Tommy Wiaduck 2014

Tommy Wiaduck Honors Biology Midterm Exam Review 2014 This study guide is an extensive collaboration of class powerpoints and independent notes. It provides a large amount of direct information. Application and use of the information ultimately depends on each individual student. It is recommended to use other resources in addition to this review. This study guide does not guarantee any scores or accuracy. If you have questions or need help in Biology, please contact Tommy Wiaduck. Topic 1: Exploring Life

The living world is a hierarchy, with each level of biological structure building on the level below.

With the additional of each new level, we get new emergent properties Atom > Molecule > Organelle > Cell > Tissue > Organ > Organ System >

Organism > Population > Community > Biosphere Biosphere:

all environments on Earth that support life Ecosystem:

all the organisms living in a particular area Community:

the array of organisms living in a particular ecosystem Population:

all the individuals of a species within a specific area Organism:

an individual life form Organ System:

composed of organs (have specific functions) Organs:

provide specific functions for the organism Tissues:

made of groups of similar cells Cells:

living entities distinguished from their environment by a membrane Organelle:

membrane­bound structures with specific functions Molecules:

clusters of atoms Living Organisms Interact with their Environments (exchanging matter and energy)

interactions between living and nonliving components is required producers:

photosynthetic organisms that provide their own food consumers:

animals/organisms that profit/eat from plants chemical nutrients:

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nonliving components required for life to be successful, an ecosystem must:

recycle chemicals necessary for life move energy through the ecosystem

energy cannot be recycled (energy enters as light ; leaves as heat)

Cells are an organism's basic units of structure and function: form generally fits function

if you change the structure, you change the function prokaryotic cells

simple and small (no membrane­bound organelles) bacteria

eukaryotic cells possess organelles seperated by membranes

plants, animals, and fungi All forms of life have common features

Order the complex organization of living things

Regulation/Homeostasis: ability to maintain an internal environment consisten with life

Growth and Development: consistent and specific pattern for growth/development controlled by DNA

Energy Utilization/Processing: organisms taking in energy and transforming it to do work (useful form)

Response to Environment: respond to stimuli from their environment (reaction)

Reproduction: organisms reproduce (life comes from life ­ biogenesis)

Evolutionary Adaptation: life evolving in response to interactions between organisms and their

environment (acquisition of traits that best suit organism in environment) Three Domains for Diversity of Life

bacteria: prokaryotic ; unicellular (often microscopic)

archaea: prokaryotic, often unicellular and microscopic

eukarya: eukaryotic and contain nucleus and organelles

fungi, animalia, plantae, protists Evolution Explains Unity and Diversity of Life:

Charles Darwin evolution:

biology's core theme and explains unity and diversity of life

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natural selection: individuals in a population inherit characterists that will help them

survive in an environment (only fit organisms are reproduced, slowly weeding out certain traits that prevent survival)

increases frequency of certain inherited variants/traits ex) food is high up... only taller animals can eat, shorter

animals die... species now are mainly tall The Process of Science

there are two main approaches to understand natural causes for phenomena discovery science:

provable observations and measurements to describe science hypothesis­based science:

uses data from discovery science to explain you must propose and test hypotheses

ex) Why doesn't the flashlight word? 1) Bulb or 2) Batteries

control group: all variables are held constant

experimental group: one factor or treatment is varied

theory vs. hypothesis theory:

supported by a large (and usually growing) body of evidence

hypothesis: proposed explanation for a set of osbservations

Biology and Everyday Life science and technology are interdependent

science wants to understand natural phenomena technology applies science for a specific purpose

Topic Review: 1) Describe life's hierarchy of organization

A: Atom > Molecule > Organelle > Cell > Tissue > Organ > Organ System > Organism > Population > Community > Biosphere

2) Describe living organisms' interactions with their environments

A: light from the sun goes to producers, which use it to make food (release heat energy), which is then eaten by consumers (release heat energy), and chemical nutrients cycle through the ecosystem.

3) Describe the structural and functional aspects of cells

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A: Prokaryotic Cells archaebacteria and bacteria small size ; DNA is not seperated from rest of cell no membrane­bound nucleus or other organelles tough external walls

Eukaryotic Cells protists, plants, fungi, animals DNA is seperated from rest of the cell (organized in chromosomes) cytoplasm surrounds nucleus and contains various organelles some have a cell wall outside plasma membrane (plant cells)

4) Explain how the theory of evolution accounts for the unity and diversity of life

A: All living species descend from ancestral species (differences reflect evolutionary change) ; natural selection

5) Distinguish between discovery science and hypothesis­based science

A: Discovery Science: use verifiable/provable observations and measurements to describe science and

phenomenas Hypothesis­Based Science:

use data from discovery science to explain science (you must propose and test) 6) Describe ways in which biology, technology, and societs are connected

A: technology improves our standard of living, but also brings about problems like population growth, acid rain, deforestation, global warning, endangered species, nuclear accidents, toxic waste, etc...

