BIOLOGY MIDTERM STUDY GUIDE 2015*Look over textbook, notes, labs, tests and quizzes to enhance your studying*

I. Scientific Methoda. Steps of scientific methodb. Hypothesisc. Theoryd. Inference vs. Observatione. Variablesf. Control

II. Tools of a Biologista. Microscope

i. Labelingii. Function of each part

b. Identifying Lab equipment

III. Characteristics of Lifea. All of the different characteristics and examples of eachb. Asexual vs. sexual reproduction

IV. Ecologya. Biodiversityb. Abiotic vs Biotic Factorsc. Levels of ogranization

i. Organims, population, community, ecosystem, biome, biosphered. Autotroph (producers)e. Heterotrophs (consumers)

i. Omnivoresii. Carnivores

iii. Herbivoresf. Competition

i. Intraspecific vs Interspecificg. Predation h. Symbotic Relationships

i. Mutualismii. Commensalism

iii. Parasitism I. Food Chain vs. Food Web

V. Cellsa. Microscopes

i. Compound light microscopeii. Scanning electron microscope

iii. Transmission electron microscopeb. Endosymbiosisc. Scientists

i. Rediii. Pasteur

iii. Hookeiv. Leeuwenhoek

d. Cell Theory e. Organization- celltissueorganorgan systemorganismf. Prokaryotes vs. Eukaryotesg. Plants vs. Animalsh. Domainsi. Organelles

i. Labelingii. Functions

VI. Biochemistrya. Elements

i. Definitionii. Examples

b. Atomsi. Definition

ii. Structure1. Protons2. Neutrons3. Electrons

c. Macromoleculesi. Carbs

ii. Lipidsiii. Proteinsiv. Nucleic Acids

VII. Cellular Transporta. Membranes

i. Labelingii. Phospholipids, proteins, cholesterol

b. Passive transporti. Diffusion

ii. Osmosis1. hypertonic2. hypotonic3. isotonic

iii. Facilitated Diffusionc. Active Transportd. Vesicular Transport

i. Endocytosis1. Pinocytosis2. Phagocytosis

ii. Exocytosise. Diffusion Lab!

i. Indicators1. Iodine- starch2. Benedict’s solution- glucose

ii. What crossed the membrane?

VIII. Cellular Energya. Types of energy

i. Chemical ii. Solar

iii. Autotrophs

iv. Heterotrophs

b. Photosynthesisi. Reaction

ii. Starting materialsiii. Processiv. Productsv. 2 Types of reactions

1. Label Diagram2. Light reactions

a. Where do they occur?b. What goes in, what comes out?

3. Dark Reactions/ Calvin Cyclea. Where does it occur?b. What goes in, what comes out?

4. Diagram of a chloroplasta. Stromab. Thylakoidc. Grana

I. What is the Scientific Method? The scientific method is a process that uses questioning, analysis, and evidence to solve a problem or answer a question.

Step 1. Make an Observation. After making an observation of the natural world, define the problem/question…Be specific and investigate one problem/question at a time. ALL scientific experimentation starts with observation!

EXAMPLE: An OBSERVATION is any perceived characteristic of the natural world that is OBJECTIVE (the same for everyone), this includes anything that can be QUANTIFIED (can be measured) or QUALIFIED (has a describable quality like color or smell)

Step 2. Research the problem (question). Use all available resources to collect data on the problem/question being investigated in order to form the most logical and informed hypothesis you can. Libraries, Internet, books, magazines, personal interviews, etc.

EXAMPLE: Any time an observation is made, the observer makes one or many conscious or subconscious INFERENCE(S). An INFERENCE is any SUBJECTIVE (may differ between people) conclusion that is drawn from an observation. Inferences take into account logic, prior experience, prior knowledge, and other factors.

Step 3. Develop a hypothesis (educated guess/proposed explanation). Make it a short definitive statement that can be proven to be true or false. Hypotheses are often presented as an “If…Then…” statement. The “if” part will establish a condition of the hypothesis and the “then” part will make a prediction that will be proven or disproven at the end of the controlled experiment. Hypotheses are often modified, or changed, over many rounds of experimentation.

A PREDICTION is an outcome that is expected based on an OBSERVATION and a given INFERENCE. Predictions may be correct or incorrect. A hypothesis is basically a testable prediction with controlled conditions. Through experimentation we can test the prediction to be correct or incorrect.

