All living cells can be divided into two groups: • Prokaryotic cells – simple cells – Single-celled ( and blue-green ) • Eukaryotic cells – more complex cells – Single-celled organisms () – Compose multi-cellular organisms (protists, fungi, and )

Feature Function Prokaryotes Eukaryotes (plasma) Regulate material entering All All membrane and exiting cell DNA Stores genetic material All All Protect cell, provide shape All Some (plants) Fluid inside cell All All Nucleus Houses DNA None All Site of synthesis All All Flagella Aid cell in locomotion Some Some Mitochondria Site of ATP synthesis None All Endoplasmic Synthesis of and None All Reticulum Golgi Storage and packaging of None All apparatus substances & Digest None All Storage of material Some Some Small pieces of DNA that Some None can exit the cell Contain or None Some (plants)

Biology 4A Prokaryotes & Eukaryotes

Prokaryotic Bacterial Cell

Eukaryotic Cell Eukaryotic Cell

Biology 4A Cellular Processes

Energy conversions – conversion of radiant () into chemical energy (), occurs in of

6CO2 + 6H2O + energy → C6H12O6 + 6O2 Chemosynthesis – conversion of unusable chemical energy () into usable chemical energy () (ATP) – which living things use to release and store energy, becomes adenosine diphosphate (ADP) when energy is released

Glycolysis – process of producing 2 ATP by breaking down glucose into pyruvic acid, first step of respiration Aerobic respiration – respiration in which, after glycolysis, pyruvic acid is broken down into and , net gain of 36 additional ATP – respiration in which, after glycolysis, pyruvic acid is broken down into either lactic acid or alcohol, does not provide ATP, allows glycolysis to continue

Biology 4B Cellular Processes

Synthesis of New DNA Replication 1. Helicases unwind and unzip DNA at replication forks 2. Free floating nucleotides bond to exposed bases 3. DNA polymerase bind nucleotides to each other in 5’ to 3’ direction a. Leading strand – elongates toward replication fork continuously b. Lagging strand – elongates away from replication fork discontinuously (called ), bonded together by DNA ligase 4. New molecules each contain one original and one new strand

Transcription – process by which a portion of DNA nucleotide sequence is used to produce a complementary mRNA strand by RNA polymerase – process by which information in mRNA strand is used to create chain (polypeptide chain) by ribosomes and tRNAs Lipogenesis – process of synthesizing lipids from intermediates of , occurs along smooth

Biology 4B Cellular Processes

Transport of Molecules – within the cell • Many molecules float freely through cytoplasm • Others are carried by motor proteins () or the endoplasmic reticulum and Intercellular transport – in and out of the cell through plasma membrane Passive transport – does not use energy, movement down concentration gradient (high to low concentration) • Diffusion – net movement of small, nonpolar molecules directly through bilayer • – net movement of larger molecules and ions through ion channels or carrier proteins • Osmosis – net movement of water molecules through membrane

Active transport – uses energy (ATP), movement up concentration gradient (low to high concentration) • Ion pumps – proteins that move ions one way • Cotransport – coupled passage of two molecules in the same direction (symport) or different directions (antiport)

Homeostasis – ability of a cell to maintain stable internal conditions independent of environment, accomplished by passive and active transport • Carbonic acid – buffer that helps regular pH

Biology 4B Biology 4C -

Parts of Viruses capsid animal

membranous tail envelope

tail fibers

Viruses vs. Cells Viruses Cells


Need for replication Can reproduce independently

Never contain Can contain organelles

Do not convert energy Convert energy

Replication Cycles

Lytic Lysogenic

Biology 4C Biology 4C - Viruses

Human Viral Diseases

AIDS • Loss of effectiveness • Caused HIV - immunodeficiency virus • Period of before loss of immune system • Prevention • No vaccine (yet) • Limit and avoid transmission

Influenza (the flu) • Fever, fatigue, and respiratory • Can be deadly • Caused a variety of influenza viruses • Can mutate rapidly and blend together • Prevention • Seasonal vaccine • Limit transmission

The Common Cold • Fever, fatigue, and respiratory infections • Caused a variety of rhinoviruses • Prevention • No vaccine • Limit transmission

Hepatitis A • Inflammation of liver, jaundice (yellow) appearance • Caused a hepatitis A virus in food and water • Prevention • Vaccine • Limit transmission

Biology 4C Cell

Cell cycle – the sequence of and division that occurs in a cell between the beginning of one and the beginning of next cell division • Interphase (G1, S, G2) – period in which cell prepares for division. DNA and organelles replicate. • Mitotic phase ( and ) – period in which cell divides into two daughter cells. Ensures that daughter cells receive correct number of .

