical/physical properties that can't be broken down* into smaller substances by ordinary chemical reactions -There are *118 elements, but only 92 occur naturally* + *25 ESSENTIAL FOR LIFE*. The remaining elements are synthesized in laboratories and are unstable -*TRACE elements* = *prevent disease* + *w/o iron theres no oxygen - anemia* -*Each element is designated by its chemical symbol* Ex: *C for carbon* and *Ca for calcium* -*Four elements to all living organisms*: *oxygen (O), carbon (C), hydrogen (H), and nitrogen (N)* = *96.3% BODY WEIGHT* -In the *non-living world* = *elements are found in diff proportions*, and some elements common to living organisms are relatively rare on the earth as a whole. -Ex: *atmosphere is rich in nitrogen/oxygen but contains little carbon/hydrogen*, while the *earth's crust contains oxygen and a small amount of hydrogen* -In spite of their differences in abundance, *all elements/chemical reactions btwn them obey the same chemical and physical laws* regardless of whether they are a part of the living or non-living world *OXYGEN* = *Life-65%*, *A-21%*, *EC- 46%* *CARBON* = *Life-18%*, *A-trace*, *EC- trace* *HYDROGEN* = *Life- 10%*, *A-trace*, *EC- 0.1%* *NITROGEN* = *Life-3%*, A-78%*, *EC-trace*

Levels of Organization of Living Things (Atom, molecule, macromolecule) Living things are highly _________. What is an atom and what does it look like? What doe atoms form and what are they held together by? What do molecules form and how are they formed by?

-*Living things* = highly *organized + structured on a small to large scale* -*ATOM* = *smallest unit of matter* w/ *nucleus surrounded by electrons* -*Atoms form molecules* which are *chemical structure consisting of 2+ atoms held together by 1+ chemical bonds* -*Macromolecules* = *biologically important* or *large molecules formed by polymerization* (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules) -*Ex: Macromolecule is deoxyribonucleic acid (DNA composed of atoms)* which contains the *instructions for the structure/functioning of all living organisms*

Monosaccharides These are the _______ sugars of glucose and fuel what? The number of carbon ranges from ___ to _____? ALDEHYDE has what carbonyl group at the ____ + ex of group KETONE has what carbonyl group at the _____ + ex of group TRIOSES, PENTOSES, HEXOSES = ? Monosachs are classified based on what positions? Chemical formula of GLUCOSE What role does glucose play in cell respiration/photosynthesis? What is a glucose ring form? If the hydroxyl group is below CARBON 1 = If the hydroxyl group is above CARBON 1 = Hexose examples: Pentose examples:

-*Monosaccharides* (mono- = "one"; sacchar- = "sweet") are *simple sugars of glucose* - fuel cell work/raw materials for org molecules -In monosaccharides, the *number of carbons usually ranges from 3-7* -*Hooked together via dehydration to form complex sugars/polysaccharides* -*Names end in -ose* -If the *sugar has an aldehyde group* (functional group w/ *R-CHO*), it is known as an *ALDOSE- carbonyl group at END*, and if it has a *ketone group* (functional group w/ *RC(=O)R'*), it is known as a *KETOSE- carbonyl group in MIDDLE* -Depending on the number of *carbons in the sugar may be known as TRIOSES* (three carbons), *PENTOSES* (five carbons), and or *HEXOSES* (six carbons) -*Monosaccharides -classified on carbonyl group POSITION* and *carbons in the backbone* Aldoses have a carbonyl group at the end of the carbon chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three, five, and six carbon backbones, respectively. -*Chemical formula* for *GLUCOSE* = *C6H12O6* -In humans, *glucose is an important source of energy* -*CELLULAR RESPIRATION* = *energy released from glucose* and that *energy is used to make adenosine triphosphate (ATP)* -*Plants synthesize glucose* w/ *carbon dioxide + water* -*Excess glucose* is often *stored as starch catabolized* (the breakdown of larger molecules by cells) *by humans/animals* that feed on plants -*Galactose* (part of lactose, or milk sugar) + *fructose* (found in sucrose, in fruit) are other common monosaccharides -*HEXOSES- Glucose, galactose (aldose), fructose (ketose)* all have the *same chemical formula (C6 H12 O6)*, but *differ structurally/chemically* (and are known as *isomers*) b/c *arrangement of functional groups around more than 1 asymmetric carbon* -*Glucose RING FORM* = *2 diff arrangements of hydroxyl group (OH)* around the *anomeric carbon (carbon 1 that becomes asymmetric* in the process of ring formation). If the *hydroxyl group is below carbon number 1* in the sugar = *alpha (α) position* and if it is *above the plane* = beta (β) position -*5/6 carbon monosaccharides* exist in *equilibrium btwn linear/ring forms*. When the ring forms, the *side chain it closes on is locked into an α or β position* -*Fructose and ribose* also *form RINGS* although they form *five-membered rings* as opposed to the six-membered ring of glucose.

Branches of Biological Study The scope of biology is _____ and has many different branches. Molecular biology studies what? Biochemistry studies what? Microbiology studies what? 2 factors of the dynamics of ecosystems?

-The *scope of biology is broad* and *contains many branches/subdisciplines* -*Biologists may pursue one subdiscipline and work in a focused field* -Ex: *MOLECULAR biology* = study *biological processes at the molecular level*, including interactions among *molecules such as DNA, RNA, and proteins*, as well as the way they are regulated -*BIOCHEMISTRY* = study *biological processes at the chemical level* -*Microbiology* = the *study of microorganisms*, is the study of *the structure/function of single-celled organisms*. It is quite a broad branch itself, and depending on the subject of study, *there are also microbial physiologists, ecologists, and geneticists, among others* -*Dynamics of ecosystems* = 1. *recycling chemicals from atmosphere thru producers, consumers and decomposer back to air* 2. *one way flow of energy*

Nonpolar covalent bond What is it (3)? Example?

-*Nonpolar covalent bonds form btwn 2 atoms of the same element or btwn diff elements that share electrons equally* -For example, *molecular oxygen (O2) is nonpolar bc the electrons will be equally distributed between the 2 oxygen atoms*. Another example of a nonpolar covalent bond is methane *(CH4)*. Carbon has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. •In molecules of only one element, *the pull toward each atom is equal*, because each atom has the *same electronegativity* -*Carbon and hydrogen do not have the same electronegativity* but are similar; thus, *nonpolar bonds form*. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule. -Figure 2.12 Whether a molecule is polar or nonpolar depends both on bond type and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out.

Nucleic Acids/ DNA AND RNA Nucleic acids hold what- what are the 2 main types? What is DNA and RNA? What is the difference between them? What is each nucleotide made of? Purines have what rings? Pyramidines? What is the phosphodiester linkage?

-*Nucleic acids* are the *most important macromolecules for the continuity of life*. They *carry the genetic blueprint of a cell* and carry *instructions for the functioning* of the cell. -*2 main types of nucleic acids* = *deoxyribonucleic acid (DNA)* and *ribonucleic acid (RNA)* -*DNA* = the *genetic material found in all living organisms* ranging from *single-celled bacteria to multicellular mammals* found in the *nucleus of eukaryotes* and *in the organelles, chloroplasts, mitochondria* -In *prokaryotes, the DNA is not enclosed in a membranous envelope* The entire genetic content of a cell is known as its genome, and the study of genomes is genomics. *In eukaryotic cells* but not in prokaryotes, *DNA forms a complex with histone proteins to form chromatin*, the substance of eukaryotic chromosomes -A chromosome may contain tens of thousands of genes. *Many genes contain the information to make protein products; other genes code for RNA products* -*DNA* = controls all of the cellular activities by *turning the genes "on" or "off'* -*RNA* is mostly involved in *protein synthesis* like *DNA molecules never leave the nucleus* but instead *use a messenger to communicate with the cell* = *(mRNA)* Other types of RNA—like *rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation* -*DNA and RNA* are made up of monomers known as *nucleotides* combine with each other to form a *polynucleotide, DNA or RNA* -Each nucleotide is made up of *three components: a nitrogenous base, a pentose (five- carbon) sugar, and a phosphate group*. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups. -*Organic molecules (carbon and nitrogen)* + *bases because they contain an amino group binding an extra hydrogen*, and thus, decreases the hydrogen ion concentration in its environment, making it more basic. Each *nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T)* -*Adenine/guanine* = *purines* = *two carbon-nitrogen rings* -*Cytosine, thymine, uracil* = *pyrimidines* = *single carbon-nitrogen ring* as their primary structure -The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose (Figure 3.31). The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as "one prime"). The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a *5′-3′ phosphodiester linkage*. The phosphodiester linkage is *not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules*: its formation involves the *removal of 2 phosphate groups*. A polynucleotide may have thousands of such phosphodiester linkages.

Scientific Method: Hypothesis and Theory What is the most important step and how is it tested by? How can it become a verified theory?

-*One of the most important aspects of scientific method* is the *testing of hypotheses by repeatable experiments* -A *hypothesis* = suggested *explanation for an event that can be tested* -*Scientific method is inherent to science*, it is *inadequate in determining what science is* b/c *easy to apply the scientific method* *to physics and chemistry*, but *not archaeology, psychology, geology b/c more *difficult to repeat experiments* -Consider *archeology* *one cannot perform repeatable experiments*, *hypotheses may be supported* -*Hypotheses could be correct/false through continued support or contradictions from findings* -A *hypothesis may become a verified theory* -*Theory* =*tested and confirmed explanation for observations* or phenomena -Science may be better defined as fields of study that attempt to comprehend the nature of the universe.

Growth and Development Figure 1.12 How do organisms grow? What do genes instruct? Difference between growth and development.

-*Organisms grow w/ specific instructions coded by their genes*. These genes provide instructions that will *direct cellular growth/development, ensuring same characteristics as its parents.* Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. - *Cell growth - irreversible change in the size* of the cells, grow in size -*Development* - if the egg doesn't *mature*/differentiate you can't form *organs*

Inert gases and Ions The periodic table is arranged on the total number of _______ + _________ What examples of elements have filled outer electron shells? What are inert gases? What element is most important to living systems? What do the columns of the periodic table represent?

