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Marketplace > University of Florida > Biology > BSC2010 > BSC 2010 EXAM ONE REVIEW
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This contains many Class notes and multiple different practice questions for the exam.
Integrated Principles of Biology 1
Gillooly,James FMiyamoto,Michael MasaoOppenheimer,David G
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This 33 page Study Guide was uploaded by Valerie Notetaker on Sunday February 7, 2016. The Study Guide belongs to BSC2010 at University of Florida taught by Gillooly,James FMiyamoto,Michael MasaoOppenheimer,David G in Fall 2015. Since its upload, it has received 261 views. For similar materials see Integrated Principles of Biology 1 in Biology at University of Florida.


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Date Created: 02/07/16
BSC 2010 EXAM ONE REVIEW. THIS IS GOING TO CONTAIN MULTIPLE REVIEW QUESTIONS AND MOST OF THE NOTES FROM THE CHAPTERS. Item: Summative Quiz for Chapter 1 Score: 20/20  (Calculated)  scaled to  10/10 100% 100% Due: Tuesday, February 09, 2016 5:00 PM Submitted: Sunday, January 17, 2016 5:29 PM Answers: 1.  Viruses can mutate. can extract energy from their environment.   have a cell membrane. can reproduce on their own. are made of cells. 2.  Earth is approximately _______ years old. 1,000–2,000 4,000–5,000   4–5 million 1–2 billion 4–5 billion 3.  An organism always contains more than one cell. does not contain genetic information.   cannot do biological work. can be generated from nonliving materials today. is either a prokaryote or a eukaryote. 4.  A cell always contains a nucleus. is found only in plants and animals.   is the fundamental unit of life. is never an entire organism. is always prokaryotic. 5.  Oceans were a good environment for early organisms because they contained ozone. shielded organisms from visible light.   obviated the need for a cell membrane. shielded organisms from ultraviolet light. were rich in oxygen. 6. Oxygen gas (O) in Earth's early atmosphere 2 allowed for the evolution of anoxic metabolism. depleted ozone in the atmosphere.   allowed more ultraviolet light reach Earth, thereby damaging organisms. allowed organisms to move from the sea to land. was not toxic to most prokaryotes. 7. The organisms that produced oxygen gas in Earth's early atmosphere paved the  way for _______ metabolism, which is used by larger organisms. anaerobic photosynthetic   aerobic endosymbiotic heterotrophic 8.  Photosynthesis indirectly permitted the evolution of bacterial cells. lipid synthesis.   ATP synthesis. cellular respiration. land plants. 9. In terms of increasing complexity, the order of parts of a multicellular organism  is cells, macromolecules, tissues, organs, organ systems. molecules, cells, tissues, organs, organ systems.   tissues, cells, macromolecules, organ systems, organs. molecules, tissues, cells, organs, organ systems. tissues, molecules, cells, organs, organ systems. 10. A community differs from a population in that a community consists of different populations of the same species. includes the abiotic environment.   consists of populations of different species. is synonymous with an ecosystem. is a group of populations of the same species that interact with one another. 11.  Earth's landscape and all of its life is known as a biome. the biosphere.   the ecosphere. the bioscape. the ecoscape. 12.  Genomes are the shared genetic information among all living cells. usually made of RNA.   made of proteins. the sum of genetic information in a cell. only found in animal and plant cells. 13.  All cells in a multicellular organism contain the same genome. have the same function.   express the same parts of the genome at the same time. form the same set of proteins. randomly express parts of the genome. 14.  Which item matters least for natural selection? Organisms must display variation. A trait must be able to be passed on to future generations.   A trait must increase survival. A trait must increase reproduction. A trait must directly affect metabolism. 15. Plants show remarkable diversity, even though they were derived from a  common ancestor. Which factor contributed to this diversity? Genetic uniformity Artificial selection   Sexual selection Lack of mitochondria Large cell size 16.  In the scientific method, a hypothesis is a final answer to a question. is formulated by deductive logic.   does not have to be testable. is the basis for making predictions. is formulated solely by speculation. 17. Scientists observed that frogs with toe pads live in trees, not in water. They  stated “toe pads are important for life in trees.” This statement is an example of a(n) hypothesis. prediction.   theory. law. experiment. 18.  The advantage of controlled experiments is that the hypothesis is proven right. all variables are held constant except for one.   the results are predictable. experiments are conducted in the field, not in a lab. a minimal amount of data are required. 19. Which statement represents a scientific point of view?   Earth was created by divine forces. The positions of the sun, moon, and stars provide guidance for making  decisions. Inner strength comes from beauty in nature. Meditation helps to solve problems. Comparing the genomes of organisms allows us to create phylogenetic  trees. 20.  Scientific explanations for a natural phenomenon cannot be tested. may be based on data that cannot be reproduced.   