EXAMPLE: I walk into a room and OBSERVE a pot of water bubbling and steaming; I make an INFERENCE that the water is boiling; I PREDICT that if the water is boiling, then I will get burned if I touch it. I can then create a hypothesis, “If I touch the water, then I will get burned”

Step 4. Develop a controlled experiment. A controlled experiment is an experiment that contains only one experimental variable. An experimental or independent variable is the thing being tested (what the scientist changes). Everything else in the experiment or all other variables must be the same. These variables are also called the controlled variables. Keeping these variables the same allows the experimenter to show that it was the experimental variable alone that caused the results. The dependent variable is what changes when the independent variable changes - the dependent variable depends on the outcome of the independent variable.  Data should be organized into charts, tables, or graphs.

EXAMPLE: If I am investigating the relationship between how much fertilizer I give a plant and how much it grows, the amount of fertilizer would be my independent variable and the amount of plant growth would be my dependent variable. Everything else must be controlled variables (amount of sunlight, water, temperature, etc.) in order to accurately measure the effect of the fertilizer on plant growth.

Step 5. Analyze the data and come up with a conclusion. Data may be quantitative (numbers) or qualitative(appearance, properties, etc.).  The conclusion may or may not support the hypothesis. Additional experimentation must then take place to build documentation concerning the problem/question. If the hypothesis is proven wrong, change the hypothesis, not the data. Scientists must be unbiased (do not take sides or make data fit their ideas).

WHAT FOLLOWS: Scientific research must be published, but first it must be reviewed by peers (other scientists) and verified for accuracy/reproducibility.  Research may result in a scientific theory or law (accepted as “fact” or the “best explanation” by the scientific community).

II. Tools of a Biologist Microscopes

1. Compound Light microscope: Uses visible light to look at a thin sample; can observe cells but not detailed organelles

Eyepiece/Ocular Lens is always 10X magnification Can have objective lenses of 4X, 10X, and 40X OR 10X, 40X, and 100X To find total magnification we multiply the 10X magnification of the eyepiece

and the magnification of whatever objective lens we are usingo EXAMPLE: 10X (eyepiece) and 40X (objective lens):10 * 40 = 400X o The weakest magnification would be 4X objective: 10 * 4 = 40X o The strongest magnification would be 100X objective: 10 * 100 = 1000X

2. Scanning Electron Microscope (SEM): Uses an electron beam to produce 3D, surface images of a specimen at up to 100,000X Total Magnification (think SCANNING=SURFACE)

3. Transmission Electron Microscope (TEM): Uses and electron beam to penetrate a thin sample and produce images of a specimen at up to 300,000X Total Magnification (think TRANSMISSION=THROUGH)

Compound Light Microscope

Identifying Laboratory Equipment Names and Functions1. Hand lens: magnifies small objects2. Dissecting Tray: hold specimens for dissection3. Dissecting Pins: hold specimen on the dissecting tray4. Forceps: grasps small objects5. Dissecting Scissors: cut specimens to be studied6. Dissecting Probe: pointed object used to examine specimens7. Scalpel: cuts specimens to be dissected8. Safety Goggles: protects eyes from fire and chemicals9. Hot Plate: heats objects10. Graduated Cylinder: measures liquids11. Test Tube: holds liquids12. Beaker: holds and measures liquids13. Test-Tube Rack: holds test tubes14. Electronic Balance: measures mass15. Dropper Pipette: measures out drops of liquid16. Pipette: transfers measured amounts of liquid17. Compound Microscope: magnifies very small objects18. Microscope Slide: holds object for examination with the compound microscope19. Coverslip: covers material on a glass slide20. Petri Dish: shallow dish used for bacterial cultures21. Thermometer: measures temperature22. Funnel: transfers liquid from one container to another; filters materials with filter paper23. Metric Ruler: measures length24. Hot Hands: protective gear to hold extreme hot or cold objects25. Weigh-Boat: used to hold materials when they are being weighed26. Spatula: used for transferring small amounts of dry/solid material27. Test-Tube Holder: grabs test tube for safe handling/holding28. Mortar and Pestle: grinds/crushes material29. Test-Tube Brush: used to clean glassware (test tubes, beakers, etc.)

III. Characteristics of LifeLiving things are/display:

A. Composed of ONE or MORE Cells…a. Unicellular: Organisms composed of only one cell

i. Directly exchange nutrients and waste with their environmentii. Example: Bacteria, Algae, Amoebae, Paramecia

b. Multicellular: Organisms composed of multiple/many cellsi. Specialized cells that have specific forms and perform specific

functions working together to maintain the life functions of an organism

ii. Living things can organism simple substances into complex ones (i.e. macromolecules)

iii. Example: Animals, Plants, most FungiB. Organized

a. Living things display organization and forms that fit the functions necessary to maintain life functions

b. Living things exhibit body plans that allow them to survive in their environment