-*Periodic table is based on the total number of protons (and electrons)* helps us know *how electrons are distributed among the outer shell*. The periodic table is *arranged* in columns and rows based *on the number of electrons* and *where these electrons are located*. Take a closer look at the some of the elements in the table's far right column. The *group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells*, making it *unnecessary to share electrons w/ other atoms* to attain stability; they are highly stable as single atoms -Their *non-reactivity* has resulted in their being named the *INERT GASES (or noble gases)*. Compare this to the group 1 elements in the left-hand column: hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can *achieve a stable configuration and a filled outer shell by donating/sharing 1 electron w/ another atom* or molecule like water -*Hydrogen will donate/share its electron to achieve this configuration*, while lithium and sodium will donate their electron to become stable. As a result of *losing a negatively charged electron, they become positively charged ions* -Ex: Group 17 elements, including fluorine and chlorine -Group 14 elements, of which *carbon is the most important to living systems*, have *four electrons in their outer shell allowing them to make several covalent bonds* with other atoms. Thus, the *columns of the periodic table* = *shared state of these elements' outer electron shells* that is responsible for their similar chemical characteristics.

Pharmaceutical Chemist What do they do?

-*Pharmaceutical chemists* = *responsible making new drugs* + and *determining the mode of action of old/new drugs* -They are *involved in every step of the drug development process* -Drugs *can be found in the natural environment* or can be *synthesized in the laboratory* -In many cases, *potential drugs* found in nature are *changed chemically in the laboratory* to make them *safer and more effective*, and sometimes synthetic versions of drugs substitute for the version found in nature -*After the initial discovery/synthesis of a drug* = the chemist then *develops the drug*, perhaps chemically altering it, *testing its toxicity*, and then *designing methods for efficient large-scale production* -Then, the *process of approval for human use begins* -In the US, *drug approval is handled by the Food and Drug Administration (FDA)* and involves a series of *large-scale experiments using human subjects to make sure the drug is not harmful* and effectively treats the condition it aims to treat. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete testing and gain approval -Ex: *Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer* discovered in the *bark of the pacific yew tree* -Ex: *Aspirin*, originally isolated *from willow tree bark*. Finding drugs often means *testing hundreds of samples of plants, fungi, and life forms* to see if any biologically active compounds are found within them -*Traditional medicine* can give *modern medicine clues to where an active compound is* -Ex: *willow bark to make medicine* has been known for thousands of years, dating back to ancient Egypt. It was not until the late 1800s, however, that the aspirin molecule, known as acetylsalicylic acid, was purified and marketed for human use. -*Drugs developed for one use are found to have unforeseen effects* that allow these drugs to be used in other, unrelated ways -Ex: *minoxidil (Rogaine)* was originally developed to *treat high blood pressure* and *when tested on humans = grow new hair* Eventually the drug was *marketed to baldness to restore lost hair* The career of the pharmaceutical chemist may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier.

Phospholipids The plasma membrane has fatty acid chains attached to?

-*Phospholipids* = *plasma membrane*, the outermost layer of *animal cells* -*LIKE FATS* = phospholipids *fatty acid chains attached to a glycerol*/*sphingosine backbone* -A phospholipid molecule consists of a *3-carbon glycerol backbone* with *2 fatty acid* molecules *attached to carbons 1 and 2, and a phosphate-containing group attached to 3rd carbon* -This *arrangement gives the molecule an area described as its head* (the phosphate-containing group), which has a *polar character or negative charge*, and an area called the *tail (the fatty acids), no charge*. The head can form hydrogen bonds, but the tail cannot. A molecule with this arrangement of a positively or negatively charged area and an uncharged, or non-polar, area is referred to as *amphiphilic or "dual-loving"* -*Instead of 3 fatty acids attached in triglycerides*, however, *there are 2 fatty acids forming diacylglycerol*, and the *3rd carbon of the glycerol backbone is occupied by a modified phosphate group* -A *phosphate group alone attached to a diaglycerol* does not qualify as a phospholipid; it *is phosphatidate (diacylglycerol 3-phosphate)*, the precursor of phospholipids -*Phosphate group* is *modified by an alcohol* -Ex: *Phosphatidylcholine and phosphatidylserine* in *plasma membranes* -*Phospholipid* = *2 fatty acids* + *modified phosphate group* attached *to glycerol backbone* -The *phosphate may be modified by the addition of charged/polar chemical groups* (*choline/serine*) -*Choline/serine attach to phosphate group* at the *position labeled R* via the *hydroxyl group* -*Phospholipid* = an *amphipathic molecule, w/ hydrophobic and a hydrophilic part* -*The fatty acid chains are hydrophobic* + *phosphate-containing group is hydrophilic* -The phospholipid bilayer is the *major component of all cellular membranes* -*Hydrophilic head* = face the *aqueous solution* -*Hydrophobic tails* are sequestered in the *middle of the bilayer* -In a membrane, *bilayer of phospholipids forms the matrix* of the structure, the *fatty acid tails of phospholipids* -If a drop of *phospholipids placed in water*, it spontaneously *forms a structure known as a micelle*, where the hydrophilic phosphate heads face the outside and the fatty acids face the interior of this structure. -When *placed in water, hydrophobic molecules tend to form a ball* or cluster = *micelles or liposomes* The *hydrophilic* regions of the phospholipids *tend to form hydrogen bonds w/ water* and other polar molecules on both the exterior and interior of the cell. Thus, the membrane surfaces that face the interior and exterior of the cell are hydrophilic. In contrast, the interior of the cell membrane is hydrophobic and will not interact with water. Therefore, phospholipids form an excellent two-layer cell membrane that separates fluid within the cell from the fluid outside of the cell.

Hydrolysis What is it? What is gained by 2 products? DEHYDRATION AND HYDROLYSIS are what by specific enzymes? What 4 enzymes break down carbohydrates? What 3 enzymes break down proteins? What enzyme breaks down lipids?

-*Polymers are broken down into monomers* in a process *HYDROLYSIS*, which means "to split water," a *reaction in which a water molecule is used* during the breakdown -During these reactions, the *polymer is broken into 2 components*: *one part gains a hydrogen atom (H+)* and the *other gains a hydroxyl molecule (OH-)* from a split water molecule -Ex: The *disaccharide maltose* is broken down to *form 2 glucose monomers w/ water molecule.* Note that this reaction is the reverse of the synthesis reaction -*Dehydration and hydrolysis reactions* are *catalyzed, or "sped up," by specific enzymes* -*Dehydration* reactions involve the formation of *NEW bonds requiring energy*, while *hydrolysis reactions break bonds release energy* -These reactions are *similar for most macromolecules*, but each monomer and polymer reaction is specific for its class Ex: our bodies, *food is hydrolyzed*, or broken down, into smaller molecules *by catalytic enzymes* in the digestive system. This allows for *easy absorption of nutrients* by cells in the intestine. Each macromolecule is broken down by a specific enzyme -*Carbohydrates* are broken down by *amylase, sucrase, lactase, maltase* -*Proteins* are broken down by the enzymes *pepsin and peptidase, hydrochloric acid* -*Lipids* are broken down by *lipases* -Breakdown of these macromolecules provides energy for cellular activities.

Protein Nature and Amino acids Proteins have different _____ and _________. Some proteins are (2)? Hemoglobin is globular but collagen is what? What about the protein depends on the chemical bonds? What is denaturation and what three factors affect it? All amino acids have what parts (CHNO) (4) and what attached to the central asymmetrical carbon? How many essential amino acids and how do humans get them and what are 3 essential ones? Nonpolar/hydrophobic side chains? VMA Polar/Hydrophilic side chains? STC Positive charged side chains: LA What has an R group to the amino group and forms a ring structure? What has a N terminal and a C/Carboxyl terminal?

-*Proteins have diff shapes/molecular weights*; some *proteins are globular* in shape whereas *others are fibrous in nature* Ex: *hemoglobin is a globular protein*, but *collagen in our skin is a fibrous protein* -*Protein shape is critical to its function*, and this *shape is maintained by many diff types of chemical bonds* -**substrate concentration/Changes in temp/pH, chemicals* = *permanent changes* in the *shape of the protein*, leading to *loss of function* = *DENATURATION* , pH, temp (body temp -All *proteins* are made up of diff arrangements of *20 types of amino acids* -*Amino acids* = the *monomers that make up proteins* -*Amino acid consist* = of a *central carbon atom (alpha (α) carbon)* + an *amino group (NH2)* + *carboxyl group (COOH)* + *hydrogen atom* -Every *amino acid the R group bonded to central atom* -*Amino acids have a central asymmetric carbon* to which *an amino group, a carboxyl group, a hydrogen atom, a side chain (R group)* are attached -"amino acid" is derived from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are *20 amino acids present in proteins*/ *10 are essential amino acids* in humans because the *human body cannot produce them and they are obtained from the diet*. For each amino acid, the R group (or side chain) is different -The *chemical nature of the side chain* = the *nature of the amino acid* (acidic, basic, polar, nonpolar) Ex: *amino acid glycine has hydrogen atom* as the R group. *Valine, methionine, alanine* are *nonpolar/hydrophobic* in nature while *Serine, threonine, cysteine are polar/hydrophilic side* chains. -Side chains *Lysine/Arginine* are *positively charged* = *basic amino acids* -*Proline has an R group linked to amino group* = forming a *ring- like structure* + *opp from reg amino acid* since its amino group is not separate from the side chain -*Essential amino acids* = *isoleucine, leucine, cysteine* = necessary for *construction of proteins* not produced by the body -The *sequence/amino acids* = ultimately determine the *protein's shape, size, function* -*Carboxyl group attached to amino group* by a *covalent bond or peptide bond* via *dehydration reaction* •A polypeptide chain contains hundreds or thousands of amino acids linked by peptide bonds. •The amino acid sequence causes the polypeptide to assume a particular shape. -*Polypeptides have a free amino group at one end* = *N terminal* and the other end has *free carboxyl group = *C or carboxyl terminal* -*Polypeptide* = *polymer of amino acids* -*Protein* = *polypeptides that have combined together* often have bound *non- peptide prosthetic groups*, *distinct shape, unique function* - Post -protein synthesis *(translation)*, most *proteins are modified*. -*Post-translational modifications* = They may undergo *cleavage, phosphorylation, addition of other chemical groups* = protein becomes functional

Proteins are one of the most abundant what molecules and have diverse functions in _______? Proteins may be (4) and serve in what? All have linear sequence of ? Steroids are the what for the carbon skeleton?