do not refer to religious or spiritual explanations. cannot be rejected. are a reflection of how things ought to be. BSC2010 NOTES 1/6/2016 Class one: introduction Class broken up into three sections: - Cells - Genetics - Evolution Instructor - Dr. Sixue Chen - Office hour location: 521 Carr Hall - Office hours: Monday and Wednesday period 7 (1:55 PM TO 2:45 PM) OR BY appointment Everything is due Feb 9 th Chapter one principles of life. *Concept 1.5 science is based on Quantifiable observations and experiments - Scientific investigations are based on observation and experimentation o Science is Based on human curiosity. - Observation is enhanced by technology: microscopes imaging, genome sequencing and satellites. o Technology drives science to move forward. - Observations must be qualified by measurement and mathematical and statistical calculations. - Inductive reasoning allows one to make to general conclusion based on limited set of observations. - These general conclusions allow the scientist to predict that the same results will be obtained in the future under similar circumstance. - Inductive reasoning example: o Observation:  I have observed that the sun rises in the east and sets in the west every day for the past month. o Generalization/ prediction:  I predict that the sun will rise in the east and set in the west every day. - Question: o why does the sun rise in the east and set in the west? - Hypothesis: o The tentative explanation I have is that the earth is rotation relative to the sun o You need to have a testable hypothesis. - Experiment: o To test this I will use a pendulum to try and observe the effects of the earth rotating. - Deductive reasoning: o Knowing the laws of motion , and believing them to be true, o If I start a pendulum moving, it will move I hand ever changing are arc if the earth rotates under it. o Alternatively, if the earth does not rotate, then the arc traced by the pendulum will not change direction. o Show that the world is rotating with the pendulum - Scientific method: o Observation o Questions o Hypothesis o Predictions o Tests of the predictions. (experiments) - The role of hypotheses in inquiry o Observation: your flashlight doesn’t work o Question: why doesn’t your flashlight work?  Hypothesis 1: the batteries are dead  Hypothesis 2: the bulb is burnt out - Both of these hypotheses are testable. - A closer Look at Hypotheses in Scientific inquiry and limitation: o Must be testable o Hypothesis based science often makes use of two or more alternative hypotheses o Failure to falsify a hypothesis does not prove that hypothesis o For example, you replace your flashlight bulb, and it now works; this supports the hypothesis that your bulb was burnt out, but does not prove it (perhaps the first bulb was inserted incorrectly) o In science, observation and experiments must be repeatable. o Science cannot support or falsify supernatural explanations, which are outside the bounds of science. - Limitation of science: o In science, observations and experimental results must be repeatable o Science cannot support or falsify supernatural explanations which are outside of the bounds of science. *Part one: Cells - Atoms Level 1: monomeric unites Level 2: Macromolecules Level 3: supramolecular complexes Level 4: the cell and its organlles Lecture 2: Life Chemistry and Energy Concept 2.1 Atomic Structure is the Basis for Life’s Chemistry - Living and Nonliving matter is composed of atoms. - Like charges repel; different charges attract. - Most atoms are neural because the number of electrons equals the number of protons. o Neutrons do not carry any charge, protons positive, electrons are negative? - Dalton – Mass of one proton or neutron o (1.7 * 10^ -24 grams) o Measured atoms mass in molecules – mass spectrometer. - Mass of electrons is so tiny (1/2000 of a proton/neutrons), it is usually ignored. - Element o Pure substance that contains only one kind of atom. - Living things are mostly composed of 6 elements: o Carbon (C) o Hydrogen (H) o Nitrogen (N) o Oxygen (O) o Phosphorus (P) o Sulfur (S) - The number of protons identifies an element. - Atomic number o Number of protons - For electrical neutrality, # protons = # electrons - Mass number o Total number of protons + Neutrons o Protons and neutrons do not always equal each other, when they don’t they are called isotopes? - Behavior of electrons determines whether a chemical bond will form and what shape the bond will have. Outside of nucleus. - First shell o 2 electrons maximum o Hydrogen – 1 - Second shell o 8 electrons maximum o Carbon- 6 o Nitrogen – 7 o Oxygen – 8 - Third shell o 18 Electrons Maximum o Phosphorus – 15 o Sulfur – 16 - Atoms with unfilled outer shells (they are not happy) tend to undergo chemical reactions to fill their outer shells. (ex: interacting with other people to get what you need or just taking it) - They can attain stability by sharing electrons with other atoms or by losing or gaining electrons - The atoms are then bonded together into molecules. Concept 2.2 Atoms Interact and Form Molecules - Octet Rule o Atoms with at least two electron shells form stables molecules so they have eight electrons in their outermost shells. - A chemical bond is an attractive force that links atoms together to form molecules. o Because the atom is unstable they do this. - There are several kinds of chemical bonds. - - Ionic bonds - Ions o Are charged particle that form when an atom gains or loses one or more electrons. - Cations o Positively charged ions - Anions o Negatively charged ions - Ionic bonds o Result from the electrical attraction between ions with opposite charges o The resulting molecules are called salts. - Ionic attractions are weak, so salts dissolve easily in water. - Covalent bonds - Covalent bonds o Form when two atoms share pairs of electrons. - The atoms attain stability by having full outer shells. - Each atom contributes one member of the electron pair. - Carbon atoms have four electrons in the outer shell- they can form covalent bonds with four other atoms. - Atoms can share equally or unequally - Electronegivity- - Properties of molecules are influenced by characteristics of the covalent bonds: o Orientation o Strength and stability o Multiple bonds o Degree of sharing electrons. - Orientation o Length, angle, and direction of bonds between and two elements are always the same. o Example:  Methane always forms a tetrahedron. - Strength and stability o Covalent bonds are very strong; it takes a lot of energy to break