A: technology extends our ability to observe and measure science (improvement) Topic 2: The Chemical Basis of Life

Chemical Elements & Compounds Life requires about 25 chemical elements

element: substance that cannot be broken down there are 92 elements, only few are in a pure state

Trace elements: elements required by organisms (only in small quantities)

although you only need little of them, they are vital ex) B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V, Zn

lack of trace elements bring about disease lack of iron: canno transport oxygen lack of iodine: holy goiter

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some are added to food/water for various reasons preserve it, more nutrious, look better

Biologically Important Elements Carbon, Oxygen, Hydrogen, and Nitrogen

C, O, H, N ­­­> make up about 96.3% of body weight/living matter Compounds

compounds are substances cosisting of two or more different elements combined in a fixed ratio

Table Salt (NaCl ­ sodium chloride) many compounds in living organisms (including DNA) include, C, H, O,

and N Atoms and Molecules

Atoms smallest possible unit of matter that retains physical and chemical

properties of its element Subatomic Particles (3 Important): proton (+), neutron (+/­)

electron (­) neutrons and protons are packed in an atom's nucleus

atomic number: number of protons in an atom neutral atoms have the same amount of protons and electrons

mass number: number of protons and neutrons in an atom add protons and neutrons for mass number subtract atomic number from mass number to find amount of neutrons

Isotopes: isotopes have the same number of protons and electrons, but different

numbers of neutrons ex) carbon containing 8 neutrons instead of 6 is 14C

radioactive isotops are unstable emit subatomic particles and/or energy as radioactivity they can help or hurt us

your body cannot detect isomers, but certain machines like the PET can

Electrons electron shells (orbitals) are energy levels where electrons are

atoms can have one, two, or three, electron shells number of atoms in the outermost shell determines

chemical properties of an atom 1st Shell: 2 e­ Max ; 2nd Shell: 8 e­ Max

chemical bonds attractions between atoms by sharing, donating, or receiving e­'s

(to fill their outer electron shells) Structural Formula: H­H

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Molecular Formula: H2 Molecules: two or more atoms held together by chemical

bonds Covalent Bonds:

formed by sharing a pair of valence electrons (outer shell electrons)

Single Covalent Bond: sharing single pair of valence electrons

Double Covalent Bond: atoms shair two pairs of valence electrons (ex: O=O)

Triple Covalent Bonds: share 3 pairs of valence e­'s electronegativity: attraction/pull for shared electrons

Nonpolar & Polar Covalent Bonds: Nonpolar Covalent Bond:

formed by equal sharing of electrons between atoms (usually of molecules made by same element ex: O2, H2)

Polar Covalent Bond: formed by unequal sharing of electrons between

atoms atoms involved have different

electronegativities forms a polar molecule

Ionic Bonds: bond formed by the attraction after the complete transfer of

an electron from a donor to an acceptor ion: charged atom or molecule

Hydrogen Bonds: bond formed by the charge attraction when a hydrogen

atom covalently bonded to an electronegative atom is attracted to another electronegative atom

positive end attracts to neighboring oppositvely charged regions

positive charged region is always a hydrogen

Water's Life Supporting Properties cohesion

molecules sticking together (formed by hydrogen bonds) surface tension

measure of how difficult it is to break the surface of a liquid adhesion

molecules sticking to other things ex) water sticking to the wall in tree to move up tree

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heat water can resist temperature change greater than other liquids

heat is the energy associated with movement of atoms and molecules in matter

temperature measures the intensity of heat ice is less dense than liquid water

ice: hydrogen bonds are stable ice floats, oceans and lakes dont freeze over

liquid: hydrogen bonds constantly break and re­form water is the universal solvent

solution: liquid consisting of a uniform mixture of two or more substances

solvent: dissolving agent solute: substance that is dissolved

pH ­ Acids and Bases water molecules can break apart into ions (both are reactice)

hydrogen ions (H+) hydroxide ions (OH­)

acids higher concentration of H+ than OH­ (removes OH­)

bases higher concentration of OH­ (reduces H+ concentration)

neutral solution equal concentration of H+ and OH­

pH Scale (pH = potential of hydrogen) describes whether a solution is acidic or basic

0 = most acidic (battery acid) 14 = most basic (bleach) 7 = neutral ; neither acidic nor basic (pure water)

acid precipitation rain, snow, or fog with a pH lower than 5.6

returning burned fossil fuels released into air as CO2 buffers

substances that minimize large and sudden changes in pH accepts H+ when too acidic donates H+ when too basic

Chemical Reactions chemical reaction

formation of water from hydrogen and oxygen making a molecule from two atoms rearranging matter

reactants used to make the product (ex: H2 and O2)

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product made from reactants in a chemical reaction (ex: H2O)

