Semester 1 Honors Biology Study Guide Chapters 1-8

Chapter 1
Important concepts: Levels of organization (ecosystem, community, population, etc.) Molecule DNA (deoxyribonucleic acid) Cell Tissue Organ Organ system Organism Population Community Ecosystem

Scientific Method Hypothesis - a tentative answer to a question AKA. educated guess Independent vs. Dependent variable - Independent Variables are the thing that scientists physically change. Usually only one thing. Dependent variables rely on the independent variable and therefore their actions are influenced by it. Controlled variables: Variables that the scientist keeps constant throughout the experiment Control group: the group where you dont apply the independent variable Standardized variables: Variables where the amount, time, type, ect are standardized throughout the entire experiment Sample size: The amount of the person/place/thing that is being tested. The more the better. Can you design an experiment? Hope so. Domains and the differences between them 3 main domains of life: Bacteria, Archaea, Eukarya. Bacteria and Archaea dont have their own nuclei, they are PROKARYOTES Eukarya are organisms with organelles and a nucleus; they are EUKARYOTES Properties common to all life Growth Reproduction Metabolism (All of chemical reactions that take place in organism) Evolution (Changes in population over generations in response to environment) Ability to respond to stimuli Regulation-the maintaining of homeostasis (Constant internal environment, pH, Basic unit is cells (whether multi-cellular or not), and DNA.

Darwins theory of natural selection: explains how evolution works. Animals adapt to the trait that allows them to survive. Example: overtime, beetles that are a dark color outlive yellow beetles, because the color allows them to blend in with their surroundings. The trait, like the color of the beetle, is inherited by the new beetles. This is the adaptation.

Chapter 2
Important concepts: Atoms 96% of humans are made of what elements? CHON: Carbon 6, Oxygen 8, and Nitrogen 7 What are the patterns in the organization of the periodic traits? (columns vs. rows) Row of elements is called a period. THESE ALL HAVE THE SAME NUMBER OF ELECTRON SHELLS A column of elements is called a group. THESE ALL HAVE THE SAME NUMBER OF VALENCE ELECTRONS. THEREFORE THEY HAVE SIMILAR CHEMICAL PROPERTIES. Trace elements Trace elements are necessary for life in certain organisms. (in very small quantities.) They make up the remaining 4%. (example, iodine in the body is necessary for the thyroid gland to function properly. w/out iodine, a goiter forms)

What is in an atom? In the nucleus? The structure of an atom: PROTONS* NEUTRONS* ELECTRONS *= in the nucleus Protons vs. electrons vs. neutrons
Protons determine the element; they have a positive charge. Electrons have a negative charge and the elements chemical properties (reactivity/behavior) are defined by them. Neutrons determine the mass, and if an atom has too many neutrons, it becomes an isotope.

Atomic # vs. Mass # Atomic #-Number of protons Mass #- Number of protons and neutrons combined. Electron shells
ELECTRON SHELL: levels of electrons. The first shell can hold up to two electrons, the second one up to eight. What elements want is to be inert, or have a balanced shell. The reactivity of a atom increases when it is closer to having a full electron shell. The last shell is also full at 8.

Isotopes
ISOTOPES: variations of a particular element. These variations are due to different numbers of neutrons.

Compounds
A compound has two or more elements. Compounds are more common than pure elements. They have different properties from their singular elemental components

Covalent vs. ionic bonds Ionic bonds: when two highly reactive atoms cross, one will strip the other of its electron. The atom who lost the electron will have a positive charge, and the atom who took the electron will have a negative charge. Each atom becomes an ion because of the charge. Negative=anion, positive=cation. After becoming ions, the two atoms are attracted by the others opposite charge. Therefore, they bond together in an ionic bond. Covalent bonds: when two atoms share electrons. Basically, in a covalent bond, two highly reactive atoms share electrons. They each have electronegativity, the attraction towards the electron. The

more electronegative an atom is, the stronger the pull on the electron.

There are two types of covalent bonds. Polar, when the electron is shared unequally, meaning that one atom has higher electronegativity; and non-polar, where the electrons are shared equally. A polar covalent bond is when one of the atoms has a stronger electronegativity, so the electrons are actually closer to this atoms nucleus. This makes one of the atoms partially negative (the one with the electrons closer to its nucleus) and the other partially positive. An excellent example of such a molecule is water.

