bio lec notes

Biology 1020
Lecture 1
 Biology = the study of life 
 Life = is a thing of macromolecular cohesion in salty water -R Gilles
= we know it when we see it
 Dening the characteristics of life:
 order
 evolutionary adaptation
 response to environment
 regulation
 energy processing
 growth and development
 reproduction
 reproductive success of individuals with _______
 Evolution: the unifying theme of biology
 nothing in biology makes sense except in the light of evolution  - Theodosius Dobzhansky
(1900-1975)
 Evolution by natural selection
 Individuals in a population vary in their traits
 heritable traits are passed from parents to offspring
 a population produces more offspring than can survive
 Individuals with traits best suited for the local environment will survive and reproduce
 The suitable traits will become more and more common in the population
 population with varied inherited traits
 elimination of individuals with certain traits
 increasing frequency of traits that enhance survival and reproductive success
 from chemical to kinetic
 DNA and the continuity of life
 cell s genetic material
 GENES: units of inheritance
 DNA --> RNA --> protein
 proteins do the work of life
 Change in a DNA sequence --> change in the function of a protein
 Levels of biological organization
 biosphere = environments inhabited by life
 ecosystems = all the living and non-living component of an area
 non-living components : soil, water, grasses, light (abiotic)
 organisms interact with each other and the environment in ecosystems
 energy conversion and processing in ecsystems:
 Nutrients = are recycled with an ecosystem
 Energy = ows from producers to consumers
 communities = all organisms in an ecosystem
 populations = all individuals of a species
 organisms = individual living things
 organs and organ systems = carry out particular functions
 tissues = groups of similar cells make up organs
 cells = fundamental unit of life
 basic units of structure and function

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 all activities of an organism performed by cells
 growth is accomplished by division of cells
 organelles = components of cells
 molecules = chemical structure
 atoms
 Reductionism and emergent properties
 reducing complexity to manageable units
 lower levels not always predictive of higher levels emergent properties
 factors at multiple levels interact : _____ biology
 The human genome project
 2003 - complete human DNA sequence
 functions known for 50% of genes
 complexity revealed
 Systems biology = investigating how changes in one or more variables affect other components and the
whole system
 interactions of proteins in a fruit y cell
 Diversity of life
 Organizing the diversity of life
 3 domains of life
 Archaea >
 bacteria > prokaryotic
 Eukarya
 Classication of life
 Domain
 kingdom
 phylum
 class
 order
 family
 genus
 species
 unity in diversity
 biology as a science
 inquiry
 discovery science= describing
 hypothesis based science = explaining
 hypothesis = tentative answer
 experimental = control
 Theory = large body of evidence, broad scope, generates hypotheses
Lecture 2
 Emergent properties
 molecules --> organelle and cells
 Essential chemistry for biology
 life processes are chemical reactions and strings of chemical reactions
 Photosynthesis, respiration, etc.
 organisms are made of matter takes up space has mass
 matter made of chemical elements (or combination of elements) cannot be broken down into other
substances by chemical reactions

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 elements combine to form compounds - two or more elements in a xed ratio
 a compound has characteristics different from those of its elements
 essential elements
 25 of the 92 elements are essential to life
 trace elements are needed in minute quantities , can be essential
 Atoms = smallest unit of matter that still retains the properties of an element
 Sub -atomic structure
 electrons = are moving about the nucleus
 atoms are mostly empty space
 neutron mass and proton mass are almost identical (1.7 * 10 ^-24 g)
 use datons (same as atomic mass unit)
 neurons and protons are ~1 Da
 atoms of elements differ in number of protons and electrons
 atomic number is the number of protons in the nucleus
 an element s mass number = the sum of protons plus neutrons in the nucleus
 atomic mass = the atom s total ass, can be approximated by mass number
 electron mass is only 1/2000 that of a proton
 mass ignored when computing total mass
 upper number = mass number
 lower number = atomic number / number of protons
 number of neutrons = mass number - number of protons
 Isotopes = all atoms of an element have the same number of protons but may differ in number of
neutrons
 isotopes differ in number of neutrons
 radioactive isotopes or radioisotopes decay spontaneously, giving off particles and energy
 stable isotopes do not
 Applications of isotopes:
 dating fossils
 tracing atoms through metabolic processes
 diagnosing medical disorders
 treatment of medical disorders
 scintillation counter = detects radiation from isotopes
 Arrangement of electrons in elements
 electrons are attracted to the nucleus
 -ve attracted to +ve
 electrons are moving around the nucleus: some closer; some further from it
 electrons differ in their amounts of potential energy
 potential energy = is energy that comes from structure or location
 an electron s state of potential energy is called its energy level, or electron shell
 Potential energy
 gravity tends to pull ball toward ground, ball is attracted  toward ground, has potential energy by
being at the top of the stairs
 energy is released when it moves downward
 ball gains potential energy if i brought back up the stairs
 Electron distribution
 behavior of an atom is determined by the distribution of electrons in electron shells
 periodic table of elements indicates the electron distribution for each element
 valence electrons are those in the outermost shell or valence shell
 the chemical behavior mostly determined by the valence electrons