them. - Multiple bonds o Single – sharing 1 pair of electrons C – H o Double – sharing 2 pairs of electrons C- _ C o Triple – sharing 3 pairs of electrons N- - - N - Degree of sharing electrons is not always equal. o Electronegativity  The attractive force that an atomic nucleus exert on electrons o It depends on the number of protons and the distance between the nucleus and electrons. - If two atoms have similar electronegativity’s, they share electrons equally, in what is called a nonpolar covalent bond - If atoms have different electronegative, electrons tend to be near the most attractive atom, in what is called a polar covalent bond. - Hydrogen bonds - Attraction between the ___ negative end of one molecule and the _____ positive hydrogen end of another molecule forms Hydrogen Bonds. o They form between water molecules o They are important in the structure of DNA and proteins. - Water molecules form multiple hydrogen bonds with each other – this contributes to high heat capacity. o A lot of heat is required to raise the temperature of water – the heat energy breaks the hydrogen bonds. o In organisms, presence of water shields them from fluctuations in environmental temperature. - Water has a high heat of vaporization – a lot of heat is required to change water from liquid to gaseous state. - Thus, evaporation has a cooling effect on the environment. - Sweating cools the body – as sweat evaporates form the skin, heat from the adjacent body is used to transform the sweat from liquid to gas. - Hydrogen bonds also give water cohesive strength, or - Cohesion – o Water molecules resist coming apart when placed under tension. - This permits narrow columns of water to move from roots to leaves of plants. - Hydrophilic (water – loving) - in aqueous solutions, polar molecules become separated and surrounded by water molecules. o Ex: salt and sugar. - Nonpolar molecules are called Hydrophobic (water- hating); o Ex: oil - The interactions between them are hydrophobic interactions. - Functional Groups (important) o Small groups of atoms with specific chemical properties. - Functional groups confer these properties to larger molecules, e.g., polarity. - KNOW: FIGURE 2.7: functional groups important to living systems. Part one and Part two&3 - One biological molecule may contain many functional groups. Lecture 3: Concept 2.2 Atom Interact and form Molecules 1/ 11/ 2016 - Macromolecules o Are large molecules formed by covalent linkages of smaller molecules. - 4 kinds of macromolecules are typically found in living organisms. o Proteins o Nucleic acids o Carbohydrates o Lipids - Except for the lipids, the other 3 kinds of Biological Macromolecules are Polymers (“poly” = many; “mer” =unit). - Polymers are created by the covalent linkage of smaller molecules called Monomers. - Polymers are formed and broken apart in reactions involving water. - Condensation o The removal of water creates a covalent band between monomers. - Hydrolysis o The addition of water breaks a covalent bond between monomers. - Two major energy source: carbohydrates and lipids. - Endergoninc- anabolic reaction - Exergoninc- catabolic reaction. Concept 2.3 Carbohydrates consist of sugar Molecules - Carbohydrates are a large group of molecules that have similar composition, but differ in several important properties. - Carbon never bonds with water. o Composition: (Cn(H2O)n’ - Some carbohydrates are small and are called simple sugars. - Some carbohydrates are large and are polymers of the simple sugars. - Five- Carbon sugars (pentoses) - Ribose (RNA) and deoxyribose(DNA) each have five carbons, but very different chemical properties and biological roles. - Six – Carbon sugars (hexoses) - These hexoses all have the formula C6H12O6, but each has distinct biochemical properties. o MANNOSE o GALACTOSE o GLUCOSE o FRUCTOSE - Glucose and fructose makes sucrose - Monosaccharides are covalently bonded by condensation reactions that form glyosidic linkages. - Sucrose is s disaccharide. (fun fact: average, American consume 100 pounds of sugar and sweeteners each year, or almost 30 teaspoons a day.) - Oligosaccharides o Contain several monosaccharides. o Many have additional functional groups o They are often bonded to proteins and lipids on cell surfaces, where they serve as recognition signals. - Polysaccharides o Are large polymers of monosaccharides; the chains can be branching. o Starches  A family of polysaccharides of glucose, the principal energy storage compound of plants. o Glycogen  Highly branched polymer of glucose; main energy storage molecule in mammals  Can be found in liver. And it is heavily branched than starches. o Cellulose  The most abundant carbon – containing (organic) biological compound on Earth; stable; good structural material, in plant cell wall - Why organisms do not store glucose, but starch or glycogen? o Glucose has very high osmosis pressure.- draw water very extensively. o Starch and glycogen has very low osmotic pressure. Which is very safe. - Cellulose is an un branching polymer of glucose with linkages that are chemically very stable - Glycogen and starch are polymers of glucose with branching of carbon. Concept 2.4: Lipids are Hydrophobic Molecules - Lipids o Are hydrocarbons (composed of C and H); they are insoluble in water because of many nonpolar covalent bonds. o Note: Gas is a Hydrocarbon. - When close together, weak but additive van der Waals interactions hold them together. - Store energy in C – C and C – H bonds. - Play a structural role in cell membranes. - Fat in animal bodies serves as thermal insulation. - Triglycerides (simple lipids). o Fats  Solid at room temperature o Oils  Lipids at room temperature - They have very little polarity and are extremely hydrophobic. - Triglycerides consist of: - Three Fatty Acids o Nonpolar hydrocarbon chain attached to a polar carboxyl group (-- COOH) (carboxylic acid) - One Glycerol o An alcohol with 3 hydroxyl (-- OH) groups. - Synthesis of a triglyceride involves three condensation