-*Proteins* = one of the *most abundant organic molecules* in living systems and have the most *diverse range of functions of all macromolecules* -*Proteins may be structural, regulatory, contractile, or protective* they may serve in *transport, storage, or membranes* or they may be *toxins/enzymes* -*Each cell* in a living system may contain *thousands of proteins w/ unique function* -Their *structures/functions vary greatly* -*They are all*, however, *polymers of amino acids* arranged in a *linear sequence* •*Steroids are lipids* in which the *carbon skeleton contains four fused rings*

Two Types of Science: Basic Science and Applied Science The scientific community debates about the ______ of these sciences. What is basic science or "____" science? What is applied science or "____" use science? Some people think it's useless while others think what about basic science?

-*Scientific community debating about the value of different types of science* and ask if it's valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question *focuses on the differences between two types of science: basic science and applied science.* -*Basic science or "pure" science* = seeks to *expand knowledge regardless of the short-term application of that knowledge* not focused on commercial value. *Immediate goal of basic science* is *knowledge for knowledge's sake*. -*Applied science or "technology"* = *use science to solve real-world problems* making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher. -Some individuals may perceive applied science as "useful" and basic science as "useless." A question these people might pose to a scientist advocating knowledge acquisition -Many scientists think that a *basic understanding of science is necessary before an application* is developed; therefore, *applied science relies on basic science*

Electron Configuration The second electron shell is what orbital and how many shaped p orbitals? What shell is filled after the 1s orbital? Larger elements have more _______? What do orbitals do?

-The *second electron shell* = *8 electrons, another spherical s orbital and 3 "dumbbell" shaped p orbitals*(2 electrons). -*After the 1s orbital is filled* = the *second electron shell is filled*, first filling its *2s orbital and then its 3 p orbitals*. -When filling the *p orbitals, each takes a single electron*; once each p orbital has an electron, a second may be added -Ex: Lithium (Li) contains three electrons that occupy the first and second shells. Two electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron configuration is 1s22s1. Neon (Ne), on the other hand, has a total of ten electrons: two are in its innermost 1s orbital and eight fill its second shell (two each in the 2s and three p orbitals); thus, it is an inert gas and energetically stable as a single atom that will rarely form a chemical bond with other atoms. -*Larger elements have additional orbitals*, making the third electron shell. -*Orbitals* - provide *more accurate depiction of electron configuration* bc the orbital model *specifies diff shapes/special orientations* of the places the electrons may occupy

Reproduction How do single-celled organisms and multicellular organisms reproduce? What is reproduction? If there is no division, then there is no _____. What are mitosis and meiosis? What do genes direct? What is sexual/asexual reproduction? What is binary fission and budding and what type of reproduction are they?

-*Single-celled organisms reproduce by first duplicating their DNA*, then *dividing it equally* as the cell prepares to divide to *form two new cells* -*Multicellular organisms often produce specialized reproductive germline cells* that will *form new individuals*. -*Reproduction* = *genes containing DNA are passed to an organism's offspring*. -These *genes ensure that the offspring will belong to the same species* and will have similar characteristics, such as size and shape - *Cell*: *plasma membrane*- entrance/exit, *organelles* (nucleus-DNA and genes - protein synthesis and *cytoplasm*) -NO division = NO growth. DNA is involved *Meiosis- gamete (germ/sex) cells* and *Mitosis- body cells* - cell divisions -Gene (*unit of inheritance*, *grouped into long DNA/chromosomes*, controls cell activities*) directs synthesis of organs in body. *Sexual reproduction- egg and sperm*. *Asexual- bacteria/plants/single parents* -*Binary fission: a single parent* and *Budding - happens in yeast*, also asexual. Cancer- abnormal cell division. Brain is the command center - develops functions. Babies get breast milk-has fat.

Regulation What organisms are the most complex to regulate and why? Two examples of internal functions regulated. What do organs do (4)? Homeostasis is what and what is the appropriate temp/pH for humans? Metabolic processes _____ w/ extremities in conditions.

-*Smallest organisms are complex & need to regulate internal functions, respond to stimuli, cope w/ environmental stresses*. -Two examples of internal functions regulated in an organism are *nutrient transport and blood flow* -*Organs* (groups of tissues working together) *carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, cooling the body* -*Homeostasis keeps a balance in the body* -Need appropriate temp (98.6), pH (7.4) -*Cells do digestion w/ enzymes* (in saliva). Enzymes are *proteins and can't perform in heat/high pH* -*Polar bears have fur to maintain homeostasis*, *we have coats* -*Snowy owls have feathers* for insulation and *keen vision/acute hearing* to hunt prey = result of *evolution* -*Metabolic processes come to a stop w/ decr temp* Maintain a stable internal environment. Hot weather - we sweat to keep stability. -*Insulin is released when sugar rises and takes up all the glucose in the cell* not blood which *breaks down into ATP*. Diabetes- internal homeostasis disturbed.

Irreversible and Reversible Reactions What are irreversible reactions? Reversible and why? When do products convert back into reactants? When does it stop, at what state? What is the law of mass action?

-*Some chemical reactions can proceed in one direction until the reactants are all used up*. These have a *unidirectional arrow and are irreversible* -*Reversible reactions* = are those that can *go in either direction* + *reactants are turned into products*, but when the concentration of *product goes beyond a certain threshold* (characteristic of the particular reaction), *some products convert back into reactants* -*This back and forth continues* until a certain relative *balance btwn reactants and products* = *equilibrium*. For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-) forming an equilibrium state with carbonic acid (H2CO3). If carbonic acid were added to this system, some of it would be converted to bicarbonate and hydrogen ions. -*Equilibrium is rarely obtained* because the *concentrations of the reactants or products constantly changing* -To return to the example of excess hydrogen ions in the blood, the formation of carbonic acid will be the major direction of the reaction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) *instead of being converted back to bicarbonate ion, thus driving the reaction to the right* by the chemical law known as *LAW OF MASS ACTION* important for *maintaining the homeostasis of our blood* = chemical law stating that the *rate of a reaction is proportional to the concentration of the reacting substances*

Electron Shells and the Bohr Model There's a connection between the number of __________, ______ _____, _________. In a neutral atom what is the same? Only electrons are involved in what? Who made the early model of the atom and when? What does the model show? These orbits form what? What is energy level 1n? Energy from a photon of life can do what? What happens to energy when it decays back to ground state?

-*There is a connection* btwn the number of *protons in an element, the atomic number that distinguishes one element from another, and the number of electrons* it has -In all electrically *neutral atoms* = the number of *electrons is the same as the protons*. Thus, the *number of electrons equal to its atomic number*. -only electrons are *directly involved in the chemical activity of an atom* -An *early model of the atom in 1913 by Danish scientist Niels Bohr* (1885-1962) -The *Bohr model shows the atom as a central nucleus containing protons/neutrons*, with the electrons in circular orbitals at specific distances from the nucleus -These *orbits form electron shells or energy levels*, which are a way of visualizing the *number of electrons in the outermost shells*. These energy levels are *designated by a number + "n"* -Ex: *1n = first energy level* located *closest to the nucleus*. *Energy from a photon of light can bump it up to a higher energy shell*, but this situation is unstable, and the *electron quickly decays back to the ground state*. In the process, a *photon of light is released*.

Steroids Unlike phospholipids, they have what structures? Cholesterol is a steroid in the bilayer, is it hydrophobic or not? Cholesterol is synthesized where? and a precursor to what 3? They are classified as what bc of the ol ending and OH functional group

-*Unlike phospholipids/fats* = *steroids have 4 FUSED RING STRUCTURES* -Although they do not resemble the other lipids, they are grouped with them because they are also *hydrophobic/insoluble in water* -All steroids have *4 linked carbon rings* and *several* like cholesterol, *have a short tail* -*Many steroids* also *have the -OH functional group* which puts them in the *alcohol classification (sterols)* Ex: Cholesterol and Cortisol -*Cholesterol* = is the *most common* steroid + *synthesized in the liver* + *precursor to many steroid hormones* such as *testosterone and estradiol* (secreted by gonads/endocrine glands) + *precursor to Vitamin D* + *precursor of bile salts* which help in the *emulsification of fats/absorption by cells* -Although cholesterol is often spoken of in negative terms by laypeople, it is *necessary for proper functioning of the body* + component of the *plasma membrane of animal cells* and is found *within the phospholipid bilayer* -*Plasma membrane* is *responsible for the transport of materials/cellular recognition* and it is involved in *cell-to-cell communication*

Water's Solvent Properties Water has slightly ______ and _______ charges. What molecules could readily dissolve in it? Water is referred to as a _________ bc it is capable of dissolving _________ molecules and _______ compounds but poor at nonpolar molecules. What is the sphere of hydration? What is dissociation and when does it occur?

-*Water is a polar molecule with slightly positive and slightly negative charges* = *ions and polar molecules can readily dissolve* in it -Therefore, *water is referred to as a solvent*, a substance *capable of dissolving other polar molecules/ionic compounds* -The *charges associated w/ these molecules will form hydrogen bonds* with water, surrounding the particle with water molecules. This is referred to as a *sphere of hydration*, or a hydration shell, and *serves to keep the particles separated/dispersed in the water* -When *ionic compounds are added to water*, the *individual ions react w/ polar regions of the water molecules* and their *ionic bonds are disrupted in the process of dissociation* -*Dissociation* = occurs when *atoms or groups of atoms break off from molecules and form ions* -Consider table salt (NaCl, or sodium chloride): when NaCl crystals are added to water, the molecules of NaCl dissociate into Na+ and Cl- ions, and spheres of hydration form around the ions. The positively charged sodium ion is surrounded by the partially negative charge of the water molecule's oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule.

Lipids LARGELY polar or nonpolar? Include mostly what bonds w what element to element? What are the 5 subtypes? They are ____x the energy of polysaccharides? What is a fat? Differ from carbs, proteins, nucleic acids bc WHAT?

-*diverse group of compounds that are largely nonpolar/insoluble* bc they're *hydrocarbons that include mostly nonpolar carbon-carbon* or *carbon-hydrogen bonds* -*Cells store energy* for long-term use *in fats -*Lipids provide insulation* from the environment for plants and animals -Ex: *aquatic birds and mammals dry when forming a protective layer over fur/feathers bc of their water- repellant hydrophobic* nature -*building blocks of many hormones* -*Lipids* = *fats, oils, waxes, phospholipids, and steroids* -*2x energy of polysaccharides* -consist mainly of *carbon + hydrogen atoms linked by nonpolar covalent bonds* -*3 types of lipids* 1.*fats*, 2.*phospholipids*, and 3.*steroids* •A fat is a *large lipid made from glycerol + fatty acids* -differ from carbs, proteins, nucleic acids = NOT BUILT FROM MONOMERS

Polysaccharides hydrophillic or hydrophobic chain of ? Chain may be __________ and functions as what? Four examples of polysaccharides? Starch is joined by a unbranched and branched what? Glycogen is found where and in what cells? Cellulose is in what organelle of the plant cell and has what linkage? Chitin is in what?