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 atoms with full valence shell are chemically inert
 electron orbitals
 electrons exist in 3 dimentional space
 an orbital is the 3d space where an electron is found 90% of the time
 s orbitals = are spherical
 p orbitals = are dumbbell shaped
 these orbitals give characteristic shape to the atoms
 rst shell = 1 orbital
 second shell = 3 orbitals
 orbitals from the two shells (four orbitals total) superimposed joining atoms in compounds results in
interaction of electrons in these orbitals
 atoms with ____ valence shells can share or transfer valence electrons with certain other atoms
 result in atoms staying close together, held by attractions called chemical bonds
 types of chemical bonds
 covalent
 ionic
 weak
 covalent bonding
 two atoms share a pair of valence electrons
 number of covalent bonds that can be formed = number of electrons in the outermost shell
 bonding capacity is called the atom s valence
 atoms with the same number of valence electrons tend to have similar behaviors
 this has implications for certain biological molecules
 in a covalent bond, the shared electrons count as a part of each atom s valence shell
 molecules are atoms joined together by covalent bonds
 a single covalent bond (single bond) is the sharing of one pair of valence electrons
 a double covalent bond (double bond) is the sharing of two pairs of valence electrons
 structural formula represents the binding between atoms
Lecture 3
 C
 Types of chemical bonds
 Covalent = sharing of electrons
 Ionic
 Weak
 Polar covalent bonds = Occurs when there is a sharing of electrons among atoms of a covalent bond
 electronegativity = attraction of the atom for electrons
 Oxygen is more electronegative, and pulls electrons toward it
 this results in it being slightly more negative, a partial negative charge
 Polarity plays an essential role in biological membrane structure
 ionic bonds occur when one of the pair of elements is so electronegative that it ____ from the partner
 the partners in the pair are called ions
 One of the partners becomes negatively charged- the anions
 The other become positively charged the cations
 Compounds formed by ionic bonds are called ionic compounds or salts
 Salts, such as sodium chloride (table salt), potassium chloride are often crystals
 Water __ salts = reduces the attraction of the cations and anions for each other
 Weak chemical bonds

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 ___, reversible
 reinforce shapes of large molecules and help molecules adhere to each other
 Can be important in ____ contact
 electrons are distributed asymmetrically in molecules or atoms
 can result in _____  of positive or negative charge
 collectively strong
 hydrogen bonding = hydrogen atom covalently bonded to one electronegative atom is also attracted
to another electronegative atom
 Molecular Shapes
 Shape important to function
 Shape determined by the positions of its atoms ____
 biological molecules interact with each other based on shape
 molecules with similar shapes can have similar biological effects
 Chemical reactions = making and breaking of chemical bonds
 reactants = starting molecules
 products = nal molecules
 Chemical reactions: photosynthesis
 conversion of carbon dioxide and water to glucose and oxygen
 6CO2 + 6H2O ---> C6H12O6 + 6O2
 all chemical reactions are reversible: products of the forward reaction become reactants for the
reverse reaction
 Chemical Equilibrium = is reached when the forward and reverse reaction rates are equal
 Water has properties that are conducive to life (on Earth)
 cohesive behavior
 H2O is a polar molecule: opposite ends have opposite charge
 water molecules from hydrogen bonds with each other
 hydrogen bonds hold water together - cohesion
 _____
 water transport in plants
 _____
 related to cohesion
 how hard it is to break the surface of a liquid
 moderates temperature
 water has a high _____ due to hydrogen bonding
 ________ is the total quantity of kinetic energy due to molecular motion
 ________ is the intensity of heat due to average kinetic energy
 Temperature moderation by water
 We apply _____ to change the ____
 specic heat of a substance = amount of heat that must be absorbed or loss for 1 g of that
substance to change its temperature by 1C
 Water has a high specic heat
 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
 Evaporation = transformation of a substance from liquid to gas
 As a liquid evaporates, its remaining surface cools, a process called evaporative cooling
 helps stabilize temperature in organisms and bodies of water
 expansion upon freezing
 Insulation = H-binding in ice i more ordered than in liquid wafer: ______