Topic 3: The Molecules of Cells

Introduction to Organic Compounds organic compounds

any carbon­based molecules ex) Methane (CH4)

four covalent bonds like 4 hydrogens to carbon molecular diversity is based on properties of carbon

composed of carbon bonded to other elements hydrocarbons

compounds composed only of carbon and hydrogen carbon skeleton

chain of carbon atoms (branched or ubranches) isomers

different compounds with the same molecular formula different structure/arrangement

if you change the structure, you change the function Functional Groups

testosterone and estrogen are similar, other than their difference in functional groups

groups of atoms attached to an organic compound Hydroxyl Group (hydrogen bonded to an oxygen)

­OH Carbonyl Group (carbon double­bonded to an oxygen atom)

­­C=O Carboxyl Group (carbon double­bonded to oxygen and hydroxyl group)

­COOH Amino Group (nitrogen bonded to two hydrogen atoms)

­NH2 Phosphate Group (phosphorus bonded to for oxygen)

­OPO3^2­ Biological Molecules

Carbohydrates, Lipids, Proteins, Nucleic Acids often called macromolecules because of large size also called polymers

made from many identical or similar subunits connected polymer building blocks: monomers

dehydration reactions

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links monomers together to form polymers results in polymer and water molecule (dehydrates two

monomers) hydrolysis

addition of water to break apart polymers adds back in water (hydro: water ; lysis: break)

enzymes speed up chemical reactions in the cell

Carbohydrates fuel and building material

carbohydrates: organic molecules made of sugars and their polymers monosaccharides

simple sugars ; simplest version of carbohydrate glucose and fructose

hook together to form polysaccharides main fuels for cellular work

used as raw materials to manufacture other organelles disaccharide

two monosaccharides bonded together thru dehydration reaction ex) glucose + fructose = sucrose

Polysaccharides polymers of monosaccharides

storage molecule or structural support cannot be used for energy in this large state

must be broken down by hydrolysis hydrophilic (water­loving)

very water absorbment (cotton fibers) starch

glucose polymer used as a storage polysaccharide in plants glycogen

glucose polymer used as a storage polysaccharide in animals hydrolyzed when glucose is needed

cellulose polymer of glucose that forms plant cell walls

structural ; cannot be digested by humans chitin

polysaccharide (that is a polymer of an amino sugar) used by insects and crustaceans to build exoskeletons

Lipids Diverse Hydrophobic Molecules

lipids: diverse grop of organic compounds that are insoluble in water, but will dissolve in nonpolar solvent

contain twice as much energy as a polysaccharide

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water fearing oil on ducks feathers repels water

Fats store large amount of energy lipids made from glycerol and fatty acids

one glycerol and three fatty acids triglycerides

fats composed of three fatty acids bonded to one glycerol Unsaturated Fats

fatty acids containing double bonds room for more hydrogen atoms (kinks/bends in carbon chain) liquid at room temperature

commercial products are artificially hydrogenated to prevent seperation Saturated Fats

maximum number of hydrogens (no double bonds) solid at room temperature

Phospholipids compounds with molecular building blocks of glycerol, two fatty acids, a

phosphate group, and usually an additional small chemical group attached to the phosphate

structurally similar to fats and are important in all cells cell membranes

cluster into a bilayer of phospholipids hydrophylic heads

in contact with the water of the environment hydrophobic tails

band in the center of the bilayer, away from water naturally arrange that way (sort of like a magnet)

Steroids lipids composed of fused ring structures with various functional groups attached cholesterol

plays a significant role in the structure of the cell membrane also synthesizes sex hormones

anabolic steroids synthetic variants of testosterone

causes buildup of muscle and bone mass can help treat disease, but also can be abused with

consequences like liver damage (leads to cancer) Proteins

Molecular Tools of the Cell protein: polymer built from various combinations of 20 amino acid monomers

contains one or more polypeptide chains polypeptide chains: polymers of amino acids arranged in a specific linear

sequence

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linked by peptide bonds enzymes

proteins that serve as metabolic catalysts speed up reactions, regular chemical reactions

Functionals of Proteins Structural Proteins

provide associations between body parts Contractile Proteins

(found within the muscle) ; movement Defensive Proteins

include antibodies of the immune system Signal Proteins

chemical messengers ; exemplified by hormones Receptor Proteins

server as antenna for outside Transport Proteins

carry oxygen ; ex: hemoglobin Proteins are made from amino acids linked by peptide bonds

amino acids: building blocks of proteins contain amino and carboxyl group (covalently bonded to a central carbon)

Hydrogen atom and the R­group (variable) are also bonded to central carbon

amino acids are hydrophobic or hydrophilic nonpolar: hydrophobic

less soluble in water polar: hydrophilic

solube in water peptide bond

covalently bonding the carboxyl group of one amino acid to the amino group of another

accomplished by an enzyme­mediated dehydration reaction create a water molecule in the process

Protein's Function depends on its specific shape amino acid sequence causes the polypeptide to assume a particular shape

this shape determines its specific function denatured proteins can no longer function

denaturation causes polypeptide chains to unravel and lose their shape (and their

function) caused by: shape change, temperature change, pH change, salt

concentration change Four Levels of Protein Structure

Primary Structure

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unique to amino acid sequence ; determined by genetic information linear shape