reactions. - Fatty acid chains can vary in length and structure. - In saturated fatty acids, all bonds between carbon atoms are single; they are saturated with hydrogens. - In unsaturated fatty acids, hydrocarbon chains contain one or more double bonds. These acids cause kinks in the chain and prevent molecules from packing together tightly. o Allow membranes to be more flexible. o Deposit In blood flow and can clog the arteries. (not good for us) - Fatty acids are amphipathic: they have a hydrophilic end and a hydrophobic tail. - Phospholipid o Two fatty acids and a phosphate compound bound to glycerol. - The phosphate group has a negative change, making that part of the molecule hydrophilic. - Head- positive charge- Hydrophilic head, and tail – hydrophobic. - Watch video on macromolecule, carbohydrates, and lipids. Concept 2.5 : Biochemical Changes Involve Energy - Chemical reactions occur when atoms have enough energy to combine, or change, bonding partners. o Involves energy. - Sucrose + H2O  Glucose + Fructose - C12h22o11 (C6H12O6) (C6H12O6) - Reactants Products - There are two basic types of energy: - All forms of energy can be considered as either: o Potential:  The energy of state or position, or stored energy  Starch and glycogen, stolen energy, o Kinetic  The energy of movement (the type of energy that does work) that makes things change. - Energy can be converted from one form to another. - There are two basic types of metabolism: - Anabolic reactions: Link simple molecules to form complex ones. o They require energy inputs (endergonic or endo thermic) o Energy is captured in the chemical bonds that form. - Catabolic reactions: energy is released (exergonic or exothermic) o complex molecules are broken down into simpler ones o Energy stored in the chemical bonds is released. - The laws of thermodynamics apply to all matter and energy transformations in the universe. o First law: Energy is neither created nor destroyed. o Second law: disorder (entropy) tends to increase. - When energy is converted from one form to another, some of that energy becomes unavailable for doing work. - Metabolism creates more disorder (more energy is lost to entropy) than the amount or order that is stored. - Example: o The anabolic reactions needed to construct 1 kg of animal body require catabolism of about 10 kg of food. - Life requires a constant input of energy to maintain order. Nucleic Acids, Proteins, and Enzymes 01/13/2016 Concept 3.1 Nucleic Acids Are Informational Macromolecules - Nucleic acids o Are polymers specialized for storage, transmission, and use of genetic information. - DNA = deoxyribonucleic acid - ATCG - RNA = ribonucleic acid - AUCG - Monomers: Nucleotides (building blocks) - Amino acid make bnds through condenstation - DNA contains deoxyribose - RNA contains ribose - Nucleotides bond in condensation reactions to form phosphodiester linkages. - Nucleic acids grow in the 5’ (5 carbon attached to phosphate) to 3’(three carbon OH) direction. - - Oligonucleotides o have about 20 monomers, and include small RNA molecules important for DNA replication and gene expression. - DNA and RNA are polynucleotides, the longest polymers in the living world. - - Memorize : table 3.1 Distinguising RNA FROM DNA. - DNA- Sugar (deoxyribose) – Base Pyrlmidliners (Cytosine and Thymine) – Base Purines (Adenine and Guanine) – Stand double. - RNA – sugar (Ribose) – Base Pyrlmidliners (Cytosine and Urcil) – Base purines (Adnine and Guanine) – Strands (Single). - - Complementary base pairing: o Adenine and thymine always pair (A-T) (double bonds) o Cytosine and guanine always pair (C-G) (triple carbon bond) - - Base pairs are linked by hydrogen bonds. - There are so many hydrogen bonds in DNA and RNA that they form a farily strong attraction, but not as strong as covalent bonds. - Thus, base pairs can be separated with only a small amount of energy. - - Top hat question: o Which of the following amino acid is basic? Lysine— - - RNA is usually single – stranded, but may be folded into 3-D structures, by hydrogen bonding. - Folding occurs by complementary base pairing, so structure is determined the order of bases. - - DNA – two polynucleotide strands form a “ladder” that twist into a double helix. - Sugar – phosphate groups form the sides of the ladder (on the outside), the hydrogen bases form the rungs (on the inside). Turn is always an right hand turn. - “central dogma” - DNA (transcription) RNA(Translation) Polypeptide (this is what we call “central dogma”). - Dna is an informational molecule: genetic information is the sequence of base pairs. - DNA has two functions: - Replication - Gene expression – o base sequences are copied to RNA, and specify amino acids sequences in proteins. - - DNA replication and transcription depend on the base pairing. - - DNA replication and transcription depend on the base pairing: - 5’- T C A G C A – 3’ – Coding strand - / / / / / / - 3’- A G T C G T – 5’ – Template strand - (polymer chain reaction) - 3’ – AGTCGT- 5’ transcribes to RNA with the sequence 5’- UCAGCA-3’ - Template strand – transcribe into Rna. - - Genome- o complete set of DNA in a living organism o Genomics- study of the genome - Genes – o DNA sequences that encode specific proteins and are transcribed into RNA and translated to specific protiens. o Gd o fdf - Not all genes are transcribed and translated in all cells of an organism. - - DNA base sequences reveal evolutionary relationships. - Closely related living species should have more similar base sequences than species that are more distantly related. - Scientists are now able to determine and compare entire genomes of organisms to study evolutionary relationships. - - Major functions of proteins: - Enzymes – o catalytic proteins o Allow us to digest food. - Defensive proteins (e.g., antibodies) o The reason that we can sense the environment. - Hormonal and regulatory proteins – o control physiological processes - Receptor proteins – o Receive and respond to molecular