Polarity of Water Polar covalent bonds: Oxygen is one of the most aggressive elements, with some of
the highest electronegativity. It pulls the two shared electrons from hydrogen and towards its nucleus; creating polarity. Keep in mind the because the hydrogens share electrons with the oxygen, it is a covalent bond. Hence the name: polar covalent bond. The polarity of water leads to hydrogen bonds: when water is formed, it has a partial negative (oxygen) and partial positive (the hydrogens) charge. Water molecules are attracted to each other because of these charges: the hydrogen to the oxygen, and vice versa. They form a bond, called a hydrogen bond. These hydrogen bonds are weak, but very consistent. They are easily broken because of how fast water molecules move, but form as easily.

Properties of Water & their importance for life

1. cohesion/adhesion

Cohesion: water molecules are attracted to each other because of the partial charges due to the polar covalent bonding. Adhesion: water is attracted to other molecules that have a partial/whole charge. capillary action: in order for plants to transport water from the roots up, plants use adhesion, waters attraction to charge, to push the water molecules up. transpiration: the movement of water through plants using processes like adhesion, cohesion, and evaporation. 2. high specific heat surface tension: the amount of force necessary to break the surface of a liquid, measured in lbs/ square inch. because of the high attraction between water molecules in hydrogen bonds, water has a high surface tension. Now, specific heat is the amount of energy required to change the temperature of 1 gram of a liquid by 1C. (both ways, as in up or down.) Temperature is the average of kinetic energy of a given object. Because water has a high specific heat, it maintains global temperature at a moderate degree. 3. less dense as a solid than a liquid water is the only substance on earth that can be found as a solid, liquid, and gas. this is once more because of hydrogen bonds. when you drop a solid into water, it generally sinks. with ice, it floats. this is because ice is less dense than water. why? when you lower the temperature of water (by freezing), you slow down and eventually stop the hydrogen bonds from forming and the bond remains broken. (at 4C) 4. versatile solvent: It is a versatile solvent because of the polarity of its molecules. Side note: Water easily breaks ionic bonds, therefore covalent bonds do the best in biological systems. Also, when water is the solvent in a solution, the solution is called an aqueous solution.

Acids vs. bases In aqueous solutions within organisms, sometimes the water molecules break apart into ions The ions formed are called hydrogen ions (H+) and hydroxide (OH-) ions. Example: hydrochloric acid in your stomach. HCI breaks apart into H+ and CIions. A chemical compound that donates H+ ions to solutions is called an ACID. A chemical compound that donates OH- ions to solutions is called a BASE We determine the acidity of a solution by the pH scale. pH stands for potential hydrogen. 1-6 is acid; 7 is neutral; and 8-14 is base Biological fluids contain BUFFERS, substances that resist changes in pH by accepting H+ ions and donating OH- to keep the pH at around 7 (neutral)

Chapter 3
Important concepts: What attributes make carbon a good building block for organic molecules? Single, Double, Triple Bonds Abundant No upper limit on size Macromolecules What are they? Big molecules that do all the major jobs in our bodies. Lipids -fats, cholesterols Carbohydrates -fiber, sugars Proteins Nucleic acids How can we distinguish them from one another? LIPIDS -Not just one unit that repeats -All hydrophobic -Non-polar b/c of C-H electrons shared equally -CHO (Phospholipid) -Not really a polymer. NUCLEIC ACIDS NUCLEOTIDES -Polymer -Phosphate group -Makes up DNA and RNA -Sugar -Sugar and phosphate are covalently bonded through -Nitrogenous base dehydration synthesis, while the nitrogenous base hangs off -Made up of multiple nucleotides bonded - Nucleotide chains has to be flipped to form double stranded helix -Sugar and phosphate covalently bonded through dehydration synthesis, while nitrogenous bases hang off. -In DNA, coding for protein structure CARBOHYDRATE SUGAR -Polysaccharide -Monosaccharide -Polymer -Monomer (Starch) (Glucose)

Bonds up to 4 times

-CHO

PROTEIN AMINO ACIDS -Polymer -Monomer -CHON (Collagen) The "R" group in amin is the only thing different from each structure. -Varies between 20 diff. amino acids Links between amino acids are called Peptide bonds. Hemoglobin-Protein in blood. ----------------------------------------------------------------------------------------------------------------------------------------------