Secondary Structure results from coiling or folding of the polypeptide

caused by hydrogen bonding between certain parts of the polypeptide chain

creates an alpha helix shape may lead to a pleated sheet structure

Tertiary Structure overall, three­dimensional shape

interactions between the R group of the amino acids Quaternary Structure

arrangement of multiple folded protein or coiling protein molecules in a multi­subunit complex

Nucleic Acids Store and Transmit Hereditary Information

composed of monomers called nucleotides nucleotides have three main parts

5­Carbon Sugar (Pentose) (RNA: ribose ; DNA: deoxyribose)

a phosphate group a nitrogenous base

DNA nitrogenous bases: Adenine (A), thymine (T), cytosine (C), and guanine (G)

RNA nitrogenous bases: A, C, G, and uracil (U)

uracil replace thymine in RNA both nitrogenous bases make up sugar­phosphate backbones

repeating and protruding nitrogenous bases double helix

two polynucleotide strands wrap around each other to form the shape of DNA

A pairs with T ; C pairs with G (base pairs) RNA is usually a single polynucleotide strand

gene particular nucleotide sequence that can instruct the formation of a

polypeptide DNA molecules consist of many base pairs (and therefore,

many genes) determine the structure of protein, and thus, life's

structures and functions Deoxyribonucleid Acid (DNA)

contains coded information that programs all cell activity

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contains directions for its own replication is copied and passed from one generation of cells to the next found primarily in the nucleus makes up genes

contain instructions for proteins synthesis Ribonucleic Acid (RNA)

actual synthesis of proteins (coded for by DNA) on ribosomes in the cytoplasm messenger RNA carries encoded genetic messages

from nucleus to cytoplasm Mutations

alterations in bases or the sequence of bases in DNA lactose intolerance is a result of these mutations the gene that dictates lactose utilization is turned off in adulthood

mutations, over time, prevent the gene from turning off Topic 4: A Tour of the Cell

Cells on the Move Cells were first observed by Robert Hooke in 1665

most cells cannot be seen without a microscope Antoni van Leeuwenhoek described moving cells

not all cells move, however, the cellular parts are actively moving Light Microscope (LM)

light passes thru specimen, then thru glass lenses into viewer's eye you can magnify up to 1,000x

resolution: the ability to distinguish between small structures light microscopes cannot provide details of a small cell's structure

Electron Microscope (EM) can magnify specimens as small as 2 nanometers up to 100,000x uses a beam of electrons (as opposed to light)

Surface Area smaller the cell, larger the surface area (relative to volume)

Prokaryotic vs. Eukaryotic prokaryotic cells are structurally simpler

bacteria and archaea both have plasma membrane and 1+ chromosomes/ribosomes eukaryotic cells have membrane­bound nucleus (and other organelles)

prokaryotes have a nucleoid and no true organelles Eukaryotic Cells

partitioned into functional compartments

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four life processes in eukaryotic cells (depend upon structures and organelles)

Manufacturing nucleus, ribosomes, ER, and golgi

Breakdown of Molecules lysosomes, vacuoles, peroxisomes

Energy Processing mitochondria (animals) ; chloroplast (plants)

Structural Support, Movement, and Communication cytoskeleton, plasma membrane, cell wall

Animals vs. Plants Cells Lysosomes and Centrioles are not found in plant cells Plant cells have a rigid cell wall, chloroplasts, and central vacuole

(animals cells do not) Membranes

Selective Permeability plasma membrane

controls movement of molecules in and out of the cell membranes made of lipids, proteins, and carbohydrates

(phospholipids) Phospholipids form a 2­layer sheet (bilayer)

hydrophilic heads face outward water loving

hydrophobic tails point inward water hating

proteins are attached to the surface Manufacturing

Endomembrane System nucleus: cell's control center (responsible for inheritence)

contains chromatin complex of proteins and DNA (makes chromosomes) DNA is copied within nucleus during interphase, before division

nuclear envelope: double membranes w/ pores allowing material to flow in and out of the nucleus

attached to a network of cellular membranes called the ER ribosomes: involved in the cell's protein synthesis ; make proteins

made in the nucleolus (inside nucleus) free ribosomes: suspended in cytoplasm bound ribosomes: attached to ER

endomembrane system: nuclear envelope, ER, golgi, lysosomes, vacuoles, and the plasma membrane

membranes in a eukaryotic cell are physically connected to compose this

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vesicles: embrane­enclosed sacs that are pinched off portions of membranes, moving from the site of one membrane to another

communication results in synthesis, storage, and export of molecules

Endoplasmic Reticulum: a biosynthetic factory Smooth ER

no attached ribosomes synthesizes lipids, phospholipids, steroids, oils detoxifies drugs and poisons (usually in liver)