signals. - Storage proteins store amino acids. - Structural proteins – o physical stability and movement - Transport proteins carry substances (e.g., hemoglobin) - Genetic regulatory proteins regulate hen, how and to what extent a gene is expressed. - - Protein monomers are amino acids (building block of protiens. - Amino and carboxylic acid functional groups allow them to act as both acid and bas. - The R Groups differs in each amino acid. GO OVER PROTIENS WATCH VIDEOS! - Amino acids with electrically charge hydrophilic side chains. - Amino acids with polar, uncharged, hydrophilic side chains. - Amino acids with nonpolar, hydrophobic side chains. - Cysteine side chains can form covalent bonds with other cysteine side chains. – disulfide bonds - This type of S ---- S bond is called a disulfide bridge, or a disulfide bond. - TAKE NOTES FROM THE CHARTS/ TABLES - Top Hat question: - Nucleotides in rna are connected to one another in the polynucleotide chian by : o They are single chains o Covalent bonds between sugar and phosphate. Chapter three: Nucleic Acids, Proteins, and Enzymes January 15, 2016 Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles. - Additional terms to know: - Oligopeptides or peptides – short polymers of 20 or fewer amino acids (some hormones and signaling molecules.) - Polypeptides or proteins range in size from insulin, which has 51 amino acids, to huge molecules such as the muscle protein titin, with 34,350 amino acids. - Amino acids are linked in condensation reaction s to form peptide linkages or bonds. - Polymerization takes place in the amino to carboxyl direction. – covalent bond - Figure 3.6 Formation of a Peptide Linkage. - There are four levels of protein structure: o Primary o Secondary o Tertiary o Quaternary - Primary structure o is a single chain - Secondary structure o Regular, repeated spatial patterns in different regions, resulting from hydrogen bonding. - There are 2 major types of secondary structure: o a (alpha) helix – right handed coil  back bond hydrogen bonds allow the alpha helix to be form. o b (beta) pleated sheet – two or more polypeptide chains are extended and aligned. - Tertiary Structure: o Is the final, folded, 3-D shape of a polypeptide. o Is determined by interactions between R- groups, rather than between backbone constituents. - Interactions between R groups determine tertiary structure. o Disulfide bridges hold a folded polypeptide together  Big player in 3-d bonds  sh o Hydrogen bonds stabilize folds o Hydrophobic interactions side chains can aggregate  Rings around o Van der Waals interactions between hydrophobic side chains o Ionic interactions from salt bridges.  Positive and negative - Top hat questions - Which of the following interactions in protein tertiary structure is covalent o Disulfide bridges - Which statement about the structure of a protein is true? - Quaternary structure o Two or more polypeptide chains (subunits) bind together by hydrophobic and ionic interactions, and hydrogen bonds. o Very week bonds NO covalent bonds!!! o These week interactions allow small changes that aid in the proteins function. o Protein that care oxygen throughout the body - THERE IS A TABLE I FORGOT TO WRITE HERE. - - Secondary and tertiary protein structure derive from primary structure. - Denaturing- o heat or chemicals are used to disrupt weaker interactions in a protein, destroying secondary and tertiary structure. o All the bonds form 3d bonds and they are disruptive.. - The protein can sometimes return to normal when cooled – all the information needed to specify the unique shape is contained in the primary structure. - - Factors that can disrupt the interactions that determine protein structure (denaturing): o Temperature o Concentration of H o High concentrations of polar substances, e.e., urea o Nonpolar substances, e.g., organic solvent, acetone.  They denature the proteins - - Chemical bonds and interactions - Primary – covalent bonds (peptide bonds) – amino acid sequences - Secondary – Hydrogen bonds – α helix, β pleated sheet - Tertiary – all five bonds and interactions – folded proteins; enzymes - Quanternary – Hydrophobic interactions between subunits; hemoglobin Concept 3.3 Some proteins act as enzymes to speed up biochemical reactions - Living systems depends on reactions that occur spontaneously, but without help at such slow rates that organisms could not survive. - Catalysts are substances that speed up reactions without being permanently altered. - No catalyst makes a reaction occur that cannot otherwise occur. - Most biological catalysis are proteins (enzymes); a few are RNA molecules (ribozymes). - - In exergonic reactions there is an energy barrier between reactions and products. - An input of energy (the activation energy of E) will put reactants into a transition state. - “not spontaneous due to energy barrier” - - Enzymes lower the activation energy – they allow reactants to come together and react more easily. - Example: A molecule of sucrose in solution may hydrolyze in hundreds of years; with sucrose present, the same reaction occurs in 1 second! - ;n - Enzymes are highly specific – each one catalyzes only one chemical reaction. - Reactants are substrates; they bind to a specific site on the enzyme – the active site. - Specificity results from the exact 3-D shape chemical properties of the active site. - The Enzyme- Substrate Complex (ES) is held together by hydrogen bonding, electrical attraction, or temporary covalent bonding. - E + S <--> ES <-> EP <-> E + P - The enzyme is not changed at the end of the reaction. BSC 2010 Notes 2 Chapter 3: Nucleic Acids, Proteins, and Enzymes January 20, 2016 Concept 3.3 some proteins act as enzymes to speed up biochemical reactants  Top hat question: o Which amino acid substitution for valine would least likely affect the three- dimensional shape of the resulting protein?  Answer: Isoleucine   How do enzymes catalyze a reaction?  Inducing strain  Bonds in the substrate are stretched, putting it in an unstable translation state.  