New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here

Midterm 1 Study Guide: Chapters 1-7

by: Aliya Amin

Midterm 1 Study Guide: Chapters 1-7 Biol 5A

Marketplace > University of California Riverside > Biology > Biol 5A > Midterm 1 Study Guide Chapters 1 7
Aliya Amin

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

These notes cover what's going to be in our upcoming midterm. I've mainly focused on information provided directly in the textbook for chapters 1-7, including information not covered in lecture.
Intro: Cell and Molecular Biology
Eugene Nothnagel
Study Guide
50 ?




Popular in Intro: Cell and Molecular Biology

Popular in Biology

This 22 page Study Guide was uploaded by Aliya Amin on Tuesday January 26, 2016. The Study Guide belongs to Biol 5A at University of California Riverside taught by Eugene Nothnagel in Winter 2016. Since its upload, it has received 74 views. For similar materials see Intro: Cell and Molecular Biology in Biology at University of California Riverside.


Reviews for Midterm 1 Study Guide: Chapters 1-7


Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 01/26/16
BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 CHAPTER 1: EVOLUTION, THE THEMES OF BIOLOGY , AND SCIENTIFIC INQUIRY Biology is the scientific study of life, with evolution, the process of change that has shaped life from its origin on Earth to today’s diversity, as its organization principle. The properties and processes of life include highly ordered structure, evolutionary adaptation, response to the environment, regulation, energy processing, reproduction, and growth and development. 1.1: The study of life reveals common themes Theme: New properties emerge at successive levels of biological organization  biology today combines the strategy of reductionism, which breaks down complex systems into simpler components, with systems biology, which studies interactions of the parts of a system and models the system’s dynamic behavior  structural arrangements of and interactions among components at each level of biological organization lead to emergent properties at the next level  the form of a structure is well matched to its function at all levels of biological organization  the cell is lowest structural level capable of performing all the activities of life  the simpler and smaller prokaryotic cell, unique to bacteria and archaea, lacks a nucleus to enclose its DNA and other membrane-enclosed organelles  the eukaryotic cell-with a nucleus containing DNA, and numerous organelles-is typical of all other living organisms Theme: Life’s processes involve the expression and transmission of genetic information  the genetic information of a cell is coded in DNA  genes are units of inheritance that transmit information from parents to offspring. They are located on chromosomes, long DNA molecules that replicate before cell division and provide identical copies to daughter cells  most genes program the cell’s production of proteins, and almost all cellular structures and actions involve one or more proteins  gene expression is the process by which a gene’s information is converted into a cellular product. Genes also code from RNA’s that serve other functions: playing a role in the cell’s protein manufacturing machinery and regulating gene expression  the genetic instruction an organism inherits make up its genome  each of the two sets of chromosomes in a human cell contains about 3 billion nucleotide pairs  proteomes are whole sets of proteins encoded by a genome  research developments contributing to genomics and proteomics: 1) “High throughput” technology that can analyze biological materials rapidly 2) Bioinformatics, which provides computational tools to process and analyze the resulting data 3) interdisciplinary research teams with specialists from many diverse fields Theme: Life requires the transfer and transformation of energy and matter  producers transform light energy to the chemical energy in sugars, which powers the cellular activities of plants 1 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  consumers eat plants and other organisms, using chemical energy in their foods to power their movement, growth, etc  in each use of energy to perform work, some energy is lost to the surroundings as heat Theme: From ecosystems to molecules, interactions are important in biological systems  molecular interactions within organisms are crucial to proper functioning  protein enzymes catalyze cell’s chemical reactions, which are often organized into chemical pathways  many biological processes are controlled through feedback regulation, in which the product of a process regulates that process  in negative feedback, the response feeds back and reduces the original stimulus  in positive feedback, an end product speeds up the process 1.2: The Core Theme: Evolution accounts for the unity and diversity of life Classifying the Diversity of Life  prokaryotes make up the domains Archaea and Bacteria  all eukaryotes are placed in the domain Eukarya Charles Darwin and the Theory of Natural Selection  natural selection: individuals with traits best suited for the environment leave more offspring; the mechanism of evolution based off of three observations 1) individuals vary in many heritable traits 2) the overproduction of offspring sets up a competition of survival 3) species are generally matched to their environments The Tree of Life  diversity of species results from natural selection acting over millions of generations as populations adapted to different environments 1.3: In studying nature, scientists make observations and form and test hypotheses