Rough ER attached ribosomes ; lines outer surface of membranes

synthesizes proteins (into gylcoprotein, usually) ships off to golgi in transport­vesicle

Golgi Apparatus finishes, sorts, and ships

the receiving side of the golgi takes in products they are then modified as they move from one side of the golgi to

the other ships off packaged products in vesicles to other sites

Breakdown

Lysosomes digestive compartments within a cell (membranous sac containing

digestive enzymes) lack of specific lysosomes can lead to disease

remove or recycle damaged cell parts damaged part is inclosed in membrane vesicle lysosome fuses with vesicle (dismantles contests... breaks down

damaged organelle) cell destruction

"suicide sac" ; can destroy a cell if necessary Vacuoles

membrane­enclosed sac that is larger than a vesicle Food Vacuole: formed by phagocytosis Contractile: pumps excess water from the cell Central Vacuole: large vacuole found in most plant cells

hydrolytic functions Summary of Endomembrane System

Rough ER ­> Vesicles ­> Golgi ­> Vesicles ­> Lysosomes/Vacuoles/Plasma Membrane

diagrams from power point may help understanding Energy Processing

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Energy Converting Organelles Mitochondria and Chloroplasts are the main energy transformers of cells

Mitochondria organelles which are the sites of cell respiration (found in nearly all

eukaryotic cells) Intermembrane Space:

narrow region between inner and outer membranes Mitochondrial Matrix:

enclosed by inner membrane contains enzymes used for cell respiration

Cristae: folds inside the mitochondria

Chloroplast convert solary energy to chemical energy (photosynthesis) Intermembrane Space:

seperates the double membrane Thylakoid Space:

space inside the thylakoids thylakoids: membranous sacs inside chloroplast grana: stack of thylakoids

Stroma: viscous fluid outside thylakoids

do not confuse with stomata Evolution Connection

Mitochondria and Chloroplasts evolved by endosymbiosis they both have 1) DNA and 2) ribosomes derived from prokaryotes

endosymbiosis mitochondria and chloroplasts were formerly small

prokaryotes that began living within larger cells Support, Movement, and Communication Between Cells

The Cytoskeleton provides structural suport to cells for motility and regulation

Cytoskeleton network of fibers thrughout cytoplasm that forms a dynamic framework for

support, movement, and regulation maintains cell shape (or changes it) motor proteins: organelle movement, muscle contraction

microtubules found inside cytoplasm of eukaryotic cells made of tubulin ; are hollow fibers shape the cell and act as motor protein tracks

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Centrosomes and Centrioles centirole: pair of cylindrical structures located in the centrosome of

an animal cell (nine sets of triplet microtubules arranged in ring) Cilia and Flagella

locomotor organelles found in eukaryotes that are formed from specialized arranged of microtubules

move by bending motor proteins called dynein arms Cilia: lots of tiny hairs working like the oars of a crew boat Flagella: undulates in a whiplike motion (sperm) basal body: cellular structure that anchors the microtubular

assembly of cilia and flagella microfilaments

support the cell's shape and are involved in motility provide cellular support participate in muscle contraction

Intermediate filaments reinforce cell shape and anchor organelles

Cell Surfaces and Junctions Extracellular Matrix of Animal Cells

functions in support, adhesion, movement, and development composed of strong fibers of collagen, which holds cells together and

protects the plasma membrane attaches through integrins

proteins that bind to membrane Tight Junctions

hold cells together tightly enough to block transport of substances thru intercellular space

prevent leakage of extracellular fluid Gap Junctions

specialized for transport between cytoplasm of adjacent cells channels allowing molecules to flow between cells

Anchoring Junctions fasten cells together into strong sheets, but permit substances to pass

freely Cell Walls

rigid cell walls are found in plant, buut not animal cells composed primarily of cellulose protects and provides skeletal support that keeps the plant upright against

gravity also prevents excess water uptake

plasmodesmata (plant cells have these instead of junctions) channels that perforate plant cell walls

small passage in cell wall

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connect cytoplasm of neighboring cells Topic 5: The Working Cell

Membrane Structure and Function Membranes are a fluid mosaic

composed of phospholipids and proteins surface looks mosaic because the proteins embedded in the

phospholipids appears fluid because the proteins can drift about in the

phospholipids many are made from unsaturated fatty acids (kinks in tails)

this prevents tight packing this keeps them liquid

aided by cholesterol wedged into the bilayer membranes contain integrins

integrins give the membrane stronger framework they attach to the extracellular matrix on the outside of the

cell, as well as span the membrane to attach to the cytoskeleton

glycoproteins identification tags

recognized by membrane proteins of other cells recognition

enables cells of the immune system to reject foreign cells, like infectious bacteria

membrane proteins function as enzymes signal transduction

messenger molecule > enzyme > activated molecule transport

passive: no energy required ; moves down concentration gradient

active: requires energy ; moves against concetration gradient

selective permeability some substances can cross or be transported easier than others

nonpolar molecules (CO2 and Oxygen) cross easily polar molecules (glucose, sugars) do not cross easily