Substrate Orientation  Substrates are bought together so that bonds can form.  Adding chemical groups  R groups may be directly involved in the reactions.   Binding of substrate to enzyme is like a baseball in a catcher’s mitt. The enzyme changes shape to make the binding tight – “induced fit.”   Shape changes upon Ca^2+ binding to CaM  Proteins are dynamic  Enzymes are really flexible   Some enzymes require ions or other molecules in order to function:  Metal ions:  Copper, Zinc, Iron  Coenzymes:  Small organic molecules (NAD, FAD, ATP), add or remove chemical groups from the substrate. They can participate in many different reactions.  Prosthetic groups:  Organic molecules permanently bound to their enzymes (heme, Flavin, retinal)   Rates of catalyzed reactions:  There is usually less enzyme than substrate present, so reaction rate levels off when the enzyme becomes saturated.  Saturated  All enzymes molecules are bound to substrate molecules.  Maximum rate is used to calculate enzyme efficiency – substrate molecules converted to products per unit time (turnover).  It ranges from 1 to 40 million molecules per second! Concept 3.4 Regulation of metabolism occurs by regulation of Enzymes  Enzyme- catalyzed reactions are part of metabolic pathways – the product of one reaction is a substrate for the next.   Homeostasis o The maintenance of stable internal conditions.  Cells can regulate metabolism by controlling the amount of an enzyme – turn synthesis of enzymes off or on.  Cells can maintain stable internal conditions by regulating the activity of an enzyme.  Chemical inhibitors can bind to enzymes and slow down reaction rates- natural inhibitors regulate metabolism; artificial inhibitors are used to trait diseases, kill pests, and study enzymes function. o Example : drugs   Irreversible inhibition – o Inhibitor covalently binds to a side chain in the active site. The enzyme is permanently inactivated.  Example: Insecticide Malathion derived from DIPF.  Example: Aspirin – can prevent from blood to clog.  Reversible inhibition (more common in cells):  A competitive inhibitor  Competes with natural substrates for active site.  Binds to the active site and preventing substrate from binding.  A noncompetitive inhibitor  Binds at a site distinct from the active site, causing change in shape and function.  Binds at a site other than the active site   Allosteric regulation -- Non-substrate molecules binds a site other than the active site (the Allosteric site)- (non- competitive inhibitor will bind to this or are related to this.)  The enzyme changes shape, which alters the chemical attraction (affinity) of the active site for the substrate.  Allosteric regulation can activate or inactivate enzymes.   Protein kinases regulate responses to the environment:  Many Enzymes are subject to allosteric regulation.  The active form regulates the activity of other enzymes, by phosphorylating allosteric or active sites on the other enzymes.   Metabolic pathways:  The first reaction is the commitment step --- other reactions then happen in sequence.  Feedback inhibition (end – product inhibition) – the final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway.  pH affects enzyme activity:  Acidic side chains generate H+ and become anions.  Basic side chains attract H+ and become cations.  Example:  Glutamic acid – COOH < -- > glutamic acid – COO + H - +  The law of mass action  The higher the H concentration, the more reaction is driven to the left to the less hydrophilic from. This can affect enzyme shape and function.  Protein tertiary structure (and thus function) is very sensitive to the concentration of H^+ (pH) in the environment.  All enzymes have an optimal pH for activity. Temperature affects activity:  Warming increases rates of the chemical reactions, but if temperature is too high, non – covalent bonds can break and inactivate enzymes.  High temp = denaturation.  To keep cells alive you need a very cold temp  Example: sperm and egg banks  All enzymes have an optimal temperature for activity.  Isozymes  Catalyze the same reaction but have different composition and physical properties.  Isozymes may have different optimal temperature of pH, allowing an organism to adapt to changes in its environment. Reviews for chapters 2 & 3  Macromolecules (polymer) formation always involve Covalent bonds  Hydrogen bonds are responsible for maintaining structures in nucleic acids (Complementary base paring) and proteins.  All five chemical bonds and interactions contribute to further structural maintenance. Hydrophilic vs. Hydrophobic  Polar and charged molecules are hydrophilic.  Nonpolar and uncharged molecules are hydrophobic.  Functional groups give hydrophilic property to molecules.  Three amino acids groups: nonpolar, polar, and electrically charged ones. Macromolecules  Carbohydrates  Lipids  Nucleic Acid  Proteins Protein: Structure and Function  Primary  Secondary  Tertiary  Quaternary Regulation of metabolisms through regulation of enzymes  Control the amount of an enzyme  Regulate the activity of enzymes o Inhibitors (competitive and noncompetitive) o Allosteric regulation  Feedback inhibition. 1/22/2016 Chapter 4: Cells: The Working Units of Life Concept 4.1 Cells Provide Compartments for Biochemical Reaction  Cell theory was the First unifying theory of biology. Cell theory states that: o Cells are the fundamental units of life o All organisms are composed of cells o All cells come from preexisting cells. o o Important implications of cell theory:  Studying cell biology is the same as studying life.  Life is continuous. Major key for chapter 4:  Prokaryotes vs. Eukaryotes  Plant cell s. Animal cell  Structure and Function of each organelle   Most cells are tiny. o This is because diffusion is a key force that moves most molecules around the cell and allows them to interact. o Diffusion can move molecules over short distances rapidly, but it takes too long to move them long distances.  