C. Growth and Developmenta. Cells can growth in size b. Cells can divide/reproduce

D. Respond to Stimulia. Living things display responses to environmental stimulib. A stimulus (plural: stimuli) is a thing or event that elicits a response from an

organismc. Example: Shivering (response) because it is cold (stimulus: drop in internal

temperature); Pulling away hand (response) from a fire (stimulus: tissue-damaging heat)

E. Require Energya. While some life processes occur spontaneously (require no input of energy),

the vast majority require an input of energyb. Cells utilize energy in the form of ATP (Adenosine Triphosphate) in order to

drive the biochemical processes necessary to maintain life functionsc. The SUN is the ultimate source of all energy used by organisms on Earthd. Cells obtain energy from their environment and produce waste

F. Reproductiona. Organisms produce offspring (new members of the parent(s)’ species)

i. Asexual Reproduction: offspring are produced by a single parent, offspring are genetically identical to the parent

1. Example: Bacteriaii. Sexual Reproduction: offspring are produced by two parents,

offspring are a mix of each parent’s genetic materialG. Heredity

a. The passing of traits/characteristics from one generation to the next (all qualities: physical, mental, behavioral, etc.) genetically

b. Genetic information is carried by molecules of DNA (Deoxyribonucleic Acid) and acts as the “blueprint” or “body plan” for an organism

c. Offspring receive DNA from one (asexual reproduction) or two (sexual reproduction) parents that dictates all aspects of their biology

H. Evolve and Adapta. Adaptation: the ability of an organism to change with its environment in

order to increase its chances of survival and reproductionb. Evolution: the modification of a species (on the genetic level) over many

generations in order to maximize survival and reproduction in a dynamic (changing) environment

i. Example: camouflage, thick fur, large brains, sharp teeth, etc.c. A series of adaptations over many generations produces evolution and the

diversification of life we see on Earth. It is the ability of life to adapt that allows it to endure catastrophes (like the meteor that wiped out the dinosaurs) and drastic climate changes (think ice age)

I. Homeostasisa. The state of stability that organisms maintain in order to continue life

functions (pH, solute concentration, temperature, etc.)b. Although the ideal stable state varies from organism to organism, all

organisms must maintain a stable internal environment despite the state of the external environment to survive

i. Example: Humans maintain an internal temperature of about 98.6 F despite living in a wide range of external temperatures

IV. EcologyEcology: The study of interactions between organisms and their environments. Ecology includes the study of individuals, populations, communities, ecosystems, biomes, and the biosphere.

Biodiversity: The degree of diversity present amongst living things on Earth. Diversity is indicated by the genetic variation (number of different species) present in the various ecosystems on Earth (biosphere).

Biotic: Anything that is, or has ever been, ALIVE. Biotic factors also include organic products of life such as waste. Examples of biotic factors in an environment include organisms, organic molecules, and cells. Biotic is the opposite of abiotic.

Abiotic: Anything that is not, nor has ever been, alive. Some examples of abiotic factors in an environment include precipitation, sunlight, and minerals. Abiotic is the opposite of biotic.

Niche: An organism's role/place in an environment, including how it uses its resources, relates to other organisms, and times its reproduction. Each individual organism has a niche in its population, community, and ecosystem, but niches are flexible and change depending on circumstances.

Habitat: The physical environment where a population of a single species lives, or inhabits. A habitat consists of all the abiotic, or nonliving, resources influencing the population. A habitat is only understood in terms of the population it describes. For instance, we say "the black bear habitat" or "the whale habitat." It doesn’t describe the entire ecosystem, or a community of organisms, or even the home of a single individual. Habitats of different species do overlap (Ex. The habitat of a lion overlaps with the habitat of a gazelle).

Autotroph: Any living organism that makes its own food by converting simple inorganic molecules into complex organic compounds like carbohydrates, fats, and proteins. Autotrophs are the "producers" in a food chain or web. Autotrophs are able to capture sunlight and convert/store it as chemical energy that is accessible to the cell (“creating” its own food in the form of glucose).

Heterotroph: An organism that cannot convert sunlight into "food" (carbohydrates). Heterotrophs must obtain their nutrients by consuming other organisms. All animals, all fungi, and some kinds of bacteria are heterotrophs. This means that all carnivores, herbivores, and omnivores are also heterotrophs.

Food Chain: A simple, direct, and trophic (eating) relationship among a group of organisms, where one organism, like a plant, is the food source for the next organism, like a cow, which in turn is the food source for the next organism, like a human, and so on and so forth. A food chain traces the flow of energy from one type of producer to one type of primary consumer (and perhaps one type of secondary consumer, etc.)