Passive Transport diffusion

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process in whichparticles spread out evenly in an available space move from an area of more concentrated particles to a less

concentrated area diffuse down the concentration gradient

particles are eventually evenly spaced out requires no energy osmosis

diffusion of water across a membrane moves down concentration gradient until concentration on each

side is equal facilitated diffusion

diffusion of solutes across a membrane with the help of transport proteins Tonicity

ability of a solution to cause a cell to gain or lose water Isotonic Solution

concentration of a solute is the same on both sides Hypertonic Solution

concentration of a solute is higher outside the cell Hypotonic Solution

higher concentration of solute inside the cell osmoregulation

process that maintains water balance in cells prevents excessive uptake or loss of water plants have difficulties with osmoregulation due to cell walls

aquaporins hourglass­shaped proteins that are responsible for entry and exit of water

through the membrane Active Transport

requires the use of energy / ATP moves a solute against its concentration gradient changes the shape of the protein thru phosphorylation

phosphate from ATP attaches and detaches Transport of Large Molecules

material that is transported is packaged within a vesicle this vesicle then fuses with the membrane

exocytosis export bulky molecules

such as proteins or polysaccharides endocytosis

import substances useful to livelihood of the cell phagocytosis

engulfment of a particle by wrapping cell membrane around it, forming a vacuole

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cell eating pinocytosis

engulfment of a fluid by wrapping cell membrane around it, forming small vesicles

cell drinking receptor­mediated endocytosis

receptors in a receptor­coated pit interact with a specific protein, initiating formation of a vesicle

Energy and the Cell energy: the capacity to do work and cause change

work is accomplished when an object is moved against an opposing force

kinetic energy: energy of motion performs work by transferring motion to other matter

ex) heat or thermal energy potential energy: energy an object possesses as a result of its location

chemical energy (energy available for release in a reaction) ex) water behind a dam

Laws of Thermodynamics thermodynamics: study of energy transformations

First Law: energy in the universe is constant

Second Law: energy conversions increase the disorder of the universe

entropy: the measure of disorder, or randomness Reaction Classification

exergonic reaction chemical reaction that releases energy

have less free energy energy is released in covalent bonds of reactants

ex) burning wood releases energy in glucose, producing heat, light, carbon dioxide, and water

ex) cellular respiration endergonic reaction

requires an input of energy yields products rich in potential energy

ex) photosynthesis metabolism

the combined make­up of thousands of endergonic and exergonic chemical reactions

metabolic pathway series of chemical reactions that either break down a complex molecule

or build up a complex molecule

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a cell's three main types of cellular work chemical work

driving endergonic reactions transport work

pumping substances across membranes mechanical work

beating of cilia energy coupling

use of exergonic processes to drive an endergonic one cells can manage energy resources this way

ATP adenosine triphosphate: energy currency of cells

immediate source of energy that powers most forms of cellular work composed of:

adenine (nitrogenous base) ribose (5­carbon sugar) three phosphate grops

hydrolysis of ATP releases energy by transferring its third phosphate from ATP to another

molecule transfer is called phosphorylation ATP energizes molecules

ATP is a renewable source of energy for the cell How Enzymes Function

energy of activation (Ea) energy available to break bonds and form new ones

enzymes catalysis (speeds us) biological reactions

speed up rate by lowering the Energy of Activation active site

where the enzyme interacts with the enzyme's substrate substrate

particular target molecule of an enzyme non­protein enzyme helpers

cofactors inorganic ­ such as zinc, iron, or copper

coenzymes organic molecules ­ often vitamins

enzyme inhibitors competitive inhibitors

inhibit because of competition for the active sit block substrates from enetering the active site

non­competitive inhibitors

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bind somewhere else, changing the shape of the enzyme substrate no longer fits in active site

feedback inhibition regulation of a metabolic pathway by its end product, which inhibits an

enzyme within the pathway Topic 6: Cellular Respiration ­ Harvesting Chemical Energy

Muscle Fibers slow twitch muscle fibers

more myoglobin make ATP aerobically (oxygen) long­distance runners

fast twitch muscle fibers less myoglobin

make ATP anaerobically (without oxygen) sprinters

Metabolic Pathway of Cellular Respiration energy is necessary for life processes

growth, transport, manufacture, movement, reproduction, etc.. photosynthesis and cellular respiration provide energy for life

breathing supplies oxygen to our cells for use in cell respiration it also removes carbon dioxide

cell respiration banks energy in ATP molecules cell respiration produces 38 ATP molecules from each glucose molecule

foods (organic molecules) can be used as a source of energy as well

C6H12O6 + 6O2 ­­­­­­­­­­­­­­­­­> 6CO2 + 6H2O + 38 ATP

Use of energy from ATP

kilocalorie (kcal) quantity of heat required to raise the temperature of 1 kg of water by 1

degree Celsius this energy is used for body maintenance and for voluntary

activities the average adult human needs about 2,200 kcal of energy per day

different activities use different amounts of kcals ex) swimming @ 2mph uses about 408 kcals for a 150­lb person