Biology 5A

Mitosis – the process by which each daughter cell receives an exact copy of chromosomes present in parent cell • Prophase – coils into chromatid, move apart, spindle fibers form • – chromosomes arranged along spindle equator by spindle fibers, attach to separate spindle fibers • Anaphase – spindle fibers shorten and pull chromatids apart at the – chromatids reach opposite poles, spindle fibers disappear, nuclear membrane forms, uncoil

Cytokinesis – the division of the cell’s cytoplasm into two daughter cells • Animal cell – pinches together, groove forms until membrane separates • extends outward until it divides cells

Biology 5A Cell Cycle

DNA replication – the process by which DNA is copied into a new strand, occurs during S phase of interphase • Semiconservative replication – each new molecule contains one original and one new strand • Helicase unwinds DNA and break bonds between complementary base pairs o Replication fork – site which separation occurs • Free-floating nucleotides bond to exposed bases (A & T, C & G) • DNA polymerase bond nucleotides to each other in 5’ to 3’ direction o Leading strand: elongates continuously toward replication fork o Lagging strand: elongates discontinuously as Okazaki fragments away from replication fork, sealed by DNA ligase

Why is the cell cycle important? • Cells are limited in size. Large organisms need to be multicellular. Proper cell division ensures daughter cells have correct DNA • Mode of for unicellular organisms • Mode of growth, maintenance, and replacement for multicellular organisms

Biology 5A Specialized Cells

Specialized Plant Cells Cell Feature Function Concentric circles of Transport water and cells vascular upward Hairs protruding from cell Absorb water and minerals Root cells walls from Concentric circles of Transport water and Stem cells vascular tissues minerals throughout plant Thick-walled cells around Stem cells Provides support outer edge Cells have many cells chloroplasts, arranged in Carry out photosynthesis layers

Specialized Animal Cells Cell Feature Function Deliver to body Red blood cells Contain cells Contain filaments that can Cause movement of body Muscle cells contract parts or substances Epithelium cells Cells packed tightly Form a protective cover (exterior skin) together Epithelium cells High surface area Exchange molecules (internal lining) Contain dendrites and Transmit electrical signals Nerve cells axon throughout body

Biology 5B Cell Differentiation

Stem cells – cells that can differentiate into a variety of specialized cell types

Specialized cells – cells with specific structure and function • Examples: blood cells, leaf cells

Cell differentiation – process of converting stem cells into more specialized cell types in multicellular organisms

How does cell differentiation occur? • Proteins are produced by the cell – Direct the modification of the cell’s structure – Allow the cell to begin carrying out specialized functions • Role of DNA – Segments not needed are coiled tightly around – Segments needed are transcribed into proteins • Role of RNA – mRNA transcript used to create protein during translation – Small RNA remove from mRNA strands • Change the protein produced – Small RNA can bind and degrade mRNA strands • Stop protein from being produced • Role of environment – Neighboring cells can send signaling proteins to alter expression – Temperate can alter – Low oxygen concentration can suppress gene expression

Biology 5C Cell Cycle and Cancer

Cell cycle – the sequence of cell growth and division that occurs in a cell between the beginning of one cell division and the beginning of next cell division • End of G1 – vital checkpoint, cell determines whether or not to replicate its DNA o in growth- regulating cause cells to divide more rapidly

Growth regulating genes Proto-oncogenes – encode proteins that stimulate cell division in normal cells •  Oncogenes – mutated proto-oncogenes that speed up cell division Tumor suppressor genes – encode proteins that turn off cell division in normal cells • Mutation  Mutated suppressor genes fail to turn off cell division

Tumors and cancer Tumor – dense mass of abnormal cells • Result of mutations in growth-regulating genes • Benign – localized tumor, cells do not invade other tissues • Malignant – cells of tumor do not remain in one area, migrate and invade other tissues Cancer – condition in which malignant cells invade and destroy body tissues • Develops overtime due to genetic changes • Can be stimulated by carcinogens

Biology 5D DNA

Components of DNA Deoxyribonucleic acid (DNA) is a double-stranded , made of building blocks called nucleotides Each nucleotide contains a • Phosphate base • • Nitrogenous base

Bonding in DNA • The sides of one DNA molecule is connected with bonds between the phosphate group and the deoxyribose sugar • The two DNA strands connect by bonds between nitrogenous bases o A always bonds with T o G always bonds with C

Role of DNA DNA is the genetic material of organisms. • Information coded in the of the bases used to create proteins • Proteins act as , cell signals, and structural elements, contributing to the traits seen in organisms. • Different DNA can lead to different proteins

Biology 6A The Universal

Genetic code – the rules by which information in genetic material is translated into proteins • Universal – almost all living things use the same translation rules (the same mRNA strand would be translated into the same protein in different organisms) • Rules can be summarized into a chart

Components of the genetic code • DNA – stores the sequence of nucleotides • RNA – carries the nucleotide sequence to the cytoplasm, aids in translation

Biology 6B & Translation

How is DNA used to create proteins? 1) Transcription – process by which DNA is used to produce mRNA a) RNA polymerase – protein that initiates and operates transcription b) mRNA – messenger RNA, carries information into cytoplasm

Use the steps below to determine an mRNA strand sequence.

2) Editing and processing – process of modifying mRNA in eukaryotes a) introns removed b) spliced together c) cap and tail added d) sent out of the nucleus

Biology 6C Transcription & Translation

How is DNA used to create proteins (cont.)? 3) Translation – process by which information in mRNA strand is used to create amino acid chain (polypeptide chain) a) – protein complex where translation occurs, made of rRNA b) tRNA – transfer RNA, bring amino acids to the ribosome

Use the steps below to determine a polypeptide chain sequence.