Science is an approach to understanding the natural world that involves inquiry, the search for explanations of natural phenomena Making Observations  data: recorded observations, quantitative and qualitative  using inductive reasoning to draw generalizations from collections of observations Forming and Testing Hypotheses  hypothesis: tentative answer to a question or an explanation of observations, leading to predictions that can be tested -must be testable -cannot be proven to be true or incorrect -gains credibility when it is tested in various ways  deductive reasoning uses “if…then” logic Theories in Science 2 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  theory: broader in scope than a hypothesis, generates many specific hypotheses, supported by a larger body of evidence. It can be modified and rejected when results and new evidence no longer support it CHAPTER 2: THE CHEMICAL CONTEXT OF LIFE 2.1 Matter consists of chemical elements in pure form and in combinations called compounds  Matter: anything that takes up space and has mass Elements and Compounds  Elements: substances that cannot be chemically broken down to other types of matter  Compound: made up of two or more elements combined in a fixed ratio The Elements of Life  About 25 out of the 92 elements are essential to life  Essential elements: needed for an organism to live and reproduce; Carbon, Oxygen, Hydrogen, and Nitrogen make up 96% of living matter o Most of the remaining 4% consists of Calcium, phosphorus, potassium, and sulfur  Trace elements: elements required in very minute quantities such as Iron and Iodine (Mn, Co, Ni, Cu, Zn, Mo, I) *Hint: 99% of all living material consist of: CHOPKINS CaFe Mg NaCl (Carbon, Hydrogen, Oxygen, Phosphorus, Potassium, Iodine, Nitrogen, Sulfur) Evolution of Tolerance to Toxic Elements  Serpentine soil contains toxic elements but some plants exhibit evolutionary adaptations that enable them to grow in such soils 2.2 An element’s properties depend on the structure of its atoms Subatomic Particles  Atom: smallest unit of matter retaining the properties of that element  Uncharged neutrons and positively charged protons are packed tightly together to form the atomic nucleus of an atom  Negatively charged electrons form a large cloud around the positively charged nucleus  Protons and neutrons have a similar mass of about 1.7 X 10^-24 gram or close to 1 dalton each  Dalton: measurement unit for atomic mass  Electrons have negligible mass 3 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 Atomic Number and Atomic Mass  Each element has a characteristic atomic number, or number of protons in each of its atoms  The mass number is equal to the number of protons and neutrons in the nucleus and approximates the mass of an atom of that element in daltons  Atomic mass: the total mass of an atom Isotopes  Isotopes: a variance in the number of neutrons of a particular element; slightly different mases but the same chemical behaviors  Radioactive isotopes: unstable isotopes, spontaneously decay, giving off particles and energy o Fixed rate of decay, referred to as its half life: amount of years it takes for 50% of the parent isotope to decay into its daughter isotope o Radiometric dating: scientists use the ratio of different isotopes to estimate how many half lives have passed since a fossil or rock was formed The Energy Levels of Electrons  Energy: the capacity to cause change, to do work  Potential energy: energy stored in matter as a consequence of its position or structure o Potential energy of an electrons increases as their distance from the positively charged nucleus increases  Electron shells/energy level: an electron’s state of potential energy Electron Distribution and Chemical Properties  The chemical behavior of an atom is determined by the number of valence electrons it has in its outermost electron shell or valence shell  Valence shell of eight electrons is complete, resulting in an unreactive or inert atom  Atoms with incomplete shells are chemically reactive  Elements in each row or period of the periodic table of elements have the same number of electron shells and are arranged in order of increasing number of electrons  Amount of energy necessary to remove an electron from its ground state is called the ionization energy o Greater the ionization energy, the more difficult it is to remove an electron o Increases from left to right and up from bottom to the top of the periodic table (except H, which has a very high ionization energy) Electron Orbitals  Orbital: 3D space or volume within which an electron is most likely to be found  the first electron shell can contain two electrons in a single spherical orbital, 1s orbital  S –1 orbital –2 electrons  P—3 orbitals—6 electrons  D—5 orbitals—10 electrons  F—7 orbitals—14 electrons 2.3The formation and function of molecules depend on chemical bonding between atoms 4 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds Covalent Bonds  Covalent bonds: when two atoms share a pair of valence electrons  Molecule: two or more atoms held together by covalent bonds  Electronegativity: attraction of a particular atom for shared electrons  Nonpolar covalent bond: if the atoms in a molecule have similar electronegativities and the electrons remain equally shared  Polar covalent bond: if one electron is more electronegative, it pulls the shared electrons closer to itself. The unequal sharing results in a polarity or separation of charges Ionic Bonds  if two atoms are very different in their attraction for valence electrons, the more electronegative atom may completely transfer an electron from