When you have smaller cells surface area increase, and small cells want to have good and faster reactivity (this is why cells are small).   The volume  of a cell determines the amount of metabolic activity it carries out per unit time.  The surface area  of a cell determines the number of substances that can enter or leave the cell  As the volume of a cell increases, the surface area does not increase as much.  Cells compensate by changing the shape of their shape to increase the surface area (by being flat instead of Spherical, or by having many invaginations.) Cells can be studied structurally and chemically  To visualize small cells, there are two types and microscopes: o Light microscopes -- use glass lenses and light  Resolution = 2.0  Electron microscopes – electromagnets focus an electron beam  Resolution = 0.1 nm.  Chemical analysis of cells  Involves breaking them open to make a cell – free extract  The composition and chemical reactions of the extract can be examined.  The properties of the cell – free extract are similar to those inside the cell. The plasma membrane:  Is a selectively permeable  barrier that allows cells to maintain a constant internal environment  Is important in communication and receiving signals  Often had protein for binding and adhering to adjacent cells  Chapter 5: cell membranes and signaling Two types of cells: Prokaryotic and eukaryotic o Prokaryotes are without membrane – enclosed compartments. o Eukaryotes have membrane – enclosed compartments called organelles, such as the nucleus. Concept 4.2 Prokaryotic Cells do not Have a Nucleus Prokaryotic Cells: o Are enclosed by a plasma membrane o Do not have Nucleus o Have DNA located in the Nucleoid o The rest of the cytoplasm consist of:  Cytosol (water, dissolved material) and suspended particles  Ribosomes – sites of protein synthesis.  Most Prokaryotes have a rigid cell wall outside plasma membrane.  Some have an additional outer membrane that is very permeable.  Others have a slimy layer of polysaccharides, called the capsule.  Some prokaryotes swim by means of flagella, made of the protein flagellin.  Example: Bacteria.  A motor protein anchored to the plasma or outer membrane spins each flagellum and drives the cell.  Some rod – shaped bacteria have a network of actin- like protein structures to help maintain their shape. Concept 4.3 Eukaryotic Cells have A Nucleus and other membrane – bound compartments Eukaryotic cells o Have a plasma membrane, cytoplasm, and ribosomes – and also membrane – enclosed compartments called organelles. o Each organelle plays a specific role in cell functioning.  Ex: like the different departments at an University.  – animal and plant cell figures were shown  KNOW THE ORGANELLES AND THERE FUNTIONS.  Plant cells:  Animal Cells:  Ribosomes are sites of protein synthesis: o They occur in both prokaryotic and eukaryotic cells and have similar structure – one larger and one smaller subunit. o Each subunit consists of ribosomal RNA (tRNA) bound to smaller Protein molecules. o Ribosomes are not membrane – bound organelles – in eukaryotes, they are free in the cytoplasm, attached to the endoplasmic reticulum, or inside mitochondria and chloroplasts. o In Prokaryotic cells, ribosomes float freely in the cytoplasm.  The nucleus is usually the largest organelle. o Site of DNA and DNA replication, DNA transcription to RNA. o It contains the nucleolus, where ribosomes begin to be assembled from RNA and proteins. o The nucleus is surrounded by two membranes that form the nuclear envelope. o Nuclear pores in the envelope control movement of molecules between nucleus and cytoplasm. o In the nucleus, DNA combines with proteins to form chromatin in long, thin threads called chromosomes.  The endomembrane system: o The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, and lysosomes. o Tiny, membrane – surrounded vesicles shuttle substances between the various components, as well as to the plasma membrane.  Endoplasmic Reticulum (ER) – network of interconnected membranes in the cytoplasm, with large surface area.  Two types of ER: o Rough endoplasmic reticulum (RER) o Smooth endoplasmic reticulum (SER)  Rough endoplasmic reticulum (RER) HAS RIBOSOMES attached to being protein synthesis. o Newly made proteins enter the (RER) LUMEN o Once inside, proteins are chemically modified and tagged for delivery. o The RER participants in the transport of proteins to other organelles. o All secreted proteins and most membrane proteins, including glycoproteins, which are important for recognition, pass through the RER.  Smooth endoplasmic reticulum (SER) – MORE TUBLUR, no ribosomes. o It chemically modifies small molecules such as drugs and pesticides. o It is the site of glycogen Degradation in animal site o It is the site of synthesis of lipids and steroids. o It stores Calcium ions required from muscle contraction  The Golgi apparatus is composed of flattened sacs (cistemae) And small membrane – endorsed vesicles. o Receives proteins from the RER – can future modify them o Concentrates, packages, and sorts, proteins. o Adds carbohydrates to proteins o Site of polysaccharide synthesis in plant cells.  The Golgi apparatus has three regions: o The cis region receives vesicles containing protein from the ER. o At the trans region, vesicles bud off from the Golgi apparatus and travel to the plasma membrane or to lysosomes. o The medial region lies in between the trans and cis regions.  Primary lysosomes originate from the Golgi apparatus. o Membrane bound organelle. o They contain digestive enzymes, and are the site where macromolecules are hydrolyzed into monomers. o Lysosomes are connected to many of the disease. Like Parkinson’s. o o Macromolecules may enter the cell by phagocytosis – part of the plasma membrane encloses the material and a phagosomes is formed. o Phagosomes then fuse with primary lysosomes to form secondary lysosomes. o Enzymes in the secondary lysosomes hydrolyze the food molecules.   