4) Editing and folding a) editing – sections of polypeptide chain removed b) folding – chain folds to make 3D shape, critical for protein function

Biology 6C Regulation of Gene Expression

Gene regulation occurs at all four levels of gene expression

Condensed DNA less likely to be used, transcription factors promote or suppress transcription

Modification (splicing) of initial mRNA transcript into mature transcript changes protein

Proteins limit export of mature mRNA from nucleus to cytoplasm

mRNA structure and proteins affect initiation, environmental factors increase or decrease translation

Biology 6D DNA Mutations

Mutation – a random change in the sequence of a gene, caused by mistakes in DNA replication process and environmental agents. Mutation Definition Example Point mutation One base replaced with another base ABCDEFG (Substitution) ABZDEFG Inversion Order of two or more bases reversed ABCDEFG ABEDCFG

Insertion Addition or one or more new bases ABCDEFG ABCHDEFG Removal or one or more bases ABCDEFG ABEFG CD Translocation Movement of one or more bases to a ABCDEFG ABCDEFG new location in a different DNA sequence ABEFG ABCDCDEFG

Determine effect of mutation during translation 1. Determine amino acid chain made by original mRNA strand 2. Determine amino acid chain made by mRNA strand 3. Compare the two chains a. No changes = silent mutation b. One amino acid changed = missense mutation c. Amino acid chain ends sooner = nonsense mutation d. Multiple amino acids changed =

Mutation in traits can be organized by their effect • Neutral mutations – no effect on survival (eye color) • Harmful mutations – decrease survival (cancer) • Beneficial mutations – increase survival (disease resistance)

Biology 6E Biology 6F - and Punnett Squares

Vocabulary character - a recognizable feature controlled by genetics (ex: fur color) trait - a version of a character (ex: white fur) allele - the section of DNA that codes for a specific trait - an ’s genetic makeup for a character (ex: Ww) phenotype - an organism’s appearance for a character (ex: white fur) homozygous - having two of the same alleles for a character (ex: WW) heterozygous - having two different alleles for a character (ex: Ww)

Types of dominance • complete dominance - heterozygous individuals display dominant trait • incomplete dominance - heterozygous individuals display an intermediate between traits • codominance - heterzygous individuals display both traits at once

Punnett Squares

GR Gr gR gr G g G GGRR GGRr GgRR GgRr R G GG Gg Organize outcomes from genetic crosses G GGRr GGrr GgRr Ggrr r

g Gg gg Each box represents an g GgRR GgRr ggRR ggRr equally likely outcome R g GgRr Ggrr ggRr ggrr r

You can use the five steps below to solve any genetics problem

Biology 6F &

Meiosis – type of cell division in which daughter cells receive only half the number of chromosomes present in parent cell • Produces – specialized cells

Homologous chromosomes – chromosomes that control the same hereditary traits, similar in size and shape • Synapsis – pairing of homologous chromosomes) o Crossing over – event during synapsis in which material is exchanged, mixing genes. • Independent assortment – homologous chromosomes have equal chance of going to either

Sexual reproduction – reproduction in which a new individual () is produced by the union (fertilization) of the nuclei of two gametes • Significance of meiosis o Produces gametes needed o Increases genetic variation through independent assortment and crossing-over

Biology 6G DNA Technology

Chromosomal analysis – procedure used to determine chromosomal abnormalities • – photograph of arranged chromosomes from a cell • Patient karyotype compared to normal karyotype to determine presence of genetic diseases

DNA fingerprinting – technique that creates a pattern of DNA fragments • Used to identify individual organisms or compare individuals • Procedure 1. Samples taken from individuals 2. DNA separated from cells, cut by restriction enzymes 3. Cut DNA run through gel electrophoreses, separates by size 4. Samples compared

Genetic engineering – direct manipulation of genes Cloning – process used to make multiple copies of a desired gene, • Used for gene , pharmaceutical drug production, increasing agricultural • Procedure 1. DNA containing gene is isolated from organism 2. Gene copies are inserted into plasmids 3. Recombinant DNA is inserted into bacteria cells 4. Bacteria cells reproduce, each contain desired gene Gene mapping – technique used to determine the location of a gene • Used to identify the location of a gene and for genetic screening • Procedure 1. Radioactive or fluorescent DNA probe created to match sequence of desired gene 2. Organism’s DNA is unwound 3. DNA probe base-pairs with complementary sequence

Biology 6H Common Ancestry

Common ancestry – scientific theory that groups of related organisms share a common ancestor

Fossils – preserved traces of remains of living organisms from the past Evidence for common ancestry • When are arranged chronologically, can see a progressive change in organisms from shared ancestor • Generally less diversity further in record, indicating shared ancestors Limitations • Significant gaps in records because of low fossilization rates • Limited conclusions (no function or behavior)