the other atom, resulting in the formation of charged atoms called ions  cation: positively charged, atom that lost an electron  anion: negatively charged, atom that gained an electron  ionic bonds: holds cations and anions together because of the attraction of their opposite charges  ionic compounds/salts: 3D crystalline lattice arrangements held together by electrical attractions o number of ions present in a salt crystal aren’t fixed but the atoms are present in specific ratios o have strong ionic bonds when dry and dissolve in water Weak Chemical Bonds  Ionic bonds and other weak bonds may form temporary interactions between molecules  Weak bonds within many large molecules help create those molecules’ 3D functional shape  Hydrogen bond: hydrogen atom that is covalently bonded to an electronegative atom has a partial positive charge and can be attracted to a different nearby electronegative atom  All atoms and molecules are attracted to each other when in close contact by fleeting charge difference--van der Waals interactions  Momentary uneven electron distributions produce changing positive and negative regions that create van de Waals interactions Hydrogen Bonds are weak bonds important in the chemistry of life  Hydrogen bonds are attractive forces between polar molecules; when partial opposite charges in different molecules attract each other o Comparatively weak but collectively can be quite strong o Where we see hydrogen bonds: between water molecules, helping to hold DNA together, interactions between proteins Molecular Shape and Function 5 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Molecule’s shape and size affects how it interacts with other molecules  In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes  Biological molecules recognize and interact with each other with a specificity based on molecular shape  Molecules with similar shapes can have similar biological effects 2.4: Chemical reactions make and bread chemical bonds Chemical reactions: the making or breaking of chemical bonds o Reversible o Increasing concentrations of reactants can speed up the rate of a reaction Matter is conserved in chemical reactions; same number of kinds of atoms are present in both reactants and products, although the rearrangement of electrons and atoms causes the properties of these molecules to be different Chemical equilibrium: reached when the forward and reverse reactions processed at the same rate, and the relative concentrations of reactants and products no longer change CHAPTER 3: WATER AND LIFE  Water is the biological medium on Earth  All living organisms require water more than any other substance  Most cells are surrounded by water, and cells themselves are about 70-95% water o Red blood cells—60% water o Muscle—75% water o Plasma—92% water  The abundance of water is the main reason the Earth is habitable Polar covalent bonds in water molecules result in hydrogen bonding  The water molecules is a polar molecule: the opposite ends have opposite charges  Polarity allows water molecules to form hydrogen bonds with each other  The hydrogen atoms pull towards the oxygen atom in water  The unpaired electrons on a water molecule allow it to bond to other water molecules  A single water molecule can have up to 4 other water molecules bound to it  The difference between the solid and liquid form of water is the formation of H bonds and the amount of kinetic energy present 6 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 Emergent properties of water contribute to Earth’s suitability for life Some of water’s properties that facilitate an environment for life are: o Cohesive/Adhesive behavior  Surface tension and capillary action o Ability to moderate temperature, thermal stability  Specific heat and heat of vaporization o Expansion upon freezing o Versatility as a solvent o Colorless and transparent o Low viscosity—compared to other liquids Cohesion of Water Molecules Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion Cohesion helps the transport of water against gravity in plants Adhesion is an attraction between different substances, for example, between water and plant cell walls Surface tension: measure of how hard it is to break the surface of a liquid; related to cohesion o Detergents and heat lowers the surface tension of water so they can soak into our clothes. Washing in cold water requires a wetting agent in the detergent Moderation of Temperature by Water  Water absorbs heat from warmer air and releases stored heat to cooler air  Water can absorb or release a large amount of heat with only a slight change in its own temperature Heat and Temperature  Kinetic energy: energy of motion  Heat: the measure of the total amount of kinetic energy due to molecular motion  Temperature: measures the intensity of heat due to the average kinetic energy of molecules Water’s High Specific Heat  The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degree Celsius o Specific heat of water: 1 cal/g/degrees Celsius  Water resists changing its temperature because of its high specific heat o Water heats slowly and cools slowly, it has a high heat of fusion  Water’s high specific heat can be traced to hydrogen bonding o Heat is absorbed when hydrogen bonds break o Heat is released when hydrogen bonds form  The high specific heat of water minimizes temperature fluctuations to within limits that permit life Evaporative Cooling  Heat of vaporization: the heat a liquid must absorb for 1 gram to be converted to gas 7 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 o as liquid evaporates, its remaining surface cools, a process called