-*hydrophillic long chain of MONOSACCHARIDES (MORE THAN 2-disaccharide) linked by glycosidic bonds* = POLYSACCHARIDE (poly- = "many") -The *chain may be branched/unbranched* and may *function for storage/structure* -molecular weight may be 100,000 daltons or more -Ex: *Starch, glycogen, cellulose, chitin* -*1. Starch* = *(excess) stored form of sugars in plants* and is made up of a *mixture of amylose and amylopectin* (both polymers of glucose) -*used by plants for energy* + food for humans and animals. The starch that is consumed by *humans is broken down by enzymes (salivary amylases)*, into smaller molecules, such as maltose/glucose for cells absorb the glucose -*Starch* = glucose monomers joined by *unbranched amylose α 1-4* + *branched amylopectin α 1-6 glycosidic bonds* -*2. Glycogen* = *storage form of glucose in humans/animals* and is made up of monomers of glucose. Animal equivalent of starch and is a highly branched molecule *usually stored in liver and muscle cells* -Whenever *blood glucose levels drop* = *glycogen is broken down to release glucose in a process known as glycogenolysis* -*3. Cellulose* = is the *most abundant natural biopolymer*. The *cell wall of plants made of cellulose* this provides *structural support to the cell*. *Wood and paper* are mostly cellulosic in nature.*linked by β 1-4 glycosidic bonds* -*While the β 1-4 linkage cannot be broken down by human digestive enzymes* = *herbivores* such as cows, koalas, buffalos, and horses *are able, w/ specialized flora* digest plant material that is rich in cellulose and use it as a food source. In these animals, *certain species of bacteria and protists reside in the rumen* (part of the digestive system of herbivores) and *secrete the enzyme cellulase* *Cellulases can break down cellulose* into glucose monomers that can be used as an energy source by the animal(and Termites) 4. Chitin: *polysaccharide-containing nitrogen* + has *repeating units of N-acetyl-β-d-glucosamine*, a modified sugar. In *insects and crustaceans build an exoskeleton* + in *fungal cell walls*; fungi are neither animals nor plants and form a kingdom of their own in the domain Eukarya.

Fats and Oils What is a fat molecule made of? What is glycerol made of C:H:OH? How many carbons are there usually in fatty acids? Fatty acids attach 3 Carbons to and how? GLYCEROL + FATTY ACID = ? Fatty acids could be Un/____ Saturated/Single bonds have what? Unsaturated/Double bonds have what?

-A *fat molecule consists of 2 parts*: * 1 glycerol + 3 fatty acids* -*Glycerol* = *organic compound (alcohol)* w/ 3 carbons, 5 hydrogens, 3 hydroxyl (OH) -*Fatty acids* = have a *long chain of hydrocarbons + carboxyl group* is attached, hence the name "fatty acid." -*The number of carbons in the fatty acid* = *4 to 36* but usually *12-18* carbons -FAT = *fatty acids attach to each 3 carbons of glycerol via dehydration* w/ *ester bond via oxygen atom* -*GLYCEROL* + *FATTY ACID* = *TRIACYLGLYCEROL* -*Ester bond formation* = *3 water molecules released* -*Fats called triacylglycerols/triglycerides bc of chemical structure* -Some fatty acids have common names that specify their origin. Ex: *palmitic acid, a saturated fatty acid* = the *palm tree* or *Arachidic acid*= Arachis hypogea (groundnuts or peanuts) -*Fatty acids= saturated or unsaturated* -*SINGLE bonds btwn carbons in the hydrocarbon chain* = *SATURATED* - *max number of hydrogens attached to carbon* - Ex: *ANIMAL FATS + Stearic acid* -*DOUBLE bond(s)* = *UNSATURATED*. Ex: *OILS + Oleic acid* - *one fewer hydrogen on each carbon* + *bends in carbon chain preventing tight packing* -*Long, single bonded fatty acids* = *pack tightly* -*1 double bond is MONOUNSATURATED* -*2 double bonds is POLYUNSATURATED* -*Unsaturated fats/oils* are usually *plant origin* + *contain cis unsaturated fatty acids* -*If hydrogens are present in the same plane* = *cis fat*; if the *hydrogen atoms are on two diff planes* = *trans* fat -*Unsaturated fats* help to *lower blood cholesterol* levels whereas *saturated fats clog arteries*

Proposing and Testing a Hypothesis How do you solve a problem w/ hypotheses, should you make just one? Difference between hypothesis and prediction. A valid hypothesis is what 2 things and to test a hypothesis you must? Variable and Control group?

-A hypothesis is a suggested explanation that can be tested. *To solve a problem*= *several hypotheses may be proposed* -Ex: "The classroom is warm because no one turned on the air conditioning." But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, "The classroom is warm because there is a power failure, and so the air conditioning doesn't work." -*Once a hypothesis has been selected, the student can make a prediction w/ "If, then"* -*Valid hypothesis must be testable*/falsifiable* -Science does not claim to "prove" anything b/c scientific understandings are always subject to modification with further information. Ex: supernatural is neither testable nor falsifiable -*To test a hypothesis* = a *researcher conducts 1+ experiments to eliminate 1 or more hypotheses* -Each experiment will have one or more variables and one or more controls. -*Variable* = *tests hypothesis* and *part of the experiment that can change during the experiment* -*Control group* = *stays the same* and *every feat of the experimental group except the manipulation hypothesized about* -Results of experimental group differ from the control group due to hypothesized manipulation, rather than some outside factor. -*Each hypothesis should be tested by carrying out appropriate experiments*

Example of Basic/Applied Research: DNA replication and The Human Genome Project Figure 1.9 What are the strands of DNA and what happens during DNA replication? DNA replication allows us to now? What is the HUMAN GENOME PROJECT? What research did it rely on? Some discoveries are made by what? What's an example?

-After the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication -*Strands of DNA, unique in every human, are found in our cells (correlate to structure/function), where they provide the instructions necessary for life*. -*During DNA replication*, DNA makes *new copies of itself, shortly before a cell divides*. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to *identify genetic diseases*, pinpoint individuals who were at a crime scene, and determine paternity. -*Human Genome Project - 13yr collab among researchers working in several fields of science, a study in which each human chromosome was analyzed/mapped to determine the precise sequence of DNA subunits and exact location of each gene*. (The gene is the basic unit of heredity; an individual's complete collection of genes is his or her genome.) Other *less complex organisms have also been studied*. The Human Genome Project *relied on basic research carried out with simple organisms* and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases. -*Some discoveries are made by serendipity*, that is, by means of a *fortunate accident/lucky surprise* -*1928 Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open and mold grew on the dish, killing the bacteria*.

Chemical Reactions and Molecules -When are elements most stable? -What do elements do when they don't have enough to stabilize?

-All *elements are most stable when their outermost shell is filled with electrons* according to the octet rule. This is because it is *energetically favorable for atoms* to be in that configuration and it makes them stable. However, since *not all elements have enough electrons to fill their outermost shells*, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration -When *two or more atoms chemically bond* with each other, the *resultant chemical structure is a molecule*. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom; these bond together to form water, as illustrated in Figure 2.9. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.

Levels of Organization of Living Things [atom, molecule, organelles, cell (prokaryotes/eukaryotes) tissues, organs, organ system, organisms, population, community, ecosystem, biosphere) What is the smallest unit of matter? What is an example of a molecule? What is an example of an organelle? What are all living things made of? What are the types? What do tissues combine for? What is an organ system? What has all abiotic and biotic things? Three components of biosphere.

-Atom -Molecule- cluster of *atoms held together by a chemical bond* (H20, Glucose- molecule) -*ORGANELLES* = some *cells w/ aggregates of macromolecules surrounded by membranes* + *small structures within cells* performs *specific functions* -Ex: *mitochondria (energy to power the cell)* and chloroplasts* (green plants to utilize the energy in sunlight to make sugars) -*CELLS* = *what all living things are made of* + *smallest unit of structure/function in living organisms* (why viruses aren't living: they are not made of cells) To make new viruses, they have to invade and hijack the reproductive mechanism of a living cell; only then can they obtain the materials they need to reproduce.) -*PROKARYOTES* = are *single-celled organisms w/o membrane-bound nuclei* like *bacteria and archaea*, *first to evolve* and *smaller* -*EUKARYOTES* = *plants/animals/fungi/protists*, *membrane-bound organelles* and a membrane-bound *nucleus* like *nucleus carries DNA*, *mitochondria synthesizes ATP*, *ER synthesizes proteins*, *golgi apparatus modifies proteins* -*TISSUES* = *larger organisms' cells combine for similar/related functions* -*ORGANS* = *collections of tissues perform common function* -*ORGAN SYSTEM* = *several organs cooperating in a specific function* + *higher level of organization* of *functionally related organs*. Mammals have this. Ex: Circulatory System (transports blood from body to/from lungs) nervous, cardiovascular, respiratory, digestive, excretory, reproductive -*ORGANISMS* = *individual living entities* Ex: Tree, single-celled prokaryotes/eukaryotes (microorganisms) -*POPULATION*= *all individuals of a species* living in a specific area collectively - *More resources, more suitable environment* -*COMMUNITY* = *sum of populations in an area* + the *entire array of organisms* living in a particular ecosystem (Ex: forest) -*ECOSYSTEM* = all the organisms living in a particular area + physical components the organisms interact *All abiotic and biotic things* -*BIOSPHERE* = *collection of all ecosystems + zones of life on earth* all of the *environments on Earth* that support life including *land, water, air interactions* Important to *regulate climate*.

Chemical Reactions What is it? What are the substances used in the beginning of a chemical reaction called? What are the substances found at the end of the reaction called? What forms hydrogen peroxide? What is the law of conservation of matter?