Anatomical homologies – similar structures between different organisms Evidence for common ancestry • Homologous structures – similar structures that share an ancestral form (ex: forearms in vertebrates) • Vestigial structures – degenerated and/or nonfunctional structures Limitations • Must differentiate between homologous and analogous structures

Biology 7A Common Ancestry

Molecular homologies – similar stretches of genetic material and/or proteins between different organisms Evidence for common ancestry • Universal genetic code (same bases, same codon table) • Similar between related • Conserved vital proteins (ribosomes) Limitations • Mutation rates difficult to accurately analyze • Gene regulation hard to study

Developmental homologies – similar features in of different species Evidence for common ancestry • Ancestral forms during development (teeth in baleen whales) • Similar hox genes (code for development) Limitations • Gene regulation hard to study

Biogeography – the study of the distribution of species, organisms, and through geological Evidence for common ancestry • Similar organisms found in similar environments across the world • Splintered on islands Limitations • Depends on other methods to verify hypotheses

Biology 7A The Fossil Record

Fossils – preserved traces or remains of living organisms • Require specific conditions to form

How can groups suddenly appear in the fossil record? • Some organisms don’t fossilize well • Species may evolve into form that is more favorable for fossilization o Organisms may appear suddenly when new form is reached • Gap in record may exist between two forms

Why does stasis appear in the fossil record? • Stasis – a period in which species exhibits limited morphological change • If no trait is being selected for, no occurs, no change will occur (stasis) o Ex: crocodile, horseshoe crab

Why do groups seem to appear and change sequentially in the fossil record? • Slow response to constant natural selection pressure o Ex: coiled oysters became larger, thinner, flatter to be more stable in disruptive water

Biology 7B Natural Selection in Populations

Natural selection – process whereby organisms with favorable variations survive and produce more offspring than less well-adapted organisms • Individuals with most adaptive variations survive and pass on traits • Over time, shifts to have more offspring with trait

Genetic Equilibrium – the genetic makeup of a population will remain relatively stable unless something happens to make it change • Populations in genetic equilibrium do not change or evolve • For to take place something must upset the genetic equilibrium of a population • Natural selection upsets genetic equilibrium and causes changes in populations

Example: Natural selection in giraffe population • Giraffe population had short necks and ate grass • Some had longer necks than others – Could eat lower of when grass was scarce – More likely to survive – Offspring would inherit favorable variation of a longer neck • Over generations, average neck length in population increases • No individual evolved to have a longer neck during its lifetime, the population slowly evolved to having a longer neck on average

Mutations occur in individuals Mutations enable natural selection to occur Natural selection is a process that affects a population Individuals do not evolve

Biology 7C Differential Reproductive Success

Differential reproductive success – phenomenon in which one group has more offspring than another • Caused by natural selection acting on variations within a population o Organisms with favorable variations have a higher chance of living and producing offspring with these variations

Biotic potential – the highest rate of reproduction possible for a population under idea conditions

Carrying capacity – the number of individuals of a given population that the environment can support • Caused by limited food, , and • Limits create , winners survive and reproduce

Example: giraffe evolution via differential reproductive rates • Giraffe population had short necks and ate grass o Variation: some had longer necks o Population: large herds o Limitation: food sources • Longer-necked giraffes had a higher reproductive rate • Over time, population evolved longer necks

Biology 7D Natural Selection, , & Diversity

Adaptation – trait that helps an organism survive and/or reproduce in its unique environment • Natural selection favors variations of traits that increase organism’s ability to survive and reproduce Natural selection can increase or decrease variation within a species Directional selection – a single variation of a trait that was not previously favored is now favored in a species, usually a result of migration or environmental changes • May increase or decrease diversity within a species Diversifying selection – multiple variations of a trait are favored in a single species • Increases diversity within a species, might lead to separate species Stabilizing selection – a single variation of a trait is favored in a species • Decreases diversity within a species

Natural selection can increase or decrease variation among species • If different traits are favored in different species, diversity increases o Different food sources for , different beaks across species • If similar traits are favored in different species, diversity decreases o Same need to retain water in plants, same leaves across species

Biology 7E Evolutionary Mechanisms

Gene pool – all of the genes in a population • Allelic frequency – the frequency of a specific allele • Evolution – change in frequencies of alleles in a population over time

Genetic drift – changes in allele frequencies because of random events • Generally affects smaller populations because of probability Effects on gene pools • Frequency of each allele changes • Rare mutations can become lost or more common

Gene flow – preserved traces of remains of living organisms from the past • Caused by migration or transfer Effects on gene pools • New allele added to gene pool

Biology 7F Evolutionary Mechanisms

Mutation – a change in the nucleotide sequence of DNA • Frame shift mutation – codon divisions are moved, changing the rest of the DNA sequence - Insertion – a nucleotide is added to the sequence - Deletion – a nucleotide is removed from the sequence • Substitution – a different nucleotide is used, only affect the codon they occur within Effects on gene pools • New allele could be added

Recombination – exchange of DNA between two chromosomes Effects on gene pools • Alleles moved, but no net change on gene pool

Biology 7F Cell Complexity

Prokaryote – “before nucleus,” simple cell lacking nucleus (bacteria) – “true nucleus,” more complex cell containing nucleus (plant)