Food Web: A complex trophic relationship among a group of organisms, consisting of interactions among multiple food chains (see definition above). A food web describes how multiple producers and consumers directly or indirectly interact in a community.

Herbivore: An organism that only eats autotrophic organisms, like plants and algae. Some examples of herbivores include members of the bovine family, like cows, bison, antelope, and sheep; members of the deer family, like moose, reindeer, and elk; and many insects, like leaf beetles, lady bugs, and aphids.

Carnivore: An organism that only eats animals. Most predators and scavengers are exclusively carnivorous. Some examples of carnivores include members of the feline family—like lions, tigers, and house cats, and birds of prey—like eagles, hawks, and owls. 

Omnivore: An organism that eats both plants and animals. Some examples of omnivores include members of the hominid family—like humans, chimpanzees, and orangutans, and many bird species—like chickens, ducks, and woodpeckers.

Decomposer: An organism that feeds on and breaks down dead or decaying matter in the process of ecological decomposition. Examples of decomposers include fungi—like mushrooms and molds; worms—like earthworms and some nematodes; and some bacteria. Decomposers are essential for recycling nutrients in an ecosystem.

Detritivore: An organism that consumes detritus, aka decomposing organic matter, to obtain nutrients. All decomposers are detritivores, including fungi, worms, and some bacteria. Decomposers are usually associated with eating things like dead animals (think vulture eating a carcass) while detritivores are usually associated with breaking down biotic materials (think fungus breaking down a rotting log).

Competition: An interaction where individuals of different species (interspecific competition) or the same species (intraspecific competition) fight for limited resources.

Examples of interspecific competition include trees of different species fighting for limited sunlight in a rainforest, birds of different species fighting for limited prey in a prairie, and even bacteria of different species vying for limited oxygen in your large intestine.

Examples of intraspecific competition include lions fighting for mates on the Savannah, piglets vying for limited milk from their mother, and even humans vying for limited space to build a home.

Predation: A type of species interaction where one organism, aka the predator, consumes, in part or in whole, another organism, aka the prey. Examples of predators include snakes and members of the big cat family, such as lynx. The difference between parasitism and predation is that predators kill their prey almost immediately while parasites live in or on their hosts for an extended period of time and do not necessarily kill them.

Symbiosis: An ecological interaction between individuals of different species. Symbiotic relationships include mutualism, parasitism, and commensalism. They DO NOT include predator-prey interactions or competition.

Mutualism: Two organisms interact in a way that is BENEFICIAL to both

Ex. Bees and Flowers

Commensalism: Two organisms interact in a way that is BENEFICIAL to one organism and has no impact (either beneficial or harmful) on the other.

Ex. Clownfish and Sea Anemone

Parasitism: Two organisms interact in a way that is BENEFICIAL to one organism and HARMFUL to the other

Ex. Ticks and Mosquitoes

Levels of Biological Organization:

Organism: A single living member of a species. Ex. Humans, wolf, cucumber plant, etc.

Population: A group of organisms of the same species living in the same geographic area at the same time. For example, all of the coyotes in a desert ecosystem, or all of the oak trees in a forest ecosystem.

Community: A group of two or more populations of organisms from different species inhabiting the same location at the same time. Communities are composed only of biotic factors. Abiotic factors like sunlight, temperature, and terrain are not considered part of a community; these factors are part of the ecosystem, which can contain one or more communities of organisms.

Ecosystem: A term describing all the living and nonliving things in a certain location. Ecosystem studies in ecology explore the interactions between organisms, like individuals, populations, or communities, and the abiotic components in the environment, like chemical composition, landscapes, and weather patterns.

Biome: A large grouping of area that contains a number of different ecosystems. The defining characteristics of a biome are the dominant plant life and the climate. Examples include Deserts, Rainforests, Deciduous Forests, Savannahs, etc.

Biosphere: The entire area of the earth that supports life. The biosphere is made up of all of the individuals, populations, communities, ecosystems, and biomes found on Earth.

V. CellsEndosymbiotic Theory: MITOCHONDRIA and CHLOROPLASTS were once distinct organisms that were absorbed into larger, pre-eukaryotic cells. Over billions of years, the symbiosis between MITOCHONDRIA/CHLOROPLASTS and the EUKARYOTIC HOST CELLS has evolved to the point that they are inseparable. MITOCHONDRIA are found in ALL eukaryotic cells, while CHLOROPLASTS are found only in eukaryotes that perform PHOTOSYNTHESIS. This implies that MITOCHONDRIA were acquired before the split of animals and plants and CHLOROPLASTS were acquired after.