evaporative cooling (takes away heat) o evaporative cooling of water helps stabilize temperatures in organisms and bodies of water o a liquid with a low heat of vaporization evaporates faster, such as alcohol Floating of Ice on Water  ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense  if ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth  ice occupies a larger volume because of its lattice structure but is less dense than liquid water Water: The Solvent of Life solution: liquid that is a homogenous mixture of substances solvent: dissolving agent of a solution solute: substance that is dissolved an aqueous solution is one in which water is the solvent water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily when an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell water can also dissolve compounds made of nonionic polar molecules even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions Hydrophobic and Hydrophilic Substances hydrophilic substance is one that has an affinity for water hydrophobic substance is one that does not have an affinity for water o oil molecules are hydrophobic because they have relatively nonpolar bonds Solute Concentrations in Aqueous Solutions most biochemical reactions occur in water chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution molecular mass is the sum of all of the masses of all atoms in a molecule molarity (M) is the number of moles of solute per liter of solution Acidic and Basic Conditions Affect Living Organisms  a hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other o the H atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) o the molecule with the extra proton is now a hydronium ion (H3O+) o the molecule that lost the proton is now a hydroxide ion (OH-)  water is in a state of chemical equilibrium in which water molecules dissociate at the same rate at which they are being reformed  changes in concentrations of H+ and OH- can drastically affect the chemistry of a cell 8 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  concentrations of H+ and OH- are equal in pure water Acids and Bases  acid: any substance that increases the H+ concentration of a solution; ionize in an aqueous solution. Proton donor  base: any substance that reduces the H+ concentrati0on of a solution. Proton acceptor  Most biological fluids have a pH in the range of 6 to 8  Acids and bases that ionize completely are considered strong acids and bases Buffers  Buffers: substances that minimize changes in concentrations of H+ and OH- in a solution o most buffers consist of an acid-base pair that reversibly combines with H+ Acidification: A Threat to Water Quality Human activities such as burning fossil fuels threaten water quality CO2 is the main product of fossil fuel combustion About 25% of human-generated CO2 is absorbed by oceans CO2 dissolved in sea water forms carbonic acid; this process is called ocean acidification As seawater acidifies, H+ ions combine with carbonate ions to produce bicarbonate Carbonate is required for calcification by many marine organisms CHAPTER 4: CARBON AND THE MOLECULAR DIVERSITY OF LIFE Organic Chemistry is the study of carbon compounds Although cells are 70-95% water, the rest consists mostly of carbon based compounds Organic compounds range from simple molecules to colossal ones Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atom’s characteristics Electron configuration determines the kinds and number of bonds an atom will form with other atoms The formation of bonds with Carbon  Carbon can form 4 covalent bonds with a variety of atoms  This tetravalence makes large, complex molecules possible  In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape  However, when two C atoms are joined by a double bond, the molecule has a flat shape Molecular Diversity Arising from Carbon Skeleton Variation 9 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Carbon chains form the skeletons of most organic molecules  Carbon chains vary in length and shape  Hydrocarbons are organic molecules consisting of only carbon and hydrogen  Many organic molecules, such as fats, have hydrocarbon components  Hydrocarbons can undergo reactions that release a large amount of energy Isomers  Compounds with the same molecular formula but different structures and properties  Structural isomers have different covalent arrangements of their atoms; same chemical formula but different structures of atoms and bonds  Geometric isomers have the covalent bonds to the same atoms, but differ in spatial arrangement ( cis and trans)  Enantiomers are isomers that are mirror images of each other o Important in the pharmaceutical industry o Two enantiomers of a drug may have different effects o Different effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules  Central carbon with 4 different groups bound to it is called the chiral center carbon; present in amino acids Functional groups are the parts of molecules involved in chemical reactions  Distinctive properties of organic molecules depend not only on the carbon skeletons but also on the molecular components attached to it  Certain groups of atoms are often attacked to skeletons of organic molecules. These functional groups have distinct chemical and physical properties  Functional groups are the components of organic molecules that are most commonly involved in chemical reactions o The number and arrangement of functional groups give each molecule its unique properties  the 7 functional groups that are most important in the chemistry of life: o hydroxyl group o carbonyl group o carboxyl group o amino group o sulfhydryl group o phosphate