How are their functions in the body different? Lipids are used in cell membrane structure (Phospholipid bilayer), energy storage Carbohydrates are bonded together to form: -starch = how a plant stores energy long-term - cellulose = creates plant structure Proteins are used to provide structure, transport in and out of cell, communication (hormones) and enzymes (a type of protein) are used to catalyze chemical reactions. Nucleic Acids: make up DNA and RNA and code for protein structure in cells Examples of each? Monomers vs. polymers for each Lipids are lipids, they dont have specific monomers/polymers Carbohydrates = monosaccaride (monomer) and starch (polymer) Protein = proteins are the polymers, amino acids are the monomers Nucleic Acids = the acids are the polymers, nucleotides are the monomers Dehydration synthesis and hydrolysis Dehydration Synthesis: How you link monomers to form a polymer. Removes water molecules from both monomers to form one polymer. Requires energy and a enzyme. Hydrolysis: Using water to break the bonds formed by dehydration synthesis. Releases energy. Hydrophilic vs. hydrophobic Hydrophillic- substances that are easily dissolved in water. This is because they are polar Hydrophobic- substances that do not mix or dissolve in water. Lipids are an example.

USEFUL VOCAB TO KNOW: Organic- Carbon containing molecules, products of cells. Isomer- Same molecular formula, different structure. Monomer- single unit that repeats to form a polymer. Polymer- formed by repeating units bonded together

Chapter 4 Important concepts: Parts of a microscope Ocular (eyepiece) Body tube Fine adjustment knob Nosepiece High/low power objective Diaphragm (iris) Mirror (light) Base Coarse adjustment Arm Stage clip Inclination joint Differences between prokaryotic and eukaryotic cells Prokaryotic: no organelles that have own membrane. Not multi-cellular. Earliest cells. All bacteria are prokaryotic. Has free ribosomes, no mitochondria. Eukaryotic: Plants, animals, fungi, protists. Partitioned into organelles. Efficient, make more, specific tools/ environment for job in organelle, diff. enzymes for each job. Main structures in a Prokaryotic cell Plasmids-few genes low of DNA, transfers good genes through sex pili. Sex pili: allow bacteria to stick to one another and exchange plasmids. Flagella: whiplike tail for movement. also have in prokaryotic. Pili: used for sticking to surfaces. Capsule: extra layer, but only some prokaryotic cells.

Why is there an upper and lower limit on cell size? Upper limit: Cell sizes increase=volume increases much faster than surface area. Therefore, cell cannot import/ export fast enough to meet needs of cell. Lower limit: Cells must have-chromosomes, cell membrane, cytoplasm, ribosomes, so cells must be big enough to house above structures and ingredients to make stuff. Differences between animal and plant cells Plant cells have chloroplasts. Chloroplasts produces sugar for the cell through photosynthesis, the conversion of light energy to the chemical energy of sugar. Animal cells do not have central vacuoles, while plant cells do. The function of a central vacuole is to digest in a cell, like a lysosome, store food units, and store water. Plant cells also have cell walls for structure and protection, which animal cells don't have because they are fairly rigid, and animal cells need to be flexible. Eukaryotic cell structure Know what the following structures are, what their function is in a cell, and know locations: Nucleus, Nucleolus, Ribosomes, Cytoplasm, ER (smooth & rough), Golgi, Vacuoles, Lysosomes, Mitochondria, Chloroplasts Nucleus: has nuclear membrane (nuclear envelope). Has pores to allow import/export of materials. Function: protective container for