Scientists (make sure you know what they discovered and what their experiment was)

1. Robert Hooke:

Observed dead cork cells under a microscope Called what he saw “cells” after the cells that monks occupied in

monasteries 2. Anton von Leeuwenhoek

First person to observe living cells Observed living cells in a sample of pond water

3. Francesco Redi

Spontaneous Generation : In Redi’s time—the 1600s—it was commonly believed that living organisms would randomly come in to being from non-living materials.

Fly/Meat Experiment : A commonly-held assumption by Redi’s contemporaries was that maggots (fly larvae) were generated in decaying meat and dead flesh. In order to test this hypothesis, Redi placed rotten meat in both an OPEN CONTAINER and in a CLOSED CONTAINER. Although adult flies tried to get into BOTH containers, they could only

gain access to the meat in the OPEN CONTAINER. After some time, maggots appeared ONLY on the meat in the open container, suggesting that THE ADULT FLIES WERE THE SOURCE OF THE MAGGOTS and SPONTANEOUS GENERATION DID NOT OCCUR!!

4. Louis Pasteur

Pasteurization : Process developed by Louis Pasteur after discovering that bacteria in the air could contaminate food. By superheating and then rapidly cooling food items, bacterial concentrations can be greatly reduced—prolonging shelf-life and reducing spoilage/infection.

Bacteria/Broth Experiment : Preparing two flasks containing a broth (proteins, carbohydrates, etc. to support bacterial growth), Pasteur then sterilized them using high heat to kill any bacteria potentially present in the broth. Now, with both flasks bacteria free, Pasteur left one flask OPEN and left one flask CLOSED AIR-TIGHT. After some time, the OPEN FLASK HAD BACTERIAL GROWTH, while the CLOSED FLASK HAD NO BACTERIAL GROWTH. After opening the closed flask and exposing it to air, it went on to DEVELOP BACTERIAL GROWTH. This was strong evidence that bacteria is present in the air around us and led Pasteur to develop the technique for sanitizing foods called Pasteurization (see above). The results of this experiment also demonstrated that CELLS MUST COME FROM OTHER CELLS!!!!

CELL THEORY: 3 Parts

1. ALL LIVING THINGS ARE COMPOSED OF ONE OR MORE CELLS2. THE CELL IS THE MOST BASIC STRUCTURAL AND FUNCTIONAL UNIT

OF LIFE3. ALL CELLS ARISE FROM EXISTING, LIVING CELLS

Levels of Organization within an Organism:

SimplestMost Complex

CellTissueOrganOrgan SystemOrganism

Prokaryotes vs. Eukaryotes

Prokaryote: Means “before nucleus” and includes the domains Bacteria and Archaea

Eukaryote: Means “true nucleus” and includes the domain Eukarya

Biological Domain: The highest and most inclusive classification for life on Earth.

Bacteria: this domain includes all bacteria, which are PROKARYOTIC Archaea: similar to bacteria but unique in a number of ways, also PROKARYOTIC Eukarya: this domain includes all plants, animals, and fungi, which are EUKARYOTIC

ORGANELLE STRUCTURE, FUNCTION, and LOCATION:

Centriole organelles made of microtubules involved in cell division

Golgi Apparatus process materials manufactured by the cell

Smooth Endoplasmic Reticulum Site of lipid synthesis

Rough Endoplasmic Reticulum Site of protein synthesis

Ribosome produces proteins

Cilia and FlagellaUsed for movement/moving substances around outside of the cell

Central Vacuole Maintains shape of cell, stores water, nutrients and waste

Chloroplast Captures light energy and converts to sugar

Cell WallMaintains cell shape, works with central vacuole to maintain turgor pressure

Cell Membranesupport, protection, controls movement of materials in/out of cell

Nucleus controls cell activities

Mitochondrion breaks down sugar molecules into energy

Cytoplasm fluid substance that fills the interior of the cell

Lysosomebreaks down cellular waste products and debris (contains enzymes)

VI. Biochemistry

HINT: ATOMIC MASS will always be larger than ATOMIC NUMBER, this will help with deciding which one is which!!!!

ELEMENT: A substance that cannot be broken down into simpler substances by chemical means. An element is composed of atoms that have the same atomic number, that is, each atom has the same number of protons in its nucleus as all other atoms of that element.

MATTER: Anything that has mass and takes up space.

COMPOUND: A compound is a substance formed when two or more chemical elements are chemically bonded together.

Acids and Bases:

Acid: Solution containing a higher concentration of H+ ions than OH- ions

Base: Solution containing a higher concentration of OH- ions than H+ ions

Neutral: Solution containing an equal concentration of H+ and OH- ions

pH SCALE:

*****Alkali is another word for BASIC*****

NEUTRALIZATION REACTION: The reaction of an acid and base to form a neutral solution…Hydrogen Ions (H+) and Hydroxide Ions (OH-) are balanced to produce a pH 7 solution.