group o methyl group ______________________________________________ _________________ CHAPTER 5: STRUCTURE AND FUNCTION OF LARGE BIOLOGICAL MOLECULES How cells use organic compounds  Biological organisms use the same types of building blocks  All macromolecules have specific functions in cells  Other than water, macromolecules make up the largest percent mass of a cell Condensation and Hydrolysis 10 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Condensation/Dehydration synthesis o two molecules combine with loss of water to form larger molecules o requires enzymes and energy; enzymatic reaction o forms a strong covalent bond o 1 OH and H removed by DNA polymerase  Hydrolysis o A molecule splits into two smaller ones with the addition of water o Breaks bonds The Molecules of Life  Living cells synthesize: o Carbohydrates o Lipids o Proteins o Nucleic acids *Large polymers form from smaller monomers. New properties emerge Carbohydrates Used as energy and structural molecules (structural polymers); backbone Are soluble in water to provide energy Main types: o Monosaccharides o Disaccharides o Polysaccharides Monosaccharides (CH2O) o Major cell nutrient produced during photosynthesis, raw material for other molecules o 6 Carbon sugars (hexoses)  Glucose, fructose, galactose o 5 Carbon sugars (pentose)  Deoxyribose, Ribose Disaccharides o Sucrose (glucose + fructose); table/cane sugar o Lactose (glucose + galactose); milk sugar, unabsorbed in intestines if individuals lack lactase—leading to diarrhea o Maltose (glucose + glucose); beer, formed during the hydrolysis of starch by amylase o Formed by condensation reactions (glycosidic linkages created) o Broken down by specific enzymes Polysaccharides (complex carbohydrates) o 100s/1000s monosaccharides long o Made of same subunit o Energy storage  Starch (amylose/amylopectin) Digestible In plants only Forms ring in aqueous solutions  Glycogen (highly branched) In animals only o Structural support 11 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Cellulose Forms rings in aqueous solutions  Chitin Lipids  Large hydrocarbons; insoluble in water  Don’t form polymers  Dissolve in nonpolar substances (chloroform, ether)  Used for energy storage, structural, and chemical messenger  Lipids with fatty acids o Glycerides o Phospholipids o Waxes  Lipids with no fatty acids o Steroids Fatty Acids  Carbon backbone (4-24 carbon atoms)  Carboxyl group (-COOH)  Methyl group makes it nonpolar  Unsaturated o One or more double bonds in backbone  Double bonds adds kinks  Saturated o All single bonds in backbone Triglycerides  Fats/neutral fats o Three fatty acids and a glycerol molecule o Condensation reactions forms ester linkage o Most abundant lipid o Non polar; contain no charged/polar functional groups  Functions o Energy storage in adipocytes o Insulation Phospholipids  Glycerol backbone  Two fatty acid tails (hydrophobic)  Phosphate-containing head (negatively charged therefore hydrophilic)  Amphipathic (both hydrophilic and hydrophobic)  Main materials of cell membranes Sterols  Steroids/sterols o No fatty acid tails o Four carbon ring o In eukaryotic cell membranes o Cholesterol in animal tissues  Precursor to sex hormones and bile salts 12 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 Waxes  Long chained fatty acids linked to alcohols or carbon rings  Cover plant parts (cuticle) o Help conserve water o Fend off parasites  Animals o Protect, lubricate, impart pliability to skin and hair o Repel water (bird feathers, exoskeleton of insects) Amino Acids and the Primary Structure of Proteins  Proteins o Enzymes (metabolism); create reactions in a timely manner o Structures (collagen and silk) o Transport and movement (lipoproteins, hemoglobin, actin/myosin, tublin) o Nutritious (egg whites, casein) o Hormones (chemical messengers, ex: insulin/growth hormone) o Immune system (antibodies)  Two classes: globular and fibrous  Proteins are made from a pool of amino acids Structure of Amino Acids  Central carbon atom  An amino group  A carboxyl group  A hydrogen atom  One or more atoms “R group”  Organisms use L form but not D Peptide Bond Formation  A type of condensation reaction  DNA holds instructions for RNAs, mRNA determines order of amino acids Protein Conformation  Conformation (shape) is determined by genes and it determines function and is the result of linear sequence of amino acids in a polypeptide  Folding, coiling and interactions of multiple polypeptide chains create a functional protein  4 levels of protein structure o Primary o Secondary o Tertiary o Quaternary Primary Structure  The unique, linear sequence determined by the mRNA  A change in one a.a. can affect every other level of structure  One letter change may or may not have a change Secondary Level of Protein Structure  Hydrogen bonding occurs between amino and carboxyl groups of amino acids 13 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Structures formed: o Alpha helix. Common in fibrous proteins, creates elastic properties o Beta Sheet. Antiparallel chains form sheet  Core of many globular proteins and inelastic fibrous proteins Tertiary Level of Protein Structure  Additional folding of secondary structure and bonding between R groups o Hydrogen bonds o Disulfide bridges (Strong) o Hydrophobic interactions o Ionic bonding Quaternary Level of Protein Structure  Two or more polypeptide chains joined by o Weak bonds (H-bonds) o Covalent bonds between sulfur atoms and R groups  Collagen (3 helical polypeptides)  Insulin (2 polypeptides)  Hemoglobin (4 globular polypeptides) Structural Changes by Denaturation  Denaturation: altering