chromosomes (DNA, proteins) inside. Nucleolus: Inside Nucleus. Function: Construct ribosomes. Ribosomes: Made of protein and rRNa. No membrane. Two types: FREE (in cytoplasm, makes proteins for use internally in cell) BOUND (In Rough ER membrane, make secretory protein for use outside of cell. Rough ER: Continous with nuclear envelope, rough because studded with ribsomes. Cells can have multiple Rough ERs. Functions: Works with ribosomes to make secretory protein outside of cell. Makes more membrane (replace defective membrane) then used to make more organelles. Smooth ER: No studded ribosomes. Functions: Breaks down toxin. Makes carbs, lipids. Golgi: Take proteins produced in Rough ER and tags them chemically for shipping so proteins go where supposed to go. Not interconnected liek Rough ER. Just for secretory proteins. Lysosome: Membrane surrounding an organelle that contains hydrolytic enzymes. Stomach of cell Cytoplasm: Gel like substance that holds organelles in place in cell. Vacuole: 3 types: FOOD VACUOLE, carries food to lysosomes. Most plants do NOT have. CENTRAL VACUOLE, digestion, store food unit and water. Plants only. CONTRACTILE VACUOLE, collects water and forces it out of cell by flexing, ejects excess water from cell so doesnt explode. Mitochondria: makes energy for cell in form of ATP. All eukaryotes have. Unusual for organelle=has 2 separate membranes, has own DNA, divide by itself to reproduce. Chloroplast: produce sugar for organism through photosynthesis in plants. Own DNA, 2 membranes, divide by itself.

What is the path of a secretory protein through the endomembrane system? Secretory protein is made on the rough endoplasmic reticulum by ribosomes studded on the rough ER. Then is taken by a transport vesicle, which is absorbed into the Golgi when the vesicle arrives. They are chemically tagged for shipping outside of a cell; the Golgi marks what the secretory protein is and where it goes. Transport vesicles also take the secretory proteins from the Golgi to the cell membrane and is absorbed in the cell membrane and then releases the product outside.

Chapter 5 Important concepts: Kinetic vs. potential vs. chemical energy Kinetic Energy: Energy of Motion Potential Energy: Based on either location or molecular arrangement Chemical Energy: Type of potential energy in organic molecules Heat and temperature Heat: total energy of molecular motion in a substance Temperature: measure of the average energy of molecular motion in a substance The first two laws of thermodynamics First: Energy cannot be created or destroyed; only transferred or transformed. Second: Chemical reactions increase entropy (entropy=measure of disorder/ randomness) Metabolism All physical and chemical reactions in the body that convert or use energy. Energy coupling, endergonic, & exergonic reactions Energy coupling: When cells harness the energy used in an endergonic reaction and use it to fuel and power an endergonic reaction. Occurs when cells use chemical energy to perform work. Phosphorylation When ATPs bond between the 2 and 3 phosphate breaks through hydrolysis, the third phosphate is transferred to molecule that needs the bond and ATP is turned to ADP. What are enzymes and what do they do? Proteins that catalyze chemical reactions by reducing activation energy. Very, very specific. Reduces activation energy because enzymes are reusable so make enzyme and cut down on energy for long time. 3D model that clamps on and contorts both objects so they are more likely to bond. Know and be able to identify: Substrate, enzyme, active site, reactants, products Structure of the plasma membrane Phospholipids/cholesterol/proteins Phospholipids are made of phosphate group that is hydrophilic and polar and carbon/hydrogen tails that are hydrophobic and non-polar. The tails face inward in water, and phosphates face outward. Proteins on plasma membrane are specialized in shape and charge to act as a tunnel for individual solutes to get through the cell membrane. Allows polar/larger solutes through. Moves solute against concentration gradient. Cholesterol located between phospholipids. Keeps shape of phospholipid from changing when temp. changes. When warm, phospholipid spreads out and when cool, are tight against each other and kinked. Bad because then when warm, bad things let in, when cool, good things cant get in. What is selective permeability and how does this work in a cell? What does/does not pass easily? Selective permeability is when only certain things can get in a cell. This works because of the structure of the plasma membrane. The phospholipids allow non polar and small solutes through but not otherwise. Only non-polar small solutes can pass through easily. Transport proteins can pass polar, large solutes individually by creating a specialzed tunnel. Also can help move solutes against concentration gradient by pumping the solute against its concentration gradient.