MACROMOLECULES: Large, organic molecules essential for life

Proteins: Responsible for Growth, repair, enzymes, and transport.

Carbohydrates: Gives us energy. Examples include glucose and fructose.

Lipids: Can be saturated or unsaturated. Used for storing energy, signaling, and acting as structural components of cell membranes.

Nucleic Acids: Encode, transmit, and express genetic information. Found in the form of DNA and RNA.

VII. Cellular Transport

Fluid Mosaic Model: This is a model that describes the plasma (cell) membrane of animal cells (including humans). The membrane is composed of two layers of phospholipids (PHOSPHOLIPID BILAYER) which are fluid (flexible and capable of movement) at animal body temperature. The membrane functions to give the cell a definite volume (separate the components of the cell from the surrounding environment) and to moderate what goes in and out of the cell (keep/let beneficial things in and keep/send harmful things out). Because the membrane is selective in what it permits in and out of the cell, it is described as SELECTIVELY-PERMEABLE. Within the bilayer are proteins, cholesterol, and carbohydrate chains that give it the look of a mosaic (a type of art that uses many colored pieces). Because the components of the membrane can move freely through the membrane (like things floating on water), the plasma membrane is described/modeled as FLUID-MOSAIC. REMEMBER THAT PHOSPHOLIPIDS ARE A TYPE OF LIPID!!

Phospholipids: Each layer in the bilayer is composed of many units called PHOSPHOLIPIDS, and each phospholipid is composed of a hydrophilic (“water-loving”) HEAD and a hydrophobic (“water-fearing”) TAIL. The head of each phospholipid always faces towards either the watery fluid outside of the cell (extracellular fluid; extra: beyond, cellular: having to do with cellbeyond-cell fluid) or the watery fluid within the cell (intracellular fluid; intra: withinwithin-cell fluid). The tail of each phospholipid always faces away from the extra and intracellular fluids, so a bilayer forms with the heads on the outside and the tails facing each other on the inside. Think of a sandwich, with the heads representing the bread on the top and the bottom…and the middle representing the tails!

Proteins: Provide structure, enables transport of materials through the membrane, and anchor carbohydrate chains

Carbohydrate Chains: Acts a receptorsending and receiving chemical messages for the cell

Cellular Transport: The movement of materials across the plasma membrane. Transport can be either PASSIVE or ACTIVE.

Passive Transport: The movement of particles (atoms or molecules) from a higher concentration to a lower concentration (down the concentration gradient). Passive transport DOES NOT REQUIRE ENERGY and will happen spontaneously until dynamic equilibrium is reached.

DYNAMIC EQUILIBRIUM: A condition where constantly moving particles are balanced.

Equilibrium: a state in which opposing forces (motion, charges, etc.) are balanced

Dynamic: constantly changing

**In the natural world, at the molecular level, things never stop moving; because of this constant motion they tend to spread out and become balanced through random motion. Although atoms/molecules never stop moving, if the same amount are coming as are going, there is no change in concentration.**

SIMPLE DIFFUSION: The movement of particles from a higher concentration to a lower concentration. For the cell membrane, diffusion takes place across the membrane between the outside and inside of the cell. There are a number of factors which affect the rate of diffusion (how long it takes to reach dynamic equilibrium).

1. Temperature: higher temperatures= faster particles= faster diffusion2. State of matter: gasses diffuse faster than liquids, liquids diffuse faster than solids3. Concentration: The greater the difference in concentration, the faster diffusion occurs

(steeper concentration gradient). For example, diffusion would occur faster if the concentration of glucose outside of the cell is 10x that of the inside of the cell vs. 3x.

4. Size of particles: Smaller particles diffuse faster than larger particles. This makes sense because for the same amount of energy, something smaller can move faster than something bigger (What can you move faster if you give it all you got: a shopping cart or a truck?) **With a membrane, size can determine whether a substance will even be capable of diffusion. For example, O2 (oxygen gas) can readily diffuse through the cell membrane while large sugars cannot. Think of the permeability of a membrane as a net, with bigger holes letting more through than smaller holes**

OSMOSIS: The diffusion of liquid water across a semi-permeable membrane. Osmosis can only take place with liquid water and is used mostly when talking about the cell

FACILITATED DIFFUSION: To facilitate something is to help it occur. Remember how some particles where too large to cross the cell membrane by SIMPLE DIFFUSION, or move too slowly? This is where membrane protein channels help out by FACILITATING the diffusion of these particles.