-Chemical reactions *occur when 2 or more atoms bond together to form molecules or when bonded atoms are broken apart* -The substances used in the *beginning of a chemical reaction* = *REACTANTS* (usually found on the left side of a chemical equation), and the *substances found at the end of the reaction* = *PRODUCTS* (usually found on the right side of a chemical equation). For the creation of the water molecule shown above, the chemical equation would be: 2H + 0 -> H20 -*Simple chemical reaction* = *breaking down of hydrogen peroxide molecules*, each of which consists of *two hydrogen atoms bonded to two oxygen atoms* (H2O2). The *reactant hydrogen peroxide is broken down into water*, containing one oxygen atom bound to two hydrogen atoms (H2O), and oxygen, which consists of two bonded oxygen atoms (O2). -2H2O2 -> 2H2O + O2 is a *balanced chemical equation*, wherein the number of *atoms of each element is the same on each side of the equation*. -*Law of conservation of matter* = the *number of atoms before/after a chemical reaction should be equal* and no atoms created or destroyed. •*Chemical reactions do not create or destroy matter* they *only rearrange matter* -Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other atom), in this reaction only hydrogen peroxide and water are representatives of *COMPOUNDS*: they *contain atoms of more than 1 type of element* + *more common than pure elements* (H2O, NaCl) -Molecular oxygen, on the other hand, consists of two doubly bonded oxygen atoms and is not classified as a compound but as a mononuclear molecule.

Introduction of the Synthesis of Biological Macromolecules What are biological macromolecules? What are they made of? 4 classes? Combined, what do these molecules make up? Proteins have how many amino acids? How many nucleotides are in nucleotides?

-Critical *nutrients from food* are *biological macromolecules*, or large molecules, *necessary for life* -*Macromolecules (polymers) are built from diff combinations of smaller organic molecules (monomers)* -What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? -Biological macromolecules are *large molecules built from smaller organic molecules* -*Four major classes* of biological macromolecules (*carbohydrates, lipids, proteins, and nucleic acids*); each is an important cell component and *performs a wide array of functions* -Combined, these molecules *make up majority of a cell's dry mass* (recall that water makes up the majority of its complete mass) -Biological macromolecules are *organic, meaning they contain carbon*. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements. -*Cells make polymers from a small group of monomers* -*PROTEINS - 20 amino acids* -*DNA - 4 nucleotides*

Water's Cohesive and Adhesive Properties Water can stay above the glass bc of _______ where the same kind of molecules stick together. Cohesion allows for surface tension which is what? Cohesion and surface tension keep the______ ________ intact. What is adhesion and which one is stronger when there are charged surfaces? How do plants pull water up from roots, what is this process?

-Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms a dome-like shape above the rim of the glass. This *water can stay above the glass because of the property of cohesion*- tendency of *molecules of the same kind to stick together* + *stronger for water* than for other liquids -In *cohesion* = *water molecules are attracted to each other* (because of *hydrogen bonding*), keeping the *molecules together at the liquid-gas (water-air) interface*, although there is no more room in the glass -Cohesion allows for the development of *surface tension* = the *capacity of a substance to withstand being ruptured when placed under tension or stress* given by *hydrogen bonds* -This is also why water forms droplets when placed on a dry surface rather than being flattened out by gravity. When a small scrap of paper is placed onto the droplet of water, the paper floats on top of the water droplet even though paper is denser (heavier) than the water -*Cohesion and surface tension* keep the *hydrogen bonds of water molecules intact* and support the item floating on the top. It's even possible to "float" a needle on top of a glass of water -These *cohesive forces are related to water's property* of *ADHESION* = or the *attraction btwn water molecules and other molecules*2 kinds of molecules -This *attraction is sometimes stronger than water's cohesive forces*, *especially when the water is exposed to charged surfaces* (*inside of thin glass tubes known as capillary tubes*) -*Adhesion is observed when water "climbs" up the tube* placed in a glass of water: notice that the water appears to be higher on the sides of the tube than in the middle. This is because the *water molecules are attracted to the charged glass walls* of the capillary more than they are to each other and therefore adhere to it. This type of adhesion is called *capillary action* = in a glass tube is *caused by adhesive forces exerted by the internal surface of the glass exceeding the cohesive forces* between the water molecules themselves -*Cohesive and adhesive forces* = are *important for the transport of water from the roots to the leaves* in plants -These forces *create a "pull" on the water column*. This *pull results from the tendency of water molecules being evaporated* on the surface of the plant to stay connected to water molecules below them, and so they are *pulled along* -Plants use this natural phenomenon to help *transport water from their roots to their leaves*. Without these properties of water, *plants would be unable to receive the water and the dissolved minerals they require*. In another example, insects such as the water strider, use the surface tension of water to stay afloat on the surface layer of water and even mate there.

Electron Microscopes Electron Microscopes are more advanced than light microscopes but when did they come out? Specimens can be magnified up to how many times? The methods used to view specimens can do what to them? Electrons have short ___________ and move best in a __________ In a scanning electron microscope - you can view the _____________ In a transmission electron microscope - you can view the ____________

-In contrast to light microscopes, *electron microscopes starting from 1950s use a beam of electrons not beam of light* -This allows *ultrastructure of cells* + *for higher magnification (100,000x) /detail/ resolving power* -The method used to *prepare the specimen for viewing* with an electron microscope *KILLS the specimen* -*Electrons have short wavelengths (shorter than photons)* that *move best in a vacuum*, so *living cells cannot be viewed* -In a *scanning electron microscope* = a *beam of electrons moves back/forth across a CELL'S SURFACE*, creating details of cell surface characteristics -In a *transmission electron microscope* = the *electron beam penetrates the cell* and provides details of a *CELL'S STRUCTURES* -*Differential interference light microscopes* = amplify *differences in density so that living cells structures appear 3D* -As you might imagine, *electron microscopes are more bulky/expensive than light microscopes*

Introduction of Studying Cells What is your body composed of? What are epithelial cells, bone cells, immune system cells, blood cells? What are the two types of cells?

-Like a brick wall, *your body is composed of basic building blocks* = *cells* -*Your body has many kinds of cells*, each specialized for a *specific purpose* -Just as a home is made from a variety of building materials, *the human body is constructed from many cell types* -Ex: *epithelial cells: protect the surface of the body/organs/body cavities* -*Bone cells:* help to *support/protect* the body. -Immune system cells: fight invading bacteria* -*Blood cells: carry nutrients/oxygen throughout the body* + *remove CO2* -Each plays a vital role during the *growth, development, day-to-day maintenance* of the body. -*Cells from all organisms*—even ones as diverse as *bacteria, onion, and human*—*share certain characteristics* -*Cell* = the *smallest unit of a living thing* -*A living thing*, whether *made of 1 cell* (like *bacteria*) or *many cells* (like a *human*) = *organism* -*Cells* are the *basic building blocks* of all organisms -*Several of one kind perform a shared function* - *form tissues*, several *tissues combine to form an organ* (your stomach, heart, or brain), and *several organs make up an organ system* (such as the digestive system, circulatory system, or nervous system). *Several systems form an organism* (like a human being) -Many types of *cells, all grouped* into one of two broad categories: *prokaryotic and eukaryotic* - *Animal and Plant cells* = *EUKARYOTIC cells* whereas *Bacterial cells* = *PROKARYOTIC*

Dehydration Synthesis What is it? What two things (involving elements) combine and release? What bonds are used? Example:

-Most *macromolecules are made from single subunits/building blocks* called *monomers* -The monomers *combine w/ each other using covalent bonds* to *form larger molecules= polymers* -In doing so, *monomers release water molecules as byproducts*. This type of reaction is known as *DEHYDRATION SYNTHESIS*, which means "to put together while losing water." -The *hydrogen of one monomer combines w/ hydroxyl group of another* monomer, releasing a molecule of water -*Monomers share electrons and form covalent bonds*. More monomers join, this chain of repeating monomers *forms a polymer* -*Diff monomers combine in many configurations* giving rise to a diverse group of macromolecules. for example, glucose monomers are the constituents of starch, glycogen, and cellulose.

Carbohydrates What do they provide and through what? What is the stoichiometric formula C:H:O? What are the 3 subtypes?

-Most people are familiar w/ carbohydrates, one type of macromolecule, especially when it comes to what we eat. -To lose weight, some individuals adhere to "low-carb" diets. Athletes, in contrast, often "carb-load" before important competitions to ensure that they have enough energy to compete at a high level. -*Carbohydrates*- an *essential part of our diet*; *grains, fruits, and vegetables* are all *natural carbohydrates* -*Carbohydrates provide energy through glucose*, a *simple sugar/component of starch* and an ingredient in many staple foods •Carbs are *small sugar molecules (monomers) to large polysaccharides* -Carbohydrates also have other important functions in humans, animals, and plants -*Carbohydrates are represented by* the stoichiometric formula *(CH2O)* ( 1:2:1 ) the components are carbon ("carbo") and the components of water (hence, "hydrate") -*Carbohydrates are classified into 3* subtypes: *monosaccharides, disaccharides, and polysaccharides*

Water's Polarity What elements make up water molecule? Is there a net charge? What are the individual charges and why? What non-polar molecules don't interact well with water and separate from it rather than dissolve?

-One of water's important properties is that it is *composed of polar molecules*: the *hydrogen and oxygen within water molecules* (H2O) form *polar covalent bonds* -While there is *no net charge to a water molecule*, the *polarity of water creates a slightly posi charge on hydrogen* and a *slightly neg charge on oxygen*, contributing to water's properties of attraction -Water's charges are generated bc *oxygen is more electronegative than hydrogen*, making it more likely that a shared electron would be found near the oxygen nucleus than the hydrogen nucleus, thus generating the partial *negative charge near the oxygen* -*Each water molecule attracts other water molecules* bc of the *opp charges btwn water molecules* forming *hydrogen bonds* -*Water also attracts* or is *attracted to other polar molecules/ions* -*A polar substance* that interacts readily with or *dissolves in water* is referred to as *hydrophilic* (hydro- = "water"; -philic = "loving") -In contrast, *non-polar molecules such as oils and fats* do *not interact well w/ water* and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution). These nonpolar compounds are called *hydrophobic* (hydro- = "water"; -phobic = "fearing").

Ions and Ionic Bonds What are ions and how are they formed? Each ion has a ____ _______. Positive ions formed by losing electrons = ________ Negative ions formed by gaining electrons = _________ What suffix do these ions have? What is an electron transfer in ionic bonds? Example of ionic bond and they are formed between ___ charges What are electrolytes?