Passive transport vs. active transport vs. Facilitated diffusion vs. endo- & exocytosis Passive transport: diffusion of substance across biological membrane. Substances do not require energy for diffusion because random movement of particles so called passive. Active transport: cell expends energy to move molecules across against concentration gradient. ATP is need after solute is inside transport protein and needs to be expelled out. Proteins cause conformational change so protein opens up other way and makes charge of protein positive. Solute not attracted to protein anymore, goes out of protein. Facilitated diffusion: transport proteins embedded in membrane allow specific polar, larger solute to protein to move in and out of cell. Does not use energy. Type of passive transport. Allows solutes to diffuse across membrane until dynamic equilibrium. Endocytosis: plasma membrane engulfs solutes that are too large to fit through protein channel and form a vesicle around it to bring into cell and take to the lysosome. Use energy. Type of active transport. Exocytosis: expels materials, especially waste from cell using vesicle to take to cell membrane to expel. Use energy. Type of active transport. Diffusion and osmosis Diffusion: net movement of solutes (moves from high (hypertonic) to low (hypotonic) Osmosis: net movement of water (moves from low to high because there are more free H20 molecules are attracted to other solutes on the hypotonic side, while bound H20 molecules on the hypertonic side are not attracted to other solutes so are unlikely to move.)

Chapters 6 & 7 Important concepts: ATP: Structure & why it is so important The structure of ATP has a very high chemical configuration. ATP=Adenosine triphosphate. Structurally, it is very similar to nucleotides, but it has two extra phosphate. There is a very strong negative charge in between the phosphates, which is why it requires lots of energy to bond them together. This is also why the ATP releases so much energy when it is broken. What is reduction and oxidation? Redox reactions: Reduction: Gains electrons Oxidation: Loses electrons Redox reactions occur simultaneously. Cellular Respiration & Photosynthesis Know the formulas for each chemical reaction Cellular Respiration: 6O2 + C6H12O6 ---> 6H20 + 6CO2 + ATP
Photosynthesis: Sunlight + 6CO2 + 6H2O --> 6O2 + C6H12O6

Major steps: Light-dependent reactions; Calvin Cycle; Glycolysis; Intermediate step; Krebs; ETC & Chemiosmosis: Know what goes into each major step, what comes out, where it happens, and what the purpose is.

Glycolysis Reactants Glucose, 2

Krebs Acetyl Coa,

ETC NADH,

Calvin CO2, ATP,

P. System II H20,

P. System I Light, e-,

ATP, NAD+ Products Pyruvate, 2 ATP, 2 NADH, H+, H20 Cytoplasm

NAD+, ADP, P, FAD, H20 CO2, ATP, FADH2, NADH, H+ Matrix

FADH2, H+ H20, ATP, NAD+, FAD Cristae

NADPH Glucose (G3P), NADP+, H+, ADP, P Stroma

Light, ADP, P H+, O2, ATP

NADP+, H+ NADPH

Location

Thylakoid

Thylakoid

Glycolysis Purpose: to produce two pyruvates, pop off hydrogens for use in ETC, and produce electron carriers for ETC, 4 ATP (2 net gain), and 2 H+ for Chemiosmosis. Int Step Purpose: produce Acetyl CoA for Krebs Cycle and electron carriers and H+ for ETC. Krebs Cycle Purpose: Produce electron carriers and ATP. ETC Purpose: produce ATP. Calvin Cycle Purpose: Make glucose Photosystem II Purpose: Break H20 to get the H+ to make ATP for the Calvin Cycle and get the electrons to Photosystem I. Photosystem I Purpose: Re-excite the electrons and using NADP+ reductase to take in NADP+ and two excited electrons to make NADPH + H+ to be used in Calvin Cycle. What major steps occur in what types of cells? (prokaryotic vs. eukaryotic, animal vs. plant) Glycolysis occurs in both prokaryotic and eukaryotic cells, and in both animal and plant, because it takes place in the cytoplasm, which is shared by all four. The intermediate step takes place in the inter-membrane space of the mitochondria, and this organelle is in eukaryotic cells (plants and animals have this organelle), and this process is shared by all eukaryotes, not prokaryotes. ETC and chemiosmosis occur in both plant and animal cells. Krebs cycle occurs in the mitochondrion matrix, and again in all eukaryotes, not prokaryotes. Photosynthesis (Photosystems I & II, Calvin Cycle) occurs plant cells.