Source of Energy cells tap energy from electrons "falling" from organic fuels to oxygen

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whenthe carbon­hydrogen bonds of glucose break, electrons and transferred to oxygen

oxygen attracts electrons energy can be released from glucose by burning it

energy is released as heat and light this energy is not available to living organisms

oxidation loss of electrons

reducation gain of electrons

cell respirations is the controlled breakdown of organic molecules energy is released in small amounts that can be stored in ATP

dehydrogenase enzyme that removes hydrogen from an organic molecule

requires a coenzyme called NAD+ to shuttle electrons NAD+ can be reduced when it accepts e­'s and oxidized

when it gives them up NAD+ reduced becomes NADH

NAD+ is the electron acceptor it eventually becomes oxidized and is then a donor

electron "carrier" molecules form a staircase where the electrons pass from one to the next down the

staircase these electron carriers are called the electron transport chain

ATP is generated as the electrons are transported down the chain

Stages of Cellular Respiration and Fermentation Glycolysis

begins respiration by breaking glucose into two molecules of a 3­carbon compound called pyruvate.

occurs in the cytoplasm Citric Acid Cycle

breaks down pyruvate into carbon dioxide and supplies the third stage with electrons

occurs in the mitochondria Oxidative Phosphorylation

electrons are shuttled through the ETC ; ATP is generated through chemiosmosis

occurs in the inner mitochondrion membrane a concentration gradient of H+ is made during transport

the energy of this gradient is called chemiosmosis it is used to make ATP

the concentration drives H+ through ATP Synthase

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energy/ATP is produce Glycolysis

a single molecule of glucose is cut in half through a series of steps this is done to create two molecules of pyruvate

2 NAD+ molecules are reduced to 2 NADH molecules 2 ATP molecules are produce by substrate­level phosphorylation

substrate­level phosphorylation enzyme transfer a phosphate group from a substrate molecule to ADP

this forms ATP which can be used immediatley NADH must be transported thru the ETC to make more

ATP recycling the ATP

this stage makes 4 ATP, but uses 2 of the ATP's in the cycle they recycle the ATP they use for work

Products 2 Pyruvate 2 ATP (net­gain) 2 NADH

Transitional Phase counted into Krebb's Cycle

pyruvate is transported to the mitochondria in preparation for the citric acid cycle...

removal of the carboxyl group that forms CO2 oxidization of the 2­carbon compound that remains coenzyme A binds to the 2­carbon fragment

this makes acetyl coenzyme A with the help of CoA, the acetyl (2­carbon compound) enters the

the citric acid cycle Citric Acid Cycle/Krebb's Cycle

Products: 2 ATP 6 CO2 8 NADH 2 FADH2

Oxidative Phosphorylation involves electron transport and chemiosmosis and requires an adequate supply

of oxygen NADH and FADH2 and the inner membrane of the mitochondria are

involved H+ ion gradient formed from all of the redox reactions provides energy for

synthesis of ATP NADH ­­> 3 ATP

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10 NADH in stage ­­> 30 ATP FADH­­> 2 ATP

2 NADH in stage ­­> 4 ATP totals to 34 ATP

hydrogens are pumped outside this is active transport

ATP Synthase "pump"

hydrogen ions enter from top spun around into ATP (adds phosphate) (chemiosmosis)

Products: 34 ATP

Toxins DNP: diet pill (dinitrophenol)

makes you lose weight... but then die of heart attacks makes membrane permeable/leaky hydrogens cannot go thru ATP synthase

cells work harder to get them thru... raises heart rate... DEAD

oligomycin for athlete's foot

blocks/inhibits ATP synthase no ATP is made

fungus dies rotenone

kills plants and fish blocks ETC stops process

cyanide/carbon monoxide works very quickly (cyanide) ; makes you sleepy (carbon

monoxide) stop electron transport chain (ETC) no energy

DEAD Fermentation (Anaerobic)

if no oxygen is present after glycolysis, fermentation undergoes Lactic Acid Fermentation

NADH is oxidized to NAD+ when pyruvate is reduced to lactate produces 2 ATP and 2 Lactate

Alcoholic Fermentation convert pyruvate to CO2 and ethanol while oxidizing NADH to

NAD+ produces 2 Ethanol and 2 ATP (releases 2CO2)

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Evolution Connection Glycolysis evolved early in the history of life on Earth

it is the universal energy­harvesting process of living organisms Interconnections Between Molecular Breakdown and Synthesis

Cells use many kinds of organic molecules as fuel for cellular respiration Three Sources of Molecules for generation of ATP:

Carbohydrates (disaccharides) Proteins (after conversion to amino acids) Fats (glycerol and fatty acids)