What began first? Theory: prokaryotes appeared first • Evidence: record o First: simple, single-celled cells without internal structures (prokaryotes) o Later: cells containing internal structures (eukaryotes)

How did the first prokaryotes evolve? Theory: bubble-like cell membranes formed naturally (bubble theory) • Evidence: o Bubble-like structures that naturally form hollow spheres

How did complex eukaryotes evolve? Theory: prokaryotes evolved into eukaryotes • Evidence: bacteria structure o Bacterial inward foldings similar to nucleus and endoplasmic reticulum Theory: prokaryotes became some organelles (endosymbiosis) • Evidence: of some organelles o Endosymbiotic bacteria exist currently o Mitochondria, chloroplasts, and centrioles contain their own DNA similar in size and character to bacterial DNA

Biology 7G

Taxonomy – the of biology that classifies and names living things • Uses characteristics of organisms and a universal system – Every organism has a specific name – Organisms are assigned to levels of classification

Common name – name given to an organism by the people in an area • An organism can have many common names leading to confusion • Examples: mountain lion, puma, cougar

Carolus Linnaeus – developed a standardized taxonomic system • Two-word (binomial) naming system • Organisms with similar structures placed in same taxonomic group

Scientific name – standard binomial name accepted by all scientists • Uses and specific name to create name of species Species Genus Specific name Felis concolor

Importance of taxonomy • Needed to orderly classify vast diversity of organisms • Allows for universal understanding • Ability for similarities to be compared • Show common ancestry

Biology 8A Taxonomy

Every organism is classified at each nested level. If two organisms share a , they are in the same and , but they might be in different lower levels.








Biology 8A Classifying Organisms

Seven levels of taxonomy • Kingdom More broard • Phylum • Class More organisms • Order • Family More speciic • Genus Less organisms • Species

The more levels two organisms share, the closer they are related.

Identifying where an organisms belongs using shared characteristics 1. For each characteristic given, determine which possible groups are eliminated a. Ex: If the organism is multicellular, it cannot be in kingdom Bacteria or 2. Once all characteristics are analyzed, there should only be one possible group left

Cladogram – branching diagram showing evolutionary descent • Each split represents appearance of new trait(s) • Related organisms are closer together

Dichotomous key – tool used to identify organisms Identifying where an organisms belongs using a dichotomous key 1. Start at number one 2. For each number, choose the trait most applicable to the organism 3. End when trait chosen provides name of group or species

Biology 8B Taxonomic Groups

Group Major Characteristics Examples (Kingdom) Archaea Prokaryotes, cell wall, may live in extreme Methane-producing archaea, environments, unicellular, autotrophs or

Bacteria Prokaryotes, cell wall made of , E. coli, unicellular, autotrophs or heterotrophs

Protista Eukaryotes, unicellular or multicellular, autotrophs or Algae, paramecia, , heterotrophs, some have cell wall, many are microscopic Fungi Eukaryotes, most are multicellular, cell walls, absorbs , molds, through cell wall, sessile

Plantae Eukaryotes, most are multicellular, cell walls , , , flowering composed of , photosynthetic, autotrophs plants

Animalia Eukaryotes, multicellular, heterotrophs, most are Mammals, birds, , worms, motile

Biology 8C

Carbohydrates – and , made of C, H, and O • Monosaccharide – subunit of carbohydrates (glucose, fructose, and galactose) • Disaccharide – molecule formed by joining two monosaccharides via dehydration synthesis (maltose, , and lactose) • – long chain of repeating sugar units (, , cellulose, and ) Structure & Function • Multiple C-H bonds: release net energy when broken (starch and glycogen) • Strong structure: forms tough, structural parts in plants, , and fungi

Lipids – fats, oils, and , non-polar and hydrophobic (insoluble in water), primarily made of C, H, and O. • No universal subunit • Glycerides (fates and oils) – combination of fatty acids and glycerol o Saturated – carbon atoms have maximum number of hydrogen atoms, pack tightly, fats o Unsaturated – contain one or more carbon-carbon double bonds, back loosely, oils • Steroids – backbone has four fused carbon ring o Anabolic steroids – increase protein synthesis o – maintain cell membrane shape and fluidity, cell signals, precursors to other molecules Structure & Function • Multiple C-H bonds: release net energy when broken (fats and oils) • Not water soluble: component of cell membranes • Act as chemical messengers

Biology 9A Biomolecules

Proteins – sugars and starches, made of C, H, N, and O • Amino acids – subunit of proteins, central carbon with amino group, hydrogen, carboxylic acid, and r group (unique to amino acid). • Dipeptide – two amino acids joined via dehydration synthesis, bond • Polypeptide – multiple amino acids joined together, folds into & Function • Modular nature allows for diversity o 20 different amino acids (different R groups) o Different amino acid sequence changes protein produced • Fibrous proteins – fiber-like, structural • Globular proteins – compact and spherical, act as , antibodies, enzymes, and transport proteins