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 Water reaches is greatest density ______
 If ice sank, all bodies of water would eventually freeze solid, making life impossible on earth
 versatility as a solvent
 Water as a solvent
 A solution is a liquid that is a homogeneous mixture of substances
 a solvent is the dissolving agent of a solution
 the solute is the substance that is dissolved
 an aqueous solution is one in which water is the solvent
 Ionic compounds dissolved in water
 each ion is surrounded by a hydration shell
 water can also dissolve compounds made of nonionic polar molecules
 large polar molecules (ex. proteins) can dissolve in water if they have ionic and polar regions
 hydrophilic substance = has an afnity for water
 hydrophobic substance = doesn t have an afnity for water
 oil = relatively non polar bonds
 a colloid is a stable suspension of ne particles in a liquid
 Solutions: some terminology
 numbers of molecules are usually measure in moles where 1 mole (mol) = 6.02 * 10 ^23 molecules
 molarity (M) is the number of moles of solute per liter of solution (concentration)
 [H] concentration of hydrogen disassosiation
 Equilibrium of water
 a hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other
 H2O molecules ______ at the same rate at which they are being reformed
 The hydrogen atom eaves its electron behind and is transferred as a proton, ore hydrogen ion (H+)
 the molecule with the extra proton is now a hydronium ion (H3O+) (often presented as H+)
 the molecule that lost the proton is now a hydroxide ion (OH-)
 Acids and bases
 acid = increase H+ concentration of a solution
 base = decrease H+ concentration of a solution
 Aqueous solution 25C
 pH = -log[H+]
 [H+][OH-] = 10 ^ -14
 [H+] is 10 ^-7 = -(-7) = 7
 Acids donate H+ in aqueous solutions
 Bases donate OH- or accept H+ in aqueous solutions
Lecture 4
 A
 Acids = donate H+ in aqueous solutions
 bases = donates OH- or accept H+ in aqueous solutions
 pH = [H+][OH-] = 10 ^-14
 change pH 1 tenfold
 most biological uids have pH values in the range 6 to 8
 changes in concentrations of H+ and OH- can drastically affect the chemistry of a cell
 acidication of biological systems: acid precipitation
 caused by mixing of different pollutants with water in the air
 can fall at some distance from the sources of pollutants
 lakes and streams, soil chemistry

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 Oceans:coral bleaching and decrease in the ability of corals to forms calcied reefs
 Threats to water quality: coral reefs
 Acidication: coral bleaching decrease in CO3 2- decrease in calcication
 buffers
 the internal pH of most living cells must remain close to Ph 7
 buffers = substances that minimize changes in concentrations of H+ and OH- in a solution
 most buffers consist of an acid-base pair that reversibly combines with H+
 pH of human blood ~7.4
 CO2 produced from cellular respiration
 reacts with water
 H2CO3 (carbonic acid
 response to rising pH ----->
 response to drop in pH <-----
 Organic chemistry = chemistry of carbon containing compounds
 Carbon based life forms 
 Proteins, DNA, Carbohydrates, etc.
 What makes carbon suitable as the backbone of biological molecules? 
 Carbon has 4 electrons in the outer shell: it can hold 8 forms of covalent bonds to complete the shell
 CAn bind with up to ___ other atoms- _____
 Carbon atoms tend to bind with each other forming a backbone or chain with other elements or branch
points
 ethane = C2H6
 propane C3H8
 HYdrocarbons
 organic molecules consisting of only carbon and hydrogen
 can undergo reactions that release a large amount of energy
 Shape of carbon molecules
 multiple carbons molecules: each carbon bonded to four other atoms has a tetrahedral shape
 double bond - molecule has a at shape
 Isomers = molecules with the same molecular formula but different arrangements
 structural = have different covalent arrangements of their atoms
 geometric = have the same covalent arrangements but different spacial arrangements
 cis isomers = the two Xs are on the same side
 trans isomers = the two Xs are on the opposite side
 enantiomers = are mirror images of each other
 important in the pharmaceutical industry
 two enantiomers of a drug may have different effects
 organisms are sensitive to even subtle variations in molecules
 Thalidomide : 1960s
 phocomelia caused by one enantiomer
 Functional groups = are the components of organic molecules that are most commonly involved in
chemical reactions
 functional groups give each molecule its unique properties
 hydroxyl, = polar hydrogen bonds
 carbonyl,
 ketone = if the group is on the C skeleton; carbon double bonded to oxygen
 aldehyde= if it is on the end
 found in sugar
 carboxyl = acidic polar bond, carbon double oxygen single OH