Topic 7: Photosynthesis ­ Using Light

Plant Power plants use water and carbon dioxide to produce a simple sugar and liberate

oxygen this is photosynthesis, a process that converts solar energy to chemical

energy plants produce 160 billion metric tons of sugar each year sugar is food for humans and for animals that we consume

biofuels plants can be used in "energy plantations" to create a fuel source to

replace fossil fuels air pollution, acid precipitation, and greenhouse gases would be

reduced 6CO2 + 6H2O ­­­­­light energy­­­­­> C6H12O6 + 6O2

Producers and Consumers of the Biosphere autotrophs

living things that are able to make their own food without using organic molecules derived from any other living thing

photoautotrophs autotrophs that use the energy of light to produce organic molecules

most plants, algae, and other protists heterotrophs

cannot synthesize their own organic molecules from inorganic raw materials

eat plants or other animals also known as consumers or decompers

Chloroplasts are the sites of Photosynthesis in Plants chlorophyll

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important light absorbing pigment in chloroplasts reflects green light ; thus making plants green

mesophyll green tissue in the interior of the leaf

this is where the chloroplasts are concentrated stomata

tiny pores in the leaf that allow carbon dioxide to enter and oxygen to exit the plant

stroma viscous/dense fluid outside the thylakoids within the chloroplast

enclosed by an envelope of two membranes thylakoids

system of interconnected membranous sacs stacks of thylakoids: grana

Redox Process a redox process involves oxidation and reduction

Photosynthesis is a redox process water molecules are split by oxidation (they lose electrons and

hydrogen ions) CO2 is reduces to sugar as electrons and hydrogens are added to

it Cellular Respiration is also a redox process

see topic 6 for details Overview: The 2 Stages of Photosynthesis are linked by ATP and NADPH

light reactions light energy is converted in the thylakoid membranes to chemical energy

and O2 water is split to provide the O2 as well as electrons NADP+ is reduced by H+ ions to NADPH

electron carrier similar to NADH shuttled into Calvin cycle to make sugar generate ATP

calvin cycle occurs in stroma of the chloroplast

builds sugar molecules from CO2 and the products of light reactions

carbon fixation CO2 is incorporated into organic compounds

also knows as the dark or light­independent reactions Calvin­Benson cycle is also used

The Light Reactions: Converting Solar Energy to Chemical Energy sunlight contains electromagnetic energy or radiation

visible light is only a small section of the electromagnetic spectrum

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the electromagnetic spectrum is the full range of electromagnetic wavelength

wavelength distance between the crests of two adjacent waves

photon packet of light energy

shorter the wavelength, greater the energy pigments

molecules that absorb light pigments are built into the thylakoid membrane they transmit light and absorb others

ex) chlorophyll transmits green this is reflected light, making plants green

responsible for absorbing photons (capturing solar power) electrons jump to an excited state (unstable) drop back down to "ground state"

release excess energy chlorophyll a

absorbs blue violet and red light reflect green

chlorophyll b absorbs blue and orange reflects yellow­green

carotenoids absorb blue­green light reflect yellow and orange

Photosystems photosystems are light­harvesting complexes surrounding a reaction center

complex energy is passed from molecule to molecule within the photosystem

it eventually reaches a reaction center where a primary electron acceptor accepts these electrons and becomes reduced

Photosystem II functions first P680

pigment absorbs light with a wavelength of 680 nm Photosystem I

functions second P700

pigment absorbs light with a wavelength of 700 nm Photosystems are connected by the ETC

Chemiosmosis power ATP synthesis in the light reactions it is involved in oxidative phosphorylation and ATP generation in chloroplasts

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photophosphorylation chemiosmotic production of ATP in photosynthesis

Calvin Cycle: Converting CO2 to Sugars The calvin cycle makes sugar within a chloroplast

Ingredients: CO2, ATP, NADPH from light reactions

G3P (glyceraldehyde­3­phosphate) uses this to make glucose and other organic molecules

RuBP (ribulose biphosphate) five­carbon sugar that starts the calvin cycle

Carbon Fixation aided by an enzyme called rubisco

this is repeated over and over, one carbon at a time Evolution Connection

C4 and CAM plants hot climates prevent plants from opening stomata during the day

if they did, they would lose water CAM plants open their stomatas in the night when it is cooler

they store CO2 until the day, when they undergo the calvin cycle C4 Plants shut stomata when the weather is hot and dry to conserve

water but is able to make sugar by photosynthesis they first fix carbon dioxide into a 4­carbon compound

Photosynthesis, Solar Radiation, and Earth's Atmosphere greenhouse effect

gases in the atmosphere reflect heat back to Earth keeps the planet warm, supporting life

too much heat being retained will result in abnormal temperatures, bringing about problems

global warming slow and steady rise in Earth's surface temperature

melting polar ice, changing weather patterns, spread of tropical disease

photosynthesis moderates global warming it could mitigate the increase in atmospheric CO2

unfortunately, due to deforestation, it will not help