Can you compare/contrast these 2 processes? ATP formation: both use ATP synthase. H+ go through ATP synthase and create lots of potential energy, forcing ADP+P to bond as ATP in both cellular respiration and photosynthesis. Difference: origin of the H+ is different. In photosynthesis, hydrogen protons are gathered by breaking H2O in P680. In cellular respiration, NADH+ H+, with hydrogen protons already in the protein complex of electron carriers, transfers electrons to the protein complex, forcing the protons out. The electrons are transferred to next protein complex that force H+ out also. Only after that does the hydrogen protons go through the ATP synthase to make ATP. PURPOSE: Cellular respiration is an aerobic process, meaning that it requires oxygen (during ETC/chemiosmosis), and in photosynthesis, oxygen is released

(during photosystems). Also, CO2 is a waste product of cellular respiration, but in photosynthesis, CO2 is necessary in the Calvin Cycle. The products and reactants of both processes are different, in fact, practically opposites. How Photosynthesis relates to the ozone layer and global warming

Global Warming Plants absorb CO2 ; CO2 is a greenhouse gas Greenhouse gas- traps heat from sun in the atmosphere Plants get cut down less CO2 absorbed global warming Plants get cut down less CO2 absorbed global warming Ozone Loss Plants give off O2 O2 is changed into O3 in the Ozone layer, high in the atmosphere Ozone layer blocks harmful UV rays from sun Plants cut down less O2 produced less O3 produced Ozone loss UVs get through

Chapter 8 Cell Cycle

Important concepts: Interphase What happens in G1, S, and G2 G1: Normal life of cell-> growing metabolism. Close to the end comes decision time. Divide or not? If divide, does not do regular job and move on to S. If not divide, goes to G0, where it continues reg. job but stop growing. S: Synthesis chromatin duplicates, chromatin duplicate but still attached at center. G2: Enzymes, organelles made for new cells. Cell is preparing to divide. Mitosis Know what happens in each stage Prophase: Chromatin condense into chromosome. Centrioles migrate to opposite poles. Mitotic spindles forms, nuclear envelope dissolve. Mitotic spindles attracted to kinetochore proteins on sister chromatids and bring chromatids towards the equator. Metaphase: Centrioles at opposite poles, chromatids lined up at equator. Kinetochore microtubules connected, non-kinetochore microtubules elongate cell. Anaphase: Enzymes take away amino acids, making kinetochore microtubules shorter and retract, exerting pressure and pull away chromatin from copy. Telephase: Nuclear envelope reforms, cleavage furrow forms in animal cells, and microtubules break down. Cytokinesis (diff. in plant vs. animal cells) Cytokinesis: Animal cell: Pinches in until touching, then it separates. Plant cell: Little vacuoles contain cellulose and are shipped to the middle of the cell where the form themselves into straight line. Membrane between bubbles of cellulose fuse together and make a new cell right on top of one anther. Structures and their functions: chromosomes, chromatin, sister chromatids, centromere, centrioles, centrosomes, kinetochore vs. non-kinetochore microtubules Chromosomes: Double-stranded DNA made up of many nucleotides (carries lots of

genes) wrapped around proteins called histones.

Meiosis Haploid vs. diploid Diploid:Two copies of every chromosome. Start of Meiosis I. Haploid: One copy of every chromosome. End of Meiosis I and II. Homologous chromosomes One homologue is actually two sister chromatids joined together and is relative another homologue. Two sister chromatids are considered one chromosome in Meiosis I. Know what happens in each stage Prophase: Centrosomes move to poles, nuclear envelopes dissolve, mitotic spindle forms, chromatin condense chromosomes. Synapsis-homologues (Pairs of sister chromatids) pair up and form tetrads. Crossing over happens, where non-sister chromatids exchange genes within each tetrad=genetic diversity. Mitotic spindle takes the tetrads towards the center. Metaphase: Tetrads are lined up at equator. Anaphase: Tetrads separated by kinetochore microtubules. Sister chromatids still connected, no longer homologous. Telephase: Nuclear envelope reform, cleavage forms in animal cells, and microtubules. Cytokenisis: Cells break apart, and cell plate forms in plant. Then cells go into Meiosis II, which is the same as mitosis. How meiosis allows for genetic recombination Independent assortment, Crossing over, Random mating SEE SEPARATE STUDY GUIDE Can you compare and contrast Meiosis & Mitosis? What are the end products of each? SEE SEPARATE STUDY GUIDE

How do bacterial cells divide? Binary fission: Chromosome duplicate. Each chromosome attaches to plasma membrane at opposite sides. Cell splits in two. Chromosomes detach from plasma membrane and recoil up. What are examples of how cell division is controlled? Anchorage dependence: Most cells will not divide unless anchored to substrate. Density dependence: at certain density, cells stop dividing.