Active Transport: The movement of particles AGAINST the concentration gradient. This REQUIRES CELLULAR ENERGY to perform. This is commonly seen in nerve cells, where ions must be pumped against their concentration gradient (by…you guessed it…membrane proteins!) in order to create an electric potential (like a battery) for signal transmission.

ENDOCYTOSIS: **”into cell” ENDO think IN** A cell envelopes an object of interest until it forms a “bubble” around the object. The cell membrane then changes shape so that the cell membrane is reestablished and a vesicle (containing the object) is on the inside of the cell. When the object is solid (Ex. White blood cell “eating” a bacterial cell) it is called PHAGOCYTOSIS (cell “eating”). When the object is some amount of liquid it is called PINOCYTOSIS (cell “drinking”).

EXOCYTOSIS: **“out of cell” EXO think EXIT** A cell moves a vesicle (typically containing wastes) towards the border of the cell membrane. The vesicle and the cell membrane merge expelling the vesicle’s contents outside of the cell and reestablishing the cell membrane. It looks a lot like endocytosis in reverse.

***When comparing the fluid within a cell and a fluid outside of a cell, we can characterize the solution a cell is in by describing it as HYPOTONIC, ISOTONIC, or HYPERTONIC**

Hypotonic solution- the concentration of solute particles is greater within the cell than outside of the cell; this will cause to water to enter the cell through osmosis, and the cell will swell (possibly bursting in the process depending on a number of factors).

Isotonic solution- the concentration of solute particles in both the inside fluid and outside fluid of the cell is in equilibrium (balanced); water content of the cell is stable and thus ideal. Although there is no observable change, water is moving in and out of the cell at the same rate. The cell and solution are in DYNAMIC EQUILIBRIUM.

Hypertonic solution- the concentration of solute particles is greater outside the cell than within the cell; this will cause water to leave the cell through osmosis, and the cell will shrivel.

DIFFUSION LAB

This lab made use of two indicators—Iodine Solution and Benedict’s Solution

What is an indicator? An indicator is a chemical/substance that produces a visible color change in the presence of another chemical/substance at certain concentrations. For instance, Phenolphthalein will turn bright pink in solution with a high OH- concentration (base indicator). Remember, indicators enable QUALITATIVE observation, not quantitative as there is nothing that can be accurately and practically measured.

Iodine Solution: Tests for the presence of STARCH. Iodine solution is an amber/yellow by itself, but in the presence of starch it turns a dark black/purple/blue. The color change can very quickly be observed at room temperature.

Benedict’s Solution: Tests for the presence of simple sugars, in the case of the lab we tested for GLUCOSE. Benedict’s Solution is a light, bright blue by itself, but in the presence of glucose sugars turns orange. BENEDICT’S SOLUTION MUST BE HEATED IN ORDER TO SEE A COLOR CHANGE!!!

EXPERIMENTAL SETUP:

Recall that we placed a solution of GLUCOSE and STARCH into dialysis tubing and tied it off to create an environment that was isolated from the outside. Dialysis tubing forms a SEMIPERMEABLE (allows some substances to diffuse, while preventing others from diffusing) membrane meant to simulate a cell. We then placed the water-tight dialysis tubing “cell” in a solution of water and iodine. After some time, it was observed that the contents of the dialysis bag turned a dark blue/black/purple. Additionally, the water in the beaker was found to test positive for glucose, and the mass of the dialysis bag increased in mass (after drying and weighing). So what happened? What was able to diffuse into and out of the bag?

ABLE TO diffuse:

A. Water: the mass of the bag increased, suggesting that water was small enough to diffuse into the bag

B. Iodine: the contents of the bag turned dark black/blue/purple, suggesting that iodine was small enough to diffuse into the bag and contact the starch

C. Glucose: the sample from the solution surrounding the bag tested positive for glucose, suggesting that glucose was small enough to diffuse out of the bag

UNABLE TO Diffuse

A. Starch: the solution surrounding the bag did not change color to dark black/blue/purple, suggesting that the starch molecules were too large to diffuse out of the bag. This was later supported when the bag was cut open, and the entire beaker solution immediately turned dark black/blue/purple.

VIII. CELLULAR ENERGY

Types of Energy: Although energy may be classified in a number of different ways and as a number of different types, two forms of energy are of particular interest to biologists: SOLAR and CHEMICAL

I. Solar Energy: Energy emitted from the Sun (essentially a nuclear fusion reactor) in the form of LIGHT and HEAT. Light can be described by its WAVELENGTH.