Nucleic acids – DNA and RNA, made of C, O, H, N, P • Nucleotide – subunit of nucleic acids, phosphate group, 5-carbon sugar, and nitrogenous base (A, G, C, T, or U) • DNA – stores genetic code, contains deoxyribose sugar, double- stranded (A pairs with T, G pairs with C) • RNA – carries genetic code to cytoplasm, acts as enzymes Structure & Function • Complementary bonding allows for replication o New cells inherit genetic material from parent cells • Sequence of bases stores information o DNA is the blueprint of genetic information

Biology 9A Biomolecules

Biomolecule Subunit Function Example Proteins Globular Amino acids Catalysis; Enzymes; transport Hemoglobin Fibrous Amino acids Support Collagen, elastin

Nucleic Acids DNA Nucleotides Genetic code Chromosomes

RNA Nucleotides Protein Messenger RNA synthesis Ribosomal RNA Enzymes Lipids Glycerides Glycerols and Energy storage Butter, corn oil fatty acids Steroids Carbon rings Messengers, Cell membrane fluidity Carbohydrates Starch Monosaccharaides Energy storage Potatoes in plants Glycogen Monosaccharaides Energy storage Liver product in animals Cellulose Monosaccharaides Structural Paper, support strings

Biology 9A Photosynthesis & Respiration

Photosynthesis – process by which some autotrophs capture energy from the environment

6CO2 + 6H2O + energy  C6H12O6 + 6O2

carbon water sunlight sugar oxygen dioxide (glucose)

Cellular Respiration – process by which some living things convert stored energy into usable energy and heat

C6H12O6 + 6O2  6CO2 + 6H2O + energy

sugar oxygen carbon water ATP (glucose) dioxide heat

Photosynthesis & Cellular Respiration is recycled within ecosystems (through trophic levels) Energy flows through ecosystems (in from the sun, out as heat and work)

Biology 9B Enzymes

Enzyme – protein or RNA molecule that acts as a biological catalyst – substance than an acts upon Product – substance that is created

Characteristics of Enzymes • Names usually end in suffix –ase • Bind to specific substrate(s) • Not consumed during the reaction • Enable cell reactions to proceed at biological o Lower the amount of activation energy required for reaction

Two binding theories • Lock-and-key model – substrate molecule fits closely into enzyme (just like a key in a lock) • Induced fit model – enzyme’s shape changes slightly to bind with substrate, more widely accepted

Process • Substrate molecule fits into active site on enzyme o “Enzyme-substrate complex” • Enzyme shape changes slightly to bind to substrate o “Induced fit” • Enzyme catalyzes a chemical reaction in the substrate o Involves breaking or forming chemical bonds • Products are released • Enzyme is ready to bind to another substrate

E + S  ES  E + P

Biology 9C Formation of Organic Molecules

Where did molecules originate? • Primordial seas (most widely accepted) o Reducing – many hydrogen atoms and , no oxygen • Surface of primordial clay o Result of chemical reactions on silicate surface o Clay might have acted as lattice to join monomers into polymers • vents o Synthesized from metal sulfides in vents

How did the molecules originate? • Primordial seas (most widely accepted) o Miller-Urey experiment reproduced conditions and found simple organic molecules, including amino acids o Disagreement: composition of early atmosphere • RNA world o RNA formed first, then allowed creation of proteins o – RNA molecules that catalyze their own assembly o Disagreement: RNA too unstable and complex to form spontaneously • Bubble theory o Bubble-like structures formed hollow bilayer spheres of water because of chemical properties (resemble cell membranes) o Disagreement: “” have never been created in lab o Disagreement: atmosphere could not have supported enzyme activity needed

Biology 9D Interactions Among Animal Systems

Regulation Regulation – process of maintaining vital body conditions within an acceptable range in order to preserve • Homeostasis – stable internal conditions required for body systems to function • Negative feedback – mechanism in which when a change is detected, the body reacts until the body is returned to a normal range

Regulatory examples: Body : integumentary, nervous, and muscular • Skin (integumentary) and brain (nervous) monitor temperature • If too high, brain signals skin’s sweat glands to cool body • If too low, brain signals muscles (muscular) to contract

Heart and respiration rates: circulatory, respiratory, and nervous • Receptors (nervous) monitor blood pressure and oxygen levels • If too high, heart (circulatory) or lungs (respiratory) decrease rate • If too low, heart (circulatory) or lungs (respiratory) increase rate

Blood concentrations: endocrine, nervous, excretory, integumentary, digestive, and circulatory • Brain (nervous) signals endocrine glands (endocrine) to produce hormones, which travel through blood (circulatory) • Kidneys (excretory) signaled to release more or less water as needed • Skin (integumentary) can sweat to lower water levels • Liver (digestive) releases glucose and to change sugar levels

Biology 10A Interactions Among Animal Systems

Nutrient absorption: digestive, muscular, and circulator • Mouth (muscular and digestive) chews food, sent through throat (muscular and digestive) to stomach • Food churned (muscular) and chemically digested (digestive) • Blood vessels (circulatory) absorb nutrients through microvilli in intestine (digestive)