-Some *atoms are more stable when they gain or lose an electron* (or possibly two) and *form IONS*. This fills their *outermost electron shell = energetically more stable* -*Electrons do not equal the number of protons*, each *ion has a net charge*. -*Cations are positive ions that are formed by losing electrons*. -*Negative ions are formed by gaining electrons* and are called *anions*. Anions are altered to *end in "-ide": the anion of chlorine is called chloride*, and the anion of sulfur is called sulfide, for example. -This *movement of electrons from one element to another* is referred to as *electron transfer*. •When the *attraction holds the ions together*, it is called an ionic bond Protons stay the same In ionic bonds just electrons change •*Salt = ionic compound* -sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (-1) charge. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or -1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom. -*Ionic bonds are formed btwn ions w/ opp charges*. -Ex: positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge. -*Certain salts are referred to in physiology as electrolytes* (including sodium, potassium, and calcium), *ions necessary for nerve impulse conduction, muscle contractions and water balance*. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.

Energy Processing Figure 1.14 The California condor gets its food from what type of energy and to power what? All organisms use energy for _________ _________ and without chemical reactions, they can't do this. Some get energy from ____ and some get it as they do what? How do humans get energy? Plants? process names? What are the reactants and products?

-The *California condor* (Gymnogyps californianus) *uses chemical energy derived from food to power flight*. California condors are an *endangered species* w/ *wing tag for identification* -All *organisms use a source of energy* for their metabolic activities *Some organisms capture energy from the sun* and convert it into chemical energy in food; *others use chemical energy in molecules they take in as food* -*W/o chemical reaction, organisms can't function or perform metabolic activity*. -*Cellular respiration- oxygen + food make ATP*- energy currency for Humans. -*Photosynthesis*- *H2O, CO2, sunlight* makes *glucose for the plants eaten by animals and decomposers*. Energy comes in the form of food which yields ATP.

The Periodic Table What is it and who was it devised by and when? The properties of elements are responsible for their what? What is chemical reactivity? The elements are grouped based on what? What's a molecule?

-The *diff elements are organized/displayed in the periodic table* devised by *Russian chemist Dmitri Mendeleev* (1834-1907) in *1869*, the *table groups elements that share certain chemical properties w/ other elements*. The *properties of elements are responsible for their physical state at room temp*: they *may be gases, solids, liquids* -*CHEMICAL REACTIVITY* = the *elements' ability to combine and chemically bond w/ each other* -*Periodic table* = *elements are organized according to their atomic number* and *arranged in a series of rows and columns* *based on shared chemical/physical properties*. In addition to providing the *atomic number* for each element, the periodic table also displays the element's *atomic mass*. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.11. -The *periodic table groups elements according to chemical properties*. The *differences in chemical reactivity btwn elements are based on the number/spatial distribution of an atom's electrons* -*MOLECULES* = are simply *two or more atoms chemically bonded together* and their *electrons come together first* as the atoms form a chemical bond

Response to Stimuli Figure 1.11 The leaves of _______ _______ will droop/fold when touches. When there is no response, there is a decr______ ____? Humans respond to food and ____ like plants respond to _____. Chemotaxis and phototaxis? Movement towards is considered a ___________ response?

-The *leaves of this sensitive plant* (Mimosa pudica) will instantly *droop and fold when touched*. After a few minutes, the plant returns to normal. *NO RESPONSE = lower survival rate* Humans to food and cold. Plants to light. *Infections happen when bacteria responds to change in environment.* -*Organisms respond to diverse stimuli* Ex: *plants can bend toward light*, *climb on fences/walls*, *respond to touch*. Even tiny *bacteria move toward/away from chemicals* (a process called *chemotaxis*) or *light* (*phototaxis*). -*MOVEMENT TOWARD* a stimulus is considered a *positive response*, while *MOVEMENT AWAY* from a stimulus is considered a *negative response*

Cell Theory In what year were microscopes first seen and who crafted them? What was he observing and where? In what year did the term "cell" come about and why? When was bacteria/protozoa discovered? In what year did the unified cell theory come about and who published it?

-The *microscopes today are more complex* than those used in the *1600s by Antony van Leeuwenhoek*, a *Dutch shopkeeper who crafed lenses* -Despite the limitations of his now-ancient lenses, *van Leeuwenhoek observed movements of protista (unicellular organism)/sperm* = *"animalcules"* from blood, sperm, pond water -In a *1665 publication called Micrographia*, experimental scientist *Robert Hooke coined the term "cell"* for the box-like structures he observed *when viewing cork tissue through a lens* -In the *1670s, van Leeuwenhoek discovered bacteria/protozoa* -Later *advances in lenses, microscope construction, and staining techniques* enabled other *scientists to see components inside cells* -By the late *1830s, botanist Matthias Schleiden and zoologist Theodor Schwann* were *studying tissues* and proposed the *UNIFIED CELL THEORY* = which states that *all living things are composed of one or more cells*, the *cell is the basic unit of life*, and *new cells arise from existing cells* -*Rudolf Virchow later made important contributions* to this theory.

pH, Buffers, Acids, and Bases What does the pH indicate of a solution? What paper is used as an indicator? What is a pH test? Hydrogen ions are spontaneously generate in water by _________. Hydrogen ions dissociate from pure water in_________ moles H+ ions per liter of water. pH is the what of log? What 2 areas in the body have near-neutral pH? What's an acid and a base? What do strong bases and acids donate? What does a buffer do? What is an antacid?

-The *pH* = of a solution indicates its *acidity or alkalinity* -*Litmus/pH paper* = filter paper that *has been treated w/ a natural water-soluble dye so it can be used as a pH indicator*, to *test how much acid (acidity)/base (alkalinity)* exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the *pH test* = measures the *concentration of hydrogen ions in a given solution* -*Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization)* of a small percentage of *water* molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH-) ions* -While the *hydroxide ions are kept in solution by hydrogen bonding w/ other water molecules*, the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules, forming hydronium ions (H30+). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water. -*Hydrogen ions dissociating from pure water* = *1 × 10-7 moles H+ ions per liter of water* -*Moles (mol)* = way to *express the amount of a substance* (which can be atoms, molecules, ions, etc), with *one mole being equal to 6.02 x 10^23 particles of the substance/molecules -The *pH is calculated as the neg base 10 logarithm* of this concentration -The *log10 of 1 × 10^-7 is -7.0*, and the negative of this number (indicated by the "p" of "pH") yields a pH of 7.0, which is also known as *neutral pH* -The *pH inside of human cells and blood* are examples of *two areas of the body where near-neutral pH is maintained* -*Non-neutral pH readings result from dissolving acids or bases in water* -Using the *neg logarithm generate positive integers* where *more hydrogen ions yield a low pH number*, whereas *low levels of hydrogen ions result in a high pH* -An *acid* = is a *substance that incr concentration of hydrogen ions (H+)* in a solution, usually by having one of its hydrogen atoms dissociate -A *base* = provides either *hydroxide ions (OH-) or other negatively charged ions that combine with hydrogen ions*, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules -The *stronger the acid, the more readily it donates H+* -Ex: *hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic*, whereas the acids in *tomato juice or vinegar* do not completely dissociate and are *considered weak acids* -*Strong bases* are those substances that readily *donate OH- or take up hydrogen ions* -Sodium hydroxide (NaOH) and many household cleaners are highly alkaline and give up OH- rapidly when placed in water, thereby raising the pH -Ex: *weak basic solution is seawater*, which has a *pH near 8.0* close enough to neutral pH that *marine organisms adapted to this saline environment* are able to thrive in it. -The *pH scale* = an *inverse logarithm and ranges from 0 to 14* -Anything *below 7.0* (ranging from 0.0 to 6.9) is *acidic*, and anything *above 7.0* (from 7.1 to 14.0) is *alkaline* -*Extremes in pH* in either direction from 7.0 are usually considered *inhospitable to life* The pH inside *cells (6.8)* and the pH in the *blood (7.4)* are both very close to neutral -However, the environment in the *stomach is highly acidic, with a pH of 1 to 2* The answer is that they cannot do it and are constantly dying. New stomach cells are constantly produced to replace dead ones, which are digested by the stomach acids. It is estimated that the lining of the human stomach is completely replaced every seven to ten days -So how can *organisms whose bodies require a near-neutral pH ingest acidic and basic substances* (a human drinking orange juice, for example) and survive? *Buffers* = readily *absorb excess H+ or OH-, keeping the pH of the body carefully maintained* in the narrow range required for survival -Maintaining a *constant blood pH is critical to a person's well-being* and the *buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3-), and carbon dioxide (CO2)* -When *bicarbonate ions combine with free hydrogen ions and become carbonic acid*, hydrogen ions are removed, moderating pH changes -excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This *prevents too many free hydrogen ions from building up in the blood* and dangerously reducing the blood's pH. Likewise, if too much OH- is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body's pH would fluctuate enough to put survival in jeopardy. -Other examples of buffers are *antacids* = used to *FOCUSES ON COMBATTING stomach ACID*. Many of these over-the-counter medications work in the same way as *blood buffers, usually w/ at least ONE ION ABSORBING HYDROGEN AND and moderating pH*, bringing relief to those that suffer "heartburn" after eating. The unique properties of water that contribute to this capacity to balance pH—as well as water's other characteristics—are essential to sustaining life on Earth.

Water's States: Gas, Liquid, and Solid In LIQUID state, what is constantly happening between hydrogen bonds and what causes it? When heat is raised to make a GASEOUS state, what does this energy form do to hydrogen bonds? What happens when the temp drops and water is in a SOLID state, do the bonds break? What is a phenomenon not seen in other liquids and why? Cells can only survive freezing water if they are replaced by another liquid like?

-The formation of *hydrogen bonds* is an *important quality of the liquid water* that is *crucial to life* as we know it -As *water molecules make hydrogen bonds* with each other, *water takes on chemical characteristics compared to other liquids* and, since *living things have a high water content*, understanding these chemical features is key to understanding life -In *LIQUID* water, *hydrogen bonds are constantly formed/broken* as the water molecules slide past each other. The *breaking of bonds is caused by the motion (kinetic energy)* of the water molecules due to the heat contained in the system -When the *heat is raised as water is boiled*, the *higher kinetic energy of water molecules causes hydrogen bonds to break* completely and *allows water molecules to escape into the air as gas* (steam or water vapor) -On the other hand, *when the temp of water is reduced/freezes*, the *water molecules form a crystalline structure by hydrogen bonding* (there is not enough energy to break the hydrogen bonds) that *makes ice less dense than liquid water*, a phenomenon not seen in the solidification of other liquids -*Water's lower density is due to the way hydrogen bonds are oriented* as it freezes: the *water molecules are pushed farther apart* compared to liquid water -With *most other liquids = solidification when the temp drops* includes the *lowering of kinetic energy btwn molecules*, allowing them to *pack more tightly than liquid form* and giving the solid a greater density than the liquid.•When water freezes, each molecule forms a stable hydrogen bond with its neighbors.•Because ice is less dense than water, it floats. -*The lower density of ice* = an anomaly, causes it to *float at the surface of liquid water*, such as in an iceberg or in the ice cubes in a glass of ice water -*In lakes and ponds, ice will form on the surface* of the water creating an insulating barrier that *protects the animals and plant life in the pond from freezing* -The detrimental effect of *freezing on living organisms is caused by the expansion of ice relative to liquid water*. The ice crystals that form upon freezing rupture the delicate membranes essential for the function of living cells, irreversibly damaging them. *Cells can only survive freezing if the water in them is temporarily replaced by another liquid like glycerol*.