a protein’s native conformation and activity o Usually at the secondary and tertiary structures  Disruption of three dimensional shape of proteins o Temperature: thermal agitation (increasing kinetic energy) o pH and salts: additional H+/OH- or ions disrupts H-bonding, ionic and disulfide bridges o non polar solvents: protein turns “inside-out”  Some proteins have organic compounds attached o Glycoproteins, lipoproteins (common on membranes) Nucleotides and the Nucleic Acids Nucleotides o Sugar—ribose or deoxyribose o Phosphate group o Bases  Single or double carbon rings with Nitrogen Subunits of coenzymes o NAD+ and FAD ATP o Energy source for chemical reactions o Contains three phosphate groups Nucleic Acids—DNA and RNA Building blocks o Four kinds of nucleotides o Differ only in component bases Single Strand of Nucleic Acid A series of covalently bonded nucleotides 14 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 DNA  Double stranded  Hydrogen bonds between strands  Twisted helically  Four kinds of nucleotide monomers (A, T, C, G)  Encodes protein-building instructions RNA  Single stranded  Four kinds of nucleotide monomers (A, U, C, G)  Do not encode protein-building instructions  Key players in the protein-building processes  mRNA, tRNA, rRNA CHAPTER 6: A TOUR OF THE CELL Cells of Living Things  Prokaryotic o Usually single celled, can form colonies o No nucleus or membrane bound organelles o Metabolism through aerobic and anaerobic means o Genetic material localized (nucleoid) o Most have cell wall composed of peptidoglycan o No cytoskeleton—proteins move nutrients around o Circular DNA, one form of RNA polymerase  Bacteria and archaea  Eukaryotic o Kingdoms: lots in what used to be called Protista, Fungi, Plants, Animals o Nucleus membrane encloses DNA o Organelles that have membrane o RNA and protein synthesized in two different locations o Linear DNA molecules with non coding introns o More than one RNA polymerase o Controlled—perfect at certain functions o Compartments—organelles Cell Size and Shape  Surface to volume ration limits size of cells. Large cells require more raw materials o Volume (V) = cm^3 o Surface Area (SA) = cm^2 o Restrictions on size and shape  Cells compartmentalize to increase SA/V, specialize reactions within, localize reactions where needed Small Compartments  Isolate areas of the cell. Allows for varied conditions in different regions (pH, concentration of solutes, etc) 15 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Each smaller structure can be specialized ( a multi-departmental large company versus small business) o Allows for increase in complexity o Leads to multicellularity  Provides surfaces for reactions (photosynthesis and respiration) Basic Aspects of Cell Structure and Function  Plasma membrane o Lipid bilayer—same basic architecture found in all membranous organelles o Proteins  Channels, transport, pumps, receptors  DNA-containing region  Cytoplasm o Area between outer membrane and nuclear membrane. The cytosol is the liquid/gel material containing water, gases, and macromolecules Major Cellular Components  Nucleus  Ribosomes  Endomembrane system o Endoplasmic reticulum, smooth and rough o Golgi body o Various vesicles  Mitochondria/chloroplasts  Cytoskeleton Components of the Nucleus  Accounts for about 6-10% of total cell volume  Membrane continuous with ER  Nuclear envelope: surrounds nucleus o Chromosomes: one DNA molecule and associated proteins, organized DNA o Chromatin: DNA molecules and histone proteins. Condenses to form chromosome.  Nucleolus: genes for rRNA that will be assembled into ribosomal subunits. Cells may have more than one The Nuclear Envelope  Double membrane system o Two lipid bilayers. 20-40nm thick o Surrounds chromatin/nucleoplasm  Nuclear pores regulate entrance/exit of ions and small proteins. Composed of a large number of proteins. It’s wider than it is thick. Passage through pore requires signal proteins and GTP  Nuclear lamina made of intermediate filaments, play a role in gene regulation Ribosomes  Smallest, most numerous organelle. Composition slightly different in prokaryotic and eukaryotic cells  Composed of rRNA (60%) and proteins (40%). Synthesized by nucleolus 16 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 o Large and small subunits  Found free and bound to E.R. Differ only in what they are making  Catalyzes formation of peptide bonds using RNA molecules The Endomembrane System  Organelles in which lipids are assembled and proteins are produced and modified  Are in direct contact or send vesicles (membrane-bound sacs)  Occupy ½ of cell volume  Nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuole The Endoplasmic Reticulum  Network of tubes and sacs that are continuous with nuclear membrane. Most extensive membrane system  Rough (ribosome studded) and smooth o Rough: production of secretory proteins. Signal sequence on polypeptide instructs ribosome to attack to ER o Smooth: lipid production, CH2O metabolism, storage of ions (Ca+), detoxification of drugs/alcohol  Proteins in membrane or within lumen catalyze reactions Golgi Bodies  Enzymatic finished on proteins and lipids, and packaging in vesicles  Cis (forming) face and trans (exit) face  Forms glycolipids, glycoproteins through the modification of proteins produced by ER. Enzymes in lumen catalyze addition/removal of parts  Produce some polysaccharides and also pectin for plant cell walls  Products of golgi leave as vesicles. From cisterna to another or out of cell Lysosomes  Membrane bound organelle that contains about 40 different hydrolytic enzymes responsible for the digestion