Reproduction: reproductive, endocrine, and circulatory • Hormones (endocrine) created, travel through blood (circulatory) to stimulate and regulate organs (reproductive) • Organs (reproductive) create and/or release gametes, allow for fertilization to occur • In mammals, blood (circulatory) delivers nutrients to developing fetus

Defense against injury: integumentary, skeletal, muscular, and nervous • Skin (integumentary) and skeleton (skeletal) protect organs from environment • Receptors in skin (integumentary) detect changes and danger, spinal (nervous) send signals for muscles (muscular) to move away

Defense against illness: integumentary, respiration, digestive, circulatory, and immune • Skin (integumentary) and mucus and hairs along passageways (respiratory) act as physical barrier to • Stomach acids (digestive) kill pathogens in food • Specialized and lymphocytes (immune) travel through blood (circulatory) and attack pathogens

Biology 10A Interactions Among Plant Systems

Plants are divided into two systems: • system – above-ground (leaves, ) • Root system – below-ground ()

Each organ within these systems has three types of tissue • Dermal – barrier • Ground – metabolic functions • Vascular - transport

These tissues interact to carry out transport, reproduction, and response

Reproduction • Asexual o Shoot or root systems produce new plant • Sexual o Shoot system produces flowers o Shoot and root systems produce hormones to control process

Biology 10B Interactions Among Plant Systems

Transport • Food o Produced in of the shoot system o Transported by throughout plant • Water & minerals o Absorbed in tissues of the root system o Transported by throughout plant • Hormones o Produced in ground tissue of both systems o Transported by phloem and xylem

Response • Hormones produces and transported in both systems allow plants to respond to and gravity o Shoot system grows toward light () o Shoot system grows away from gravity (negative ) o Root system grows toward gravity (positive gravitropism)

Biology 10B Levels of Organization

Ecologists use nested levels of organization to make interactions clear

Level Definition Example Atom smallest representative unit of an hydrogen atom element Molecule two or more atoms bonded together DNA molecule

Cell smallest unit capable of life epithelial cell made of multiple molecules Tissue similar cells working together epithelial layer

Organ different tissues working together stomach

Organ System different organs working together digestive system

Organism an individual life form flamingo composed of at least one cell Population multiple organisms of one species flock of living in one area flamingos Community different populations living in one flamingos, reeds, area and spoonbills all of the populations in one area and a Florida their environment similar ecosystems found on

Biosphere all of the ecosystems on Earth majority of Earth

Biology 10C Levels of Organization

These levels of organization are nested within each other. Each level contains the matter below it.







Organ system






Biology 10C Homeostasis

Homeostasis – maintaining a stable, internal environment • Involves body systems working together, monitoring levels of variables, and correcting changes

Negative feedback mechanism – control system that monitors and corrects changes to maintain homeostasis • Regulation occurs in reverse direction as perturbing factor • Returns body to homeostasis • Ex: when body warms up, systems work to cool body down

Positive feedback mechanism – control system used by body to push a change further in the same direction • Regulation occurs in same direction as perturbing factor • Causes body to leave homeostasis • Ex: pressure during childbirth stimulate contractions, creating more pressure, creating more contractions

Biology 11A Response to External Factors

These three levels respond to external factors • Organism – an individual life form • Population – all the individuals of a given species in a particular area • Community – all the different populations of organisms in an area

Populations are limited in size • Biotic potential – the highest rate of reproduction possible for a population under ideal conditions • Carrying capacity – number of individuals of a given population that the environment can support • Limiting factors - factors or conditions which affect the growth rate and size of populations and communities

Density-independent factors – environmental conditions that affect a population regardless of its density • Ex: Natural disasters o Organism: injured or killed o Population: size decreases from individuals killed o Community: affected as populations shrink Density-dependent factors – factors that affect population growth as a result of density • Ex: o Organism: killed (prey) or fed (predator) o Population: rises or falls depending on other population o Community: when there are too many predators, prey population shrinks causing predator population to shrink

Human growth occurs at an exponential rate because of medical advancements, agricultural technology, and improved sanitation

Biology 11B

Microorganisms – living things that cannot be seen with the naked eye • Generally single-celled but can form cell clusters • All prokaryotes (bacteria) and some eukaryotes (fungi and protists)

Maintain Health of Organisms • Help digestion by breaking down compounds • Used in for vaccines, , genetic engineering

Maintain Health of Ecosystems • Recycle carbon for plants to use • Recycle for plants to use • Create sugars in marine ecosystems

Disrupt Health of Organisms • Cause disease like malaria and ringworm

Disrupt Health of Ecosystems • When numerous, become concentrated

Images by USGOV [Public ] Biology 11C Ecological Succession

Succession – orderly change in makeup of a community over time • Primary succession – occurs in a newly formed area • Secondary succession – occurs in an area that has been disturbed • Pioneer community – first inhabitants in a new community, changing o Harsh environment, increasing, energy consumption and cycling inefficient, low species diversity • – established community, little change o Favorable environment, biomass stable, energy consumption and nutrient cycling efficient, high species diversity