Light Microscopes How big is a human red blood cell? Specimens can be magnified up to how many times? What happens in a light microscope? What does staining do to the cells and why do we use it? How much can we magnify up to and what resolution?

-To give you a sense of cell size, a *typical human red blood cell* is about eight millionths of a meter or *8 micrometers (μm) in diameter*; the *head of a pin of is about two thousandths of a meter (two mm) in diameter* -That means about *250 red blood cells could fit on the head* of a pin. -*Specimens can be magnified by up to 1,000 times* -*Student microscopes are light microscopes* = *visible light passes/bent through the lens system* to enable the user *to see the specimen* -*Light microscopes* are *advantageous for viewing living organisms* •*microorganisms, animal/plant cells, only some structures within cells*, but since *individual cells are transparent*, their components are not distinguishable *unless colored w/ special stains* -*Staining kills the cells* -*Light microscopes* (in undergrad college laboratory) *magnify up to approx 400x and resolution is 200nm* -*Two parameters in microscopy* are *magnification and resolving power* -*Magnification* = the *process of enlarging an object in appearance* -*Resolving power* = the ability of a *microscope to distinguish 2 adjacent structures as separate*: the *higher resolution, better clarity* and detail of the image -When *oil immersion lenses are used for small objects* = *magnification increases to 1,000x* In order to *understand cellular structure/function* scientists typically use electron microscopes.

Polar Covalent Bonds What are the 2 types? What is polar covalent (3)? Example? More electronegative atoms do what? Macromolecules don't have atoms that differ in _______, so what bond is often present in organic molecules?

-Two types of covalent bonds: *polar and nonpolar*. -*POLAR COVALENT BOND* = *CHARGED*, *SOLUBLE*, the *electrons are unequally shared by the atoms and are attracted more to one nucleus* than the other + a *slightly positive (δ+) or slightly negative (δ-) charge develops* -This *partial charge is an important property of water* and *accounts for many of its characteristics*. -*Water is a polar molecule*, w/ *hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge*. -The *nucleus of the oxygen atom is more attractive to the electrons of the hydrogen atoms* than the hydrogen nucleus is to the oxygen's electrons. -Thus *oxygen has a higher electronegativity (attraction for shared electrons) than hydrogen* •Atoms in a covalently bonded molecule continually compete for shared electrons. •More electronegative atoms pull harder. -Either way, the *atom's relative electronegativity contributes to the development of partial charges* whenever one element is significantly more electronegative than the other, and the *charges generated by these polar bonds may then be used for the formation of hydrogen bonds based on the attraction of opp partial charges*. (Hydrogen bonds, which are discussed in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since *macromolecules often have atoms* within them that *differ in electronegativity*, *polar bonds* are often present *in organic molecules*.

Introduction of the Science of Biology Figure 1.2 (Years of existence: MICROORGANISMS (bacteria,fungus,virus), ANIMALS/PLANTS, HUMANS)

-Viewed *from space*, *Earth offers no clues ab the life forms that reside there* -The *first forms of life on Earth* are thought to have been *microorganisms* that existed for *billions of years* in the ocean before plants and animals appeared. -*Mammals, birds, and flowers* so familiar to us are all relatively recent, originating *130 to 200 million years ago* -*Humans have inhabited this planet for 2.5 million years*, and only *in the last 200,000 years* have *humans started looking like we do today* -*Former blue-green algae* = *cyanobacteria*, shown here at 300x magnification under a light microscope, are some of *Earth's oldest life forms* -*Stromatolites along Lake Thetis in Western Australia* are *ancient structures* formed by *layering of cyanobacteria* in shallow waters

Water's Heat of Vaporization What is the heat of vaporization? How much cal is required to accomplish this change in water? Water requires more what to boil and why? Hydrogen bonding with _______ is weaker than water's. When could water break hydrogen bonds, when it reaches its _____ ________? When below its _______ ________, what process occurs? In evaporation, is energy absorbed or released?

-Water also has a *high heat of vaporization* = the *amount of energy required to change one gram of a liquid substance to a gas* -A considerable amount of *heat energy (586 cal) is required to accomplish this change* in water -This *process occurs on the surface of water* -As *liquid water heats up*, *hydrogen bonding makes it difficult to separate the liquid water molecules* from each other, which is *required to enter its gaseous phase* (steam) -As a result, *water acts as a heat sink/reservoir and requires much more heat to boil* than does a liquid such as ethanol (grain alcohol), whose *hydrogen bonding with other ethanol molecules is weaker than water's hydrogen bonding* -Eventually, *as water reaches its boiling point of 100° Celsius (212° Fahrenheit)*, the *heat is able to break the hydrogen bonds* between the water molecules, and the *kinetic energy (motion) btwn water molecules allows them to escape from the liquid* as a gas -Even *when below its boiling point, water's individual molecules acquire enough energy* from other water molecules such that *some surface water molecules can escape and vaporize*: this process is known as *evaporation* -*Hydrogen bonds need to be broken for water to evaporate* means that a substantial amount of *energy is used in the process* -As the *water evaporates, energy is taken up by the process*, cooling the environment where the evaporation is taking place. In many living organisms, including in humans, the evaporation of sweat, which is 90 percent water, allows the organism to cool so that homeostasis of body temperature can be maintained.

Water's High Heat Capacity Caused by _______ bonding. Water has the ________ heat capacity of any liquids. What is specific heat and for water, what is it? It takes water a long time to ____/_____.

-Water's high heat capacity is a *property caused by hydrogen bonding* among water molecules -Water has the *highest specific heat capacity* of any liquids -*Specific heat* = defined as the *amount of heat one gram of a substance must absorb/lose to change its temp by one degree Celsius* -*For water, this amount is one calorie* -It therefore *takes water a long time to heat and long time to cool* In fact, the specific heat capacity of water is about five times more than that of sand. This explains *why the land cools faster than the sea* -Due to its high heat capacity, *water is used by warm blooded animals to more evenly disperse heat in their bodies*: it acts in a similar manner to a car's cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature.

Introduction of Water Life's chemistry is what to water? All living organisms need ______. ______% of the human body is made up of water and _____% in cells. _________ and _________ provide water w/ special properties. Where in the cell do most of cellular metabolic activities occur? What are these special properties (5)? What determines the way water behaves?

-Why do scientists spend time looking for water on other planets? Why is water so important? It is because *water is essential to life as we know it* Water is one of the *more abundant molecules critical to life on Earth* •Life's chemistry is tied to water. •*Life first evolved in water* •All living organisms require water. -*60-70% of the human body is made up of water* + *75% in cells* -*W/o it*, *life would not exist* The *polarity* of the water molecule and its resulting *hydrogen bonding* make water a unique substance with *special properties* that are intimately tied to the processes of life -*Life orig evolved in a watery environment* and most of an *organism's cellular chemistry and metabolism occur inside cell's cytoplasm* -Special properties of water are its 1. *high heat capacity and 2. heat of vaporization*, its ability to 3. *dissolve polar molecules*, its 4. *cohesive and adhesive properties*, and its 5. *dissociation into ions that leads to the generation of pH* Understanding these characteristics of water helps to elucidate its importance in maintaining life. •Remember that the *structure of atoms and molecules determines the way they behave* •Atoms combine to form molecules. •Hydrogen and oxygen can react to form water:

Introduction of Atoms, Isotopes, Ions, Molecules: The Building Blocks The chemical basis of life is 1. and 2.? What is an element and how many are there? What are the most abundant elements in living organisms and what percentage of the body are they? Which are in proteins, lipids, sugar? What do Potassium and Sulfur do? What are the 3.7% (7) and what are the trace elements?

1. *Chemical basis of life*- *part of our bodies* 2. *chemistry of our life* - tied to the chemicals and these chemicals are tied to water 75% -*Elements (92) (substance that can't be broken down by ordinary chemical means) in various combinations comprise all matter* = including living things -*96.3% Most abundant elements (*CHNO*PS)* in *living organisms* = *carbon (iron in the bones), hydrogen, nitrogen, oxygen* -*3.7%* - *Calcium, Phosphorous, Potassium, Sodium, Sulfur, Chlorine, Magnesium* -*Fluoride, Iodine (thyroxide hormones), Iron* *Proteins -CHNO* *Lipids- C* *Sugar- CHO* *Calcium- *main iron in the bones* and phosphorous *Potassium/Sodium - nerve signals, excite muscles* -*Biologists must understand these important building blocks of the atoms* that make up molecules, *allowing for cells, tissues, organ systems, and entire organisms*. -*All biological processes follow the laws of physics/chemistry*, it is important to understand the underlying physics and chemistry -Ex: *the flow of blood in the circulatory system follows the laws of physics that regulate fluid flow*. The *breakdown of large, complex molecules of food into smaller molecules*—and the *conversion of these to release energy to adenosine triphosphate (ATP)*—is a *series of chemical reactions that follow chemical laws* -*Water properties* + *hydrogen bonds* are *key to understanding living processes*. *Recognizing acids and bases* is *important to our understanding of the digestive process*. Therefore, the *fundamentals of physics and chemistry* are *important for gaining insight into biological processes*.

Trans Fats What are they (3)? Hydrogen gas is bubbled through what to do what? What is hydrogenation?