of macromolecules, autolysis, intracellular digestion  Dead cells no longer able to maintain H+ gradient (uses H+ pump to maintain pH of 4.8), so organelle breaks down releasing contents  It works at low pHs because H+ is constantly be pumped by ATP; without it cells would die  Made by ER and Golgi o Common in white blood cells  Tay-Sachs is the result of faulty enzyme in lysosomes responsible for lipid breakdown in neurons  Carries out hydrolysis; can break down: o Nucleic acids with enzyme nuclease o Proteins with enzyme protease o Lipids with enzyme lipase o Carbohydrates to create usable monomers of macromolecules Vacuoles  Largest in plant cells  Storage of water or ions, pigments, hold food, pump out water  Are larger than vesicles from golgi/ER 17 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  In plants it is enclosed by Tonoplast (membrane) and provides cell with hydrostatic pressure Peroxisomes  H2O2, bi-product of lipid production  Contain enzymes (catalase) that break down H2O2 formed during metabolism of alcohols, fatty acids  Specialized forms (glyoxysome) found in seeds and function during germination  Self-replicating-imports proteins from cytosol Mitochondria  Production of ATP  Double-membrane system o Two distinct compartments  Have their own DNA, maternal in origin  Divide on their own, independent of cell  Have ribosomes, produce enzymes necessary for ATP production  Endosymbiont theory describes proposed origin of both mitochondria and chloroplasts Chloroplast  Two outer membranes  Semifluid stroma; site of carbon fixation  Inner thylakoid membrane system; converts light energy into chemical energy  Photosynthetic pigments found in other plastids Cytoskeleton Protein fibers that support and give shape to a cell, involved in organelle movement throughout cell, chromosome movement during cell division and large cell movements (cell motility and cytokinesis) 3 groups of fibers classified according to size: o Microtubules (thickest) o Intermediate filaments o Microfilaments (thinnest) Components of the Cytoskeleton  Microtubules o Alpha and beta tubulin subunits, form hollow tube o Provide framework for cell, organized by centrosome from which they usually originate o “rail” system for organelle transport  Component of centriole o Replicated prior to mitosis  Form cilia and flagella o 9 + 2 arrangement (eukaryotic characteristic) Cilia and Flagella and the Structural Basis of Cell Motility  Surrounded by plasma membrane  Motor proteins (dynein toward – end; kinesin toward + end) on microtubules use ATP to change shape and “ratchet” past one another 18 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1  Movement causes bending of cilia/flagella Microfilaments (actin filaments)  Solid rope of two actin proteins  Thinner and more flexible than microtubules  Principle component of muscle fibers  Provide mechanism to support cell shape. Found just inside the cellular membrane  Enable cell movement, phagocytosis and cytokinesis Intermediate Filaments  Tough and durable, made of keratin  Mechanically strengthen/reinforce cells or cell parts that are under stresses o Provide structure to long cells o Found in desmosomes o Give nucleus shape (nuclear lamina) Cell to Cell Junctions  Plants o Plasmodesmata  Perforations in cell wall that allow passage for water/solutes to adjacent cells  Animals o Tight junctions: prevent leakage between cell (in stomach) o Desmosomes: mechanically attach cells to each other, serve as anchoring sites for interfilaments in cells o Gap junctions: analogous to plasmodesma, function as common pathway between cells. Cardiac muscle, nerves Plant Cell Walls Protect plants, allow for shape and prevent excess H2O uptake o Composed of cellulose Plasmodesmata connect with neighboring cells when alive Secondary cell wall inside of primary wall, forms wood Cell secretions form pectin (polysaccharide glue) which acts as adhesive o Laid down in middle lamella to hold cells together Extracellular Matrix (ECM) Intricate network of proteins and polysaccharides that are organized into a meshwork on the outside of cells o Large polysaccharides and proteoglygans form a “gel-like” material that resist compression o Proteins like collagen (most abundant protein in animals as part of bone and skin) and elasin (stretch and recoil) provide structure and strength Adhesive-like proteins (fibronectins and laminin) help cells attach to the appropriate part of the ECM 19 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 CHAPTER 7: MEMBRANE STRUCTURE AND FUNCTION  The plasma membrane is the boundary of life. Like all biological membranes, it has selective permeability, allowing some materials to cross it more easily than others. According to the fluid mosaic model, biological membranes consist of various proteins that are attached to or embedded in a bilayer of amphipathic phospholipids The Fluidity of Membranes  Membranes are held together by weak hydrophobic interactions o Lateral movements of phospholipids is rapid o Proteins move slower and in a directed matter (most are immobile because they are attached to the cytoskeleton and extracellular membrane)  Phospholipids with unsaturated hydrocarbon tails maintain membrane fluidity at lower temperatures because the kinks in the hydrocarbon chain prevent solidification  Remains fluid until phospholipids solidify at lower temperatures  Steroid more common in plasma membranes of animals, cholesterol, restricts movement of phospholipids and thus reduces fluidity at warmer temperatures o Also prevents close packing of lipids and so it enhances fluidity at lower temperatures Evolution