Phagocytes are cells that take materials into the cells and break them down.  Autophagy is the programmed destruction of cell components and lysosomes are where it occurs.  Lysosomal storage diseases occur when lysosomes fail to digest the components.  Energy transforming organelles: o In eukaryotes, molecules are first broken down in the cytosol. o The partially digested molecules enter the mitochondria chemical energy is converted to energy – rich ATP. o Cells that require a lot of energy often have more mitochondria.  Mitochondria have two membranes: o Outer membrane – quite porous o Inner membrane – extensive folds called cristae, to increase surface area o The fluid – filled matrix inside the inner membrane contains enzymes, DNA, and ribosomes.  That means it can make protein when they have their own DNA, and ribosomes. Answer: D Answer is : a Answer: d Answer: e Item: Summative Quiz for Chapter 2 Score: 20/20  (Calculated)  scaled to  10/10 100% 100% Due: Tuesday, February 09, 2016 5:00 PM Submitted: Monday, February 01, 2016 10:16 PM Answers: 1.  Which statement best describes the difference between an element and a  molecule? An element is composed of atoms; a molecule is not. An element is composed of only one kind of atom; molecules can be  composed of more than one kind of atom.   An element is unstable; molecules are stable. Elements always have lower atomic weights than molecules. Elements exist in nature only as parts of molecules. 2.  The reactivity of an atom arises primarily from the energy difference between the electron shells. potential energy of the outermost shell.   average distance of the outermost shell from the nucleus. sum of the potential energies of all electron shells. existence of unpaired electrons in the outermost shell. 3. Which type of bonds or interactions between atoms is the strongest? Hydrophobic interactions Ionic bonds   Covalent bonds van der Waals interactions Hydrogen bonds 4. Which molecular structure is incorrect? CH —3H 3 CH =2CH 2   CH —3H 2 CH —3H 3+ CH —3H 3 5.  Covalent bond formation depends on the ability of atoms to share electrons with other atoms. donate electrons to other atoms.   receive electrons from other atoms. share electrons with ions. capture electrons from gases. 6. Table salt, NaCl, is neutral. When dissolved in water, NaCl   remains as NaCl (does not dissociate). dissociates to form Na  and Cl  molecules. dissociates to form Na  and Cl  ions that do not interact with water  molecules. dissociates to form Na  and Cl  ions that interact with water molecules. does not dissociate, but interacts with water molecules. 7. An atom that contains ten protons and ten electrons is likely to form covalent bonds with another atom. form ionic bonds with another atom.   be chemically inert (stable). be radioactive. be toxic. 8. For a covalent bond to be polar, the two atoms that form the bond must have different atomic weights. the same number of electrons.   different melting points. different electronegativities. similar electronegativities. 9. Water is essential to life. Which property of water affect(s) life less than the  others? Cohesiveness High heat capacity   High heat of vaporization Hydrogen bonds Nearly colorless 10.  Which biological molecule is smallest due to being a subunit rather than a  macromolecule? Lipid Nucleic acid   Protein Starch Glucose 11.  The “building blocks” of polysaccharides are _______, and these blocks are  covalently linked together by _______. glycerol and fatty acids; glycosidic linkages amino acids; triple bonds   monosaccharides; glycosidic linkages disaccharides; triple bonds oligosaccharides; glycosidic linkages 12. Which statement about starch is true? It is a straight­chain shaped molecule. It is a polymer of fructose.   It is formed by the condensation of monomers. The properties of starch are very similar to those of cellulose. It cannot be digested by people. 13. Oils and fats form membranes. are triglycerides.   are diglycerides. all contain the same fatty acids. have glycosidic linkages. 14. Fatty acids are carboxylic acids with long hydrocarbon tails. linked to glycerol in fats by hydrogen bonds.   always saturated. large polymers of monosaccharides. water soluble. 15.  Oils melt at a lower temperature than fats because oils and fats are not the same type of macromolecule. fats contain more saturated fatty acids than oils.   fats contain more unsaturated fatty acids than oils. oils are made by plants, fats are not. fats are common in animals, oils are not. 16. Phospholipids differ from triglycerides in that phospholipids are amphipathic. are not derivatives of glycerol.   do not have both hydrophilic and hydrophobic components. are used to store energy for the cell. do not contain fatty acids. 17.  Which statement would receive the worst grade in a biology exam covering  the first and second laws of thermodynamics? Living organisms can change the form taken by energy. Chemical energy may be converted to light energy.   The total energy of a system is available to do work. Potential energy may be used to do work. Some organisms obtain energy from the sun. 18.  The synthesis of complex molecules _______ energy, whereas their  degradation _______ energy. This synthesis occurs with _______ in  entropy. requires; releases; an increase requires; releases; a decrease   releases; requires; no change releases; requires; an increase requires; releases; no change 19.  Entropy is the total energy in a system. tends to decrease the total energy in the universe.   when multiplied times the absolute temperature, is the useable energy in a  system. is related to the disorder or randomness of a system. is free energy. 20. A reaction that releases free energy is endergonic. necessarily proceeds more rapidly than a reaction with a less negative ΔG.   is spontaneous. cannot be used to drive a reaction with a positive ΔG. is always paired with a reaction with a positive ΔG. flash-cards/


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