Wavelength is the distance between two identical points on a repeating wave, in this case peak (crest) to peak, however any repeating points could be used (for example, trough [bottom] to trough)

Wavelength directly relates to the energy carried by light, with shorter wavelengths carrying more energy than longer wavelengths. Below is the Electromagnetic Spectrum of light—a useful tool in visualizing the different forms light can take. REMEMBER SHORTER WAVELENGTH=MORE ENERGY!!

Reds---------Oranges----Yellows—Greens-----Blues--------Violets

***Note: the units of length are in nanometers which are one billionth of a meter!!

II. Chemical Energy: Type of potential energy where the energy is stored in the chemical bonds that form molecules. When certain chemical reactions takes place, bonds are broken and energy is released. Chemical reactions can be represented using a chemical equation in the form: ReactantsProducts. The Law of Conservation of Mass dictates that all matter that enters a chemical reaction must leave (although in different forms), so this helps in that we can see and track everything going in and everything going out. SOMETIMES YOU WILL SEE SOMETHING WRITTEN ABOVE THE ARROW (an enzyme, light, ATP, etc.) THIS MEANS THAT IT PLAYED A ROLE IN THE REACTION BUT DID NOT DIRECTLY PARTICIPATE. (EX. An enzyme helps a reaction take place but is not chemically altered in the process; light is essential for photosynthesis but is not matter and cannot, therefore, be accounted for in the reaction; the energy to produce ATP is provided by a chemical reaction, but the reaction itself does not involve ATP)

What we think of as food is chemical energy! Where does it come from?

Photosynthesis: photo means “light” and synthesis means “putting together”, so photosynthesis means “putting together with light”. What is being put together? MoleculesFOOD. Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy (in the form of molecular bonds) that can be later released to fuel the organisms' activities.

Photosynthesis takes place in a very specialized organelle found in plant cells called the CHLOROPLAST which contains specialized pigments that absorb visible light.

Pigment: A chemical/substance that absorbs certain wavelengths of light and reflects others.

o Absorbance: A wavelength, or series of wavelengths, of light is/are trapped by a pigment along with energy it/they contain(s) the visible light wavelengths absorbed never reach your eye and, thus, are not seen.

o Reflection: A wavelength, or series of wavelengths, of light is/are scattered by a substance the visible light wavelengths reflected are the ones that enter your eye and are seen.

o Example: A leaf that appears green absorbs all wavelengths except for green, and reflects it in all directions (some of this light enters your eye and causes you to perceive the leaf as green); something that appears black absorbs all wavelengths of visible light and appears to have no color (because no visible

light is reflected into your eye); something that appears white reflects ALL wavelengths and appears to have every color (light of all visible wavelengths is reflected into the eye and the brain perceives this as “white”)

**Now you know why light colors keep you cooler in the summer and dark colors get hot faster…dark colors ABSORB more light and ENERGY (which dissipates as heat)!!**

Important Pigments used in Photosynthesis:I. Chlorophyll- pigment with strong absorbance in the blue and violet wavelengths, and

moderate absorbance in the orange-red wavelengths. There are two types Chlorophyll-α (A) and Chlorophyll-β (B) CAUSES THE GREEN APPEARANCE OF PHOTOSYNTHESIZING PLANTSREFLECTS GREEN LIGHT!!

II. Carotenoids- pigment with moderate absorbance in the blue and green wavelengths. Causes the orange-yellow-red appearance of photosynthesizing plants. Typically seen in the Fall when plants stop replenishing their chlorophyll (absorbs orange-red wavelengths) concentrations in preparation for winter (decreased sunlight).

The Chloroplast—the Site of Photosynthesis:Thylakoid: Site of the LIGHT-DEPENDENT REACTIONS

Granum (plural Grana): Stack of thylakoids surrounded by the stroma

Stroma: Watery fluid (like the cytoplasm, but thicker), site of the LIGHT-INDEPENDENT REACTIONS

Photosynthesis takes place through two stages:

I. The Light-Dependent Reaction (aka Light Reaction)II. The Light-Independent Reaction (aka Dark Reaction aka Calvin Cycle)

The Light-Dependent Reaction:

LOCATION: THYLAKOID

Inputs (what goes in):o Light energy(from the Sun) In photosynthesis equation as reactanto Water (H2O) In photosynthesis equation as reactanto NADP+

o ADP + P Outputs (what comes out):

o Oxygen gas (O2) In photosynthesis equation as producto ATPo NADPH

The Light-Independent Reaction (Calvin Cycle):

LOCATION: STROMA

Inputs (what goes in):o Carbon Dioxide gas

(CO2) In photosynthesis equation as reactant

o NADPHo ATP

Outputs (what comes out):o Glucose (C6H12O6) In

photosynthesis equation as product