of Differences in Membrane Lipid Composition  Variations in membrane-lipid composition and the ability to change the composition in response to changing temperatures are evolutionary adaptations Membrane Proteins  Integral proteins: transmembrane proteins o Center is hydrophobic and outer edges are hydrophilic o Have hydrophilic channels through the center  Peripheral proteins: not embedded; loosely bound to integral proteins o Support for plasma membrane Functions of Proteins 1. Transport a. Hydrophilic channel b. Change shape c. Hydrolyze ATP to pump substances 2. Enzymatic Activity a. Membrane protein may be an enzyme with active site exposed 3. Signal Transduction pathway a. Membrane protein (receptor) has binding site with specific shape b. External messenger (signaling molecule) cause proteins to change shape by binding to it 4. Cell to cell recognition a. Glycoproteins serve as identification tags specifically recognized by membrane proteins of other cells b. Short-lived 5. Intracellular joining 20 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 a. Membrane proteins of adjacent cells hook through junctions b. Long-lived 6. Attachment to cytoskeleton and extracellular membrane a. Microfilaments non-covalently bound to membrane proteins b. Maintains cell shape and stabilized location of membrane proteins Diffusion  Solutes move from a high concentration to a low concentration; down concentration gradient due to thermal motion  Diffusion of one solute is unaffected by the concentration gradient of other solutes  Passive transport: diffusion of substances across biological membranes o Permits solute to move in either direction; net movement occurs down its concentration gradient H2O Balance of Cells Without Walls  Tonicity: ability of surrounding solution to cause a cell to gain or lose H2O o Depends on the solute concentration that cannot pass the membrane  Osmoregulation: control of solute concentration and water balance H2O Balance of Cells with Walls Walls help maintain H2O balance Turgor pressure: opposes further uptake of water Facilitated Diffusion  Passive transport of polar molecules or ions aided by proteins (proteins speed movement)  Channel proteins—ion channels/aquaporin o Gated channels  Carrier proteins change shape  Ligand channels Active Transport  Pump a solute against its gradient  Uses carrier proteins (allows cell to maintain a gradient different than its surroundings)  Cytoplasmic side is negatively charged and the extracellular side is positively charged  Membrane potential favors passive transport of cations into the cell and anions out  Two forces drive the diffusion of ions: o Chemical force (the ions’ gradient) o Electrical force (effect of membrane potential on ions’ movement)  Some membrane proteins that transport ions contribute to the membrane potential Electrogenic Pump  Transport protein that generates voltage across membrane by active transport of ions (stores energy for cellular work) o Na-K pump (animals): maintains osmotic balance and establishes electrochemical gradient  Antiporter: results in net negative charge in cell, hydrolyzes ATP to move ions 21 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR MIDTERM 1 o Proton pump (plants, bacteria, fungi): actively transports H+ out of cell Cotransport  Single ATP powered pump that transports specific solute and indirectly drives active transport of other solutes  Plants: load sucrose made by photosynthesis in leave veins  Animals: helps with diarrhea (Na levels drop as too much waste is expelled. NaCl and glucose allos solutes to be taken up by the Na-Glucose cotransporters and pass into the blood) Exocytosis Process by which the smooth and rough ER replace lipids and proteins lost from the plasma membrane  Cell secretes biological molecules by fusion of a vesicle with the plasma membrane  Contents of vesicles spill to the outside of the cell, vesicle becomes part of the plasma membrane  Does not move water and solutes out of the cell; only removes large, insoluble particles  Used by secretory cells to export products o Delivers proteins and carbohydrates from the golgi body to outside of the cell when making the plant cell wall Endocytosis  Cells take in biological molecules and particulate matter by forming new vesicles from the plasma membrane  Means by which large protein molecules enter cells  Small area of plasma membrane sinks inward, forms pocket and pinches in Receptor Mediated Endocytosis  Enables cells to acquire specific substances from the extracellular fluid  Human cells taken in cholesterol for membrane and steroid synthesis o Cholesterol binds to LDL receptors on plasma membrane o Act like ligands: molecule that specifically binds to receptor site on another molecule Pinocytosis  Droplets of extracellular fluid are takin into the cell in small vesicles  Uptake of water and solutes into the cell by formation of vesicles at the plasma membrane 22


Buy Material

Are you sure you want to buy this material for

50 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Steve Martinelli UC Los Angeles

"There's no way I would have passed my Organic Chemistry class this semester without the notes and study guides I got from StudySoup."

Amaris Trozzo George Washington University

"I made $350 in just two days after posting my first study guide."

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Parker Thompson 500 Startups

"It's a great way for students to improve their educational experience and it seemed like a product that everybody wants, so all the people participating are winning."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.