An *unsaturated fat*, formed artificially during *hydrogenation of oils*, containing *one or more trans double bonds* -*Food industry oils* = are *artificially hydrogenated* to make them *semi-solid*/*desirable consistency* -*1890s- Hydrogenated vegetable oils* = are *unsaturated fats* that have been *converted to saturated fats by adding hydrogen to reduce SPOILAGE* -This *hydrogenation creates TRANS FATS*, which are associated w/ health risks - *Hydrogen gas* is *bubbled via oils to solidify them* -*Hydrogenation* = *double bonds of cis*- conformation in the hydrocarbon chain may be *converted to double bonds in the trans- conformation* -*Margarine, peanut butter*, and shortening = *artificially hydrogenated trans fats* -Recent studies have shown that an *incr in trans fats* in the human diet *may lead to an incr low-density lipoproteins* (LDL), or *"bad" cholesterol* which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently banned the use of trans fats, and food labels are required to display the trans fat content. •Experimental studies have tested the health risks of consuming trans fats. •In experimental controlled feeding trials, the diets of participants contained different proportions of saturated, unsaturated, and partially hydrogenated fats. •For ethical and practical reasons, controlled feeding trials are usually fairly short in duration, involve only limited dietary changes, generally use healthy individuals, and measure intermediary risk factors, such as changes in cholesterol levels, rather than actual disease outcomes •The results indicate that •for each *5% increase in saturated fat* there was a *17% increase in the risk of heart disease* and •for each *2% increase in trans fat* there is a *93% increase in risk* •Trans fats are indeed a greater health risk than saturated fats.

DNA Double-Helix Structure What structure does a DNA have and by how many nm does the double helix separate by? What lies on the outside and what's on the inside? The two strands of the helix run in what orientation? What is the base complementary rule?

DNA has a double-helix structure -*The sugar and phosphate lie on the outside of the helix*, forming the backbone of the DNA. The *nitrogenous bases are stacked in the interior*, like the steps of a staircase, in pairs; the pairs are bound to each other by *hydrogen bonds*. Every base pair in the *double helix is separated from the next base pair by 0.34 nm*. The *two strands of the helix run opp directions*, meaning that the *5′ carbon end of one strand will face the 3′ carbon end of its matching strand*. (This is referred to as antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.) -*Native DNA is an antiparallel double helix*. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C. This is known as the *base complementary rule*. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.

Denaturation and Protein Folding What 3 factors?

Each protein has its own unique sequence and shape that are held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what is known as denaturation. Denaturation is often reversible because the primary structure of the polypeptide is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is when an egg is fried. The albumin protein in the liquid egg white is denatured when placed in a hot pan. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the digestive enzymes of the stomach retain their activity under these conditions. Protein folding is critical to its function. It was originally thought that the proteins themselves were responsible for the folding process. Only recently was it found that often they receive assistance in the folding process from protein helpers known as chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing aggregation of polypeptides that make up the complete protein structure, and they disassociate from the protein once the target protein is folded.

cis-trans isomers What may contain double bonds in the cis/trans configuration? Unsaturated fats are what and what happens at room temp? Transfats are what and what happens at room temp? Saturated fats what and what happens at room temp?

One of several compounds that have the same molecular formula and covalent bonds between atoms but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds; formerly called a geometric isomer. -In *triglycerides (fats and oils)*, long *carbon chains known as fatty acids* may contain *double bonds*, which can be in *either the cis or trans configuration* -*Fats w/ at least 1 double bond btwn carbon atoms are unsaturated fats* -When *some of these bonds are in the cis configuration* = the *resulting bend in the carbon backbone* of the chain means that *triglyceride molecules cannot pack tightly*, so they *remain liquid (oil) at room temp* -On the other hand, *triglycerides w/ trans double bonds* (popularly called trans fats), have *relatively linear fatty acids* that are able to *pack tightly together at room temp forming solid fats* -In the human diet, *trans fats are linked to an incr risk of cardiovascular disease*, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, *triglycerides w/o double bonds btwn carbon atoms are called saturated fats*, meaning that they *contain all the hydrogen atoms* available. *Saturated fats* are a *solid at room temperature and usually of animal origin* These space-filling models show a cis (oleic acid) and a trans (eliadic acid) fatty acid. Notice the bend in the molecule cause by the cis configuration.

RNA What is RNA and what kind of bonds is it linked by (NOT HYDROGEN - DNA)? What are the nitrogenous bases? What are the 4 types of RNA? Where does transcription occur and where does translation occur?

Ribonucleic acid, or RNA, is mainly *involved in the process of protein synthesis under the direction of DNA* -RNA is usually *single-stranded and is made of ribonucleotides linked by phosphodiester bonds*. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (*A, U, G, C*), and the phosphate group. There are *four major types of RNA*: *messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA)* -The first, mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. If a cell requires a certain protein to be synthesized, the gene for this product is turned "on" and the messenger RNA is synthesized in the nucleus. The RNA base sequence is complementary to the coding sequence of the DNA from which it has been copied. However, in RNA, the base T is absent and U is present instead. If the DNA strand has a sequence AATTGCGC, the sequence of the complementary RNA is UUAACGCG. In the cytoplasm, the *mRNA interacts with ribosomes and other cellular machinery* A ribosome has two parts: a large subunit and a small subunit. The *mRNA sits in between the two subunits* -A *tRNA molecule recognizes a codon on the mRNA*, binds to it by complementary base pairing, and adds the correct amino acid to the growing peptide chain. The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the ribosomes; the rRNA of the ribosome lso has an enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70-90 nucleotides long. It carries the correct amino acid to the site of protein synthesis. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain. microRNAs are the smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA messages. information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process known as transcription, and RNA dictates the structure of protein in a process known as translation. This is known as the Central Dogma of Life, which holds true for all organisms; however, exceptions to the rule occur in connection with viral infections.

Benefits of Carbohydrates

carbohydrates have been an important part of the human diet for thousands of years; artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors' storage areas. Carbohydrates should be supplemented with proteins, vitamins, and fats to be parts of a well-balanced diet. *Calorie-wise, a gram of carbohydrate provides 4.3 Kcal*. For comparison, *fats provide 9 Kcal/g, a less desirable ratio*. Carbohydrates contain *soluble and insoluble elements*; the *insoluble part is known as fiber, which is mostly cellulose*. -*Fiber has many uses*; it promotes *regular bowel movement + regulates the rate of consumption of blood glucose* + *remove excess cholesterol* from the body: fiber binds to the cholesterol in the small intestine, then attaches to the cholesterol and prevents the cholesterol particles from entering the bloodstream, and then cholesterol exits the body via the feces. Fiber-rich diets also have a protective role in reducing the occurrence of colon cancer. In addition, a meal containing whole grains and vegetables gives a feeling of fullness. As an immediate source of energy, *glucose is broken down during the process of cellular respiration*, which *produces ATP*, the energy currency of the cell. *Without the consumption of carbohydrates*, the availability of *"instant energy" would be reduced*. Eliminating carbohydrates from the diet is not the best way to lose weight. A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean meat, together with plenty of exercise and plenty of water, is the more sensible way to lose weight.

Water's hydrogen bonds moderate temperature What is thermal energy? Transfer from a ______ to_______ body is heat. To break hydrogen bonds heat must be what? To form hydrogen bonds heat must be? When warming up, water ______ heat. When cooling, heat is _______. What is evaporative cooling?

•*Thermal energy* is the energy associated with the *random movement of atoms and molecules* •Thermal energy in *transfer from a warmer to a cooler body of matter* is defined as *heat* •*Temperature measures the intensity of heat*—that is, the *average speed of molecules in a body of matter* •*Heat must be absorbed* to *break hydrogen bonds* •Heat is *released* when hydrogen bonds *form* •To *raise the temperature* of water, hydrogen bonds between water molecules must be *broken before the molecules can move* faster. Thus, •when warming up, water absorbs a large amount of heat and •when water cools, water molecules slow down, more hydrogen bonds form, and a considerable amount of heat is released •When a *substance evaporates, the surface of the liquid that remains behind cools down*; this is the process of *evaporative cooling* •This cooling occurs because the *molecules with the greatest energy leave the surface*

Scientists study the effects of rising atmospheric CO2 on coral reef ecosystems What is CO2 and what is it linked to today? What percentage of human -generated CO2 is absorbed by the ocean? What is this process called? When this happens, where do the extra hydrogen ions go to form? THE LOWER THE CONCENTRATION OF CARBONATE IONS, what else is lowered (2)?

•Carbon dioxide is •the *main product of fossil fuel combustion*, •increasing in the atmosphere, and •linked to *global climate change* •About *25% of this human-generated CO2 is absorbed by the vast oceans* CO2 dissolved in seawater *lowers the pH of the ocean in a process known as = ocean acidification* •As seawater acidifies, the *extra hydrogen ions* (H+) combine with carbonate ions (CO32-) to form *bicarbonate ions (HCO3-)* •This reaction *reduces the carbonate ion concentration available to corals and other shell-building animals* •In a controlled experiment, scientists looked at the effect of decreasing carbonate ion concentration on the rate of calcium deposition by reef organisms. •The *lower the concentration of carbonate ions, the lower the rate of calcification*, and thus the *slower the growth of coral animals* •The results from experimental and observational field studies of sites where pH naturally varies have dire implications for the health of coral reefs and the diversity of organisms they support.

natural selection In what year did Charles Darwin publish his book? What two main points were made? What 2 observations were made about natural selection being a mechanism? What 2 inferences were made about favorable traits?

•In *1859, Charles Darwin published the book On the Origin of Species by Means of Natural Selection*, which articulated two main points. 1. *Species living today descended from* ancestral species in what Darwin called *"descent with modification."* 2. *Natural selection* is a mechanism for *evolution* •Natural selection was *inferred by 2 observations* 1. *Individual variation*: Individuals in a population *vary in their traits*, many of which are *passed on* from parents to offspring. 2. *Overprod of offspring*: A *population can produce more offspring than environment* can support. •From these observations, Darwin *2 inferences* 1. *Unequal reproductive success*: Individuals with *heritable traits best suited* to the environment are *more likely to survive* and reproduce than less well-suited individuals. 2. *Accumulation of favorable traits over time*: As a result of this unequal reproductive success over many generations, an increasing proportion of individuals in a population will have the advantageous traits. •Darwin realized that *numerous small changes in populations as a result of natural selection could alter species*. •The fossil record provides evidence of such diversification of species from ancestral species.

Biology, technology, and society are connected in important ways What is the goal of science? What is the goal of tech (applied science)? They are what of eachother if tech advances stem from scientific research?

•Many issues facing society are *related to biology* and often *involve our expanding technology*. •The basic goals of science and technology differ •The *goal of science* = is to *understand natural phenomena* •The *goal of technology* = is to *apply scientific knowledge* for some *specific purpose* •*Science and technology* = are *interdependent* •*Research benefits* from new *technologies* •*Technological advances* stem from *scientific research* •Technologies of DNA manipulation are the results of scientific discovery of the structure of DNA.