Species, populations, and communities change over time • Unfavorable environment  Favorable environment • Few food sources  Many food sources • Few species  Many species  Diverse populations • Pioneer community  Climax community

Example: a new pond is formed (primary succession) 1. No organisms 2. Algae and bacteria invade 3. Heterotrophic protists and small invertebrates arrive 4. Floating plants (pondweed) grow 5. Larger plants (cattails) grow around edges 6. Larger animals arrive 7. Might become marsh and fill in 8. and trees can grow

Biology 11D Biology 12A - Ecological Relationships

Ecological Relationships

Predatation - one organism hunts and kills another for nutrition

Commensalism - one organism benefits and the other is not affected

Parasitism - one organism benefits and the other is harmed

Mutualism - both organisms benefit

Competition - both organisms are harmed

You can use the four steps below to determine the relationship

Clues for determining faces

benefits not affected harmed killed nutrition unaffected not fatal dies eats not hurt loses prey gains not helped host fatal Biology 12A

Variation – a difference that exists among individuals of a group of organisms

Adaptation – any variation in an organism that makes it better suited to its environment, usually fulfills a survival requirement

Animal Survival Requirements Plant Survival Requirements Habitat Food and water Water and nutrients Protection from predators Sunlight Protection from consumers

Different ecosystems require different adaptations Examples: • : cold, soil frozen o Plants: short to avoid o Animals: migrate to avoid coldest periods • Desert: very little water, can be very hot o Plants: long roots to find water o Animals: large ears to radiate heat • Marine coasts: dry out during day, harsh waves o Plants on coast: holdfasts to stay on rocks o Animals on coast: close tightly to hold in water • Marine deep: no light o Animals: glow to attract prey

When comparing adaptations of organisms: • Consider the challenges in their environment • How do they combat these challenges? o These may be adaptations

Biology 12B Energy Flow Through Trophic Levels

General Trophic Levels Term Level Definition Type Example Producer 1 Organism which produces Grass its own food

Primary 2 Organism which primarily , Grasshopper consumer eats producer(s)

Secondary 3 Organism which primarily Heterotroph, Lizard consumer eats primary consumer(s) or Tertiary 4 Organism which primarily Heterotroph, Snake Consumer eats secondary consumer(s) carnivore or omnivore Decomposer N/A Organism which breaks Heterotroph Fungi down dead matter and returns nutrients to soil

Matter cycles through ecosystems (returned by decomposers) Energy flows through ecosystems (enters from sun, lost as heat) • Food chain – sequence of organisms feeding on a lower – network of interacting food chains in an ecosystem

Ecological pyramids visualize food chains • Pyramid of energy – amount of energy in organisms o Organisms use 90% of energy obtained for o Only 10% of energy obtained is passed onto next level • Pyramid of numbers – number of organisms • Pyramid of biomass – total mass of dry, • In all pyramids, amounts typically decrease as trophic levels increase because of energy loss

Biology 12C Limiting

Environmental factors – components of the environment that affect a species survival • Biotic factors – living components of an environment o Example: food • Abiotic factors – non-living components of an environment o Example: water • Density-dependent factors – effects vary based on density o Example: disease travels better in a dense population • Density-independent factors – affects all populations equally o Example: drought hurts all populations

Limiting resources – environmental factors that are needed by a species, but exist in limited quantities • Create competition • Food (biotic), affected by changes in prey population, seasonal cycles, natural disasters, and human activity • Water (abiotic), affected by seasonal weather cycles, natural disasters, and human activities • Space (abiotic), affected by natural disasters and human activities

Biology 12D Matter Cycles

Carbon – key element in organic matter, in all biomolecules Carbon cycle – means by which carbon is cycled between the environment (carbon dioxide) and living tissues (biomolecules)

Disruptions to the cycle • Burning of fossil fuels – release excess carbon dioxide • Deforestation – release excess carbon dioxide, decrease in photosynthesis • Additional and animals – release excess carbon dioxide

Biology 12E Matter Cycles

Nitrogen – essential element for life, in all proteins – means by which nitrogen gas converted to usable form then cycled through ecosystem

Disruptions to the cycle • Burning of fossil fuels – release excess nitrogen into atmosphere • Excessive and – washes away nitrogen from soil • Fertilizing – excess nitrogen, algal blooms • Ranching – waste releases excess nitrogen, poor and plant growth

Biology 12E Environmental Change

Ecosystem – physically distinct, self-supporting unit of interacting organisms and their surrounding environment

Conditions for stable ecosystem • Source of energy • Producers using energy sources to synthesize organic compounds • Materials cycling between organisms and environment

When analyzing how an event will change an ecosystem, keep these questions in mind 1. Are producers affected? 2. Did nutrient/ levels change? 3. Are any organisms directly hurt/killed? 4. Did habitat loss occur?

Example: Oil Spill 1. Are producers affected? Yes, toxic oil can kill producers. 2. Did nutrient/mineral levels change? No, they are not affected. 3. Are any organisms directly hurt/killed? Yes, oil is toxic to all life. 4. Did habitat loss occur? Yes, areas of and shore contaminated with toxic oil.

Biology 12F