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 amino, = acts as a base can pick up an H+, nitrogens single bonded to 2 hydrogens
 also has a carboxylic group
 sulfhydryl = cross link  proteins, sulfur single hydrogen
 Cysteine = an important sulfur-containing amino acid
 phosphate = contributes -ve charge reacts with water releasing energy
 phosphorus double oxygen single 3 oxygen
 Adenosine triphosphate
 methyl = non reactive, carbon single 3 hydrogens
 molecules are two or more atoms held together by covalent bonds
 they share one or more pairs of electrons, resulting in single or multiple bond
 The arrangement of electrons in orbitals in the individual atoms, and in the molecule determines it s
shape, which can be important in function
 Life on earth is carbon based; molecules are formed with a carbon skeleton and functional groups
Lecture 5
 E = oxygen is more electronegative than hydrogen
 Macromolecules
 macro - large
 thousands of small organic molecules joined together to form larger molecules
 joined together in a process called Polymerization
 A polymer isa long molecule consisting of smaller units called monomers
 monomers are joined together by condensation or hydrolysis
 polymers are formed by dehydration reactions
 Dehydration refers to the loss of a water molecule
 Hydrolysis of polymers
 hydro - water
 lysis - decomposition or breakdown
 hydrolysis adds a water molecule,breaking a bond
 many polymers can be made from a small set of monomers
 5 monomers: A B C D E F
 6+5+4+3+2+1 = 21 dimers AA, AB, AC, AD,..., FF
 Biological macromolecules
 Carbohydrates
 sugars and their polymers
 Monosaccharides are the simplest they are the monomers of the carbohydrate polymers
 have the formula CH2O
 glycosidic linkage
 Monosaccharides :
 hydroxyl and carbonyl
 Most names of sugars end in ose : ribose, glucose, lactose etc.
 Ribose - C5H10 O5
 grouped based on
 number of ____ in the skeleton
 ______ enantiomers
 Aldose: aldehyde sugar
 Ketose: ketone sugar
 Trioses

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 Pentoses
 Hexoses
 Disaccharide polymerization
 The covalent bond joining monosaccharides - GLYCOSIDIC linkage
 polysaccharides are hundreds to thousands of monosaccharides joined by these linkages
 biological roles of polysaccharides
 structural
 plants: cellulose
 arthropods, fungi: _____
 storage of surplus
 plants: starch
 _____: glycogen
 Storage polysaccharides
 starch
 Stored within chloroplast o plants as _____
 composed entirely of ______ monomers
 simplest starch is amylose unbranched helical
 Other forms are highly branched: amylopectin
 glycogen
 highly branched
 vertebrates store a days supply in the liver and muscles
 carbo loading  by athletes helps to ensure that the liver and the muscle glycogen stores
are high
 Structural polysaccharides
 cellulose
 composed of glucose monomers in a different arrangement than in starch
 cellulose molecules are straight because of this
 difference forms of starch and cellulose results from this difference in ring structure
 alpha glucose: helical polymers
 beta glucose: straight polymers
 What makes cellulose tough to digest?
 Cellulose: H+ atoms on one strand can bond with with OH- groups on other
 parallel cellulose molecules held together in microbrils
 building materials
 cows = cellulase
 Chitin
 Structural polysaccharide of arthropods and fungi
 LIpids
 Have little to no afnity for water - hydrophobic
 consist of mostly of hydrocarbons
 non-polar covalent bonds
 do not form polymers; but do store energy
 Are formed from dehydration reactions
 Glycerol = see gure at book
 Fatty acid
 a long hydration skeleton usually 16 or 18 carbons
 at one end is a carboxyl group
 the C-H bonds are non-polar: hydrophobic
 Fats

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 Triacylglycerols
 Three fatty acids linked to one glycerol
 Types of lipids
 Saturated/ Unsaturated (poly-unsaturated)
 some fatty acids have one or more double bonds
 no double bonds:
 maximum possible number of H
 Carbon skeleton: saturated with H
 Double bonds present: Unsaturated- contain less than the maximum number of H on the
carbon skeleton
 more than one double bond: polyunsaturated
 Double bonds add kinks to unsaturated fatty acids
 This results in the two types having different properties
 compare butter and olive to canola oil
 Plant and sh oils are liquid at room temperature: cis bonds prevent the molecules from
packing closely together
 Many animal fats are solid at room temperature
 Trans fats
 manufacturers hydrogenated vegetable oils to make them more solid at room
temperature
 This process produces saturated fats and unsaturated fats with trans double bonds
trans fats
 Phospolipids
 two fatty acids, and a phosphate group (charged) attached to glycerol
 small molecules can be attached to the phosphate groups
 Triacylglycerol
 Phospholipids self-assemble into a bilayer assemble in water
 hydrophobic tails pointing toward the interior
 cell membranes
 Steroids
 Lipids with a carbon skeleton made of four rings
 cholesterol is a steroid
 Synthesized in liver
 cell membranes
 precursor to other steroids such as sex hormones
Lecture 6
 E
 Biological macromolecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic acids
 Protein
 functional biological molecules
 one or more polypeptides
 folded and coiled
 3D

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