UNIT ONE

Chapter One: The Science of Biology

Darwin’s Theory of evolution is the core of Biology.

• Biology - the study of living things

  • The diversity of life is overwhelming.

  • All living things share common features.

Biological Diversity

• divided into 3 domains.

  • organisms in domains share similar characteristics.

    • Bacteria

    • Archaea

    • Eukarya

      • can be divided into 3 multicellular kingdoms.

        • Fungi

        • Plantae

        • Animalia

        • Protists - mostly unicellular, diverse

no common ancestor unlike the eukaryotic kingdoms

Life Defies Simple Definition

• Living and non-living organisms share properties.

• All living things share fundamental properties passed down from the first organisms that evolved on earth.

Fundamental Properties of Life

Cellular organization

• All living things have 1 or more cells.

• cells carry out the basics of living.

• some are more complex.

Energy Utilization

• All living things use energy.

• Moving, growing, and thinking requires energy.

• Energy is captured from sunlight by plants and algae through photosynthesis.

• Other organisms extract energy from plants or from plant-eating animals.

Homeostasis

• All living things maintain relatively constant internal conditions.

• Organisms keep their interior conditions relatively constant even when the environment varies.

Growth, Development, and Reproduction

• Bacteria increase in size and simply split into two.

• Multicellular organisms grow by increasing the number of cells and develop by producing different kinds of cells.

Heredity

• All organisms possess a genetic system based on the replication and duplication of DNA.

• DNA transmits the characteristics of an organism from parent to offspring.

Hierarchical Organization

Cellular level

• Atoms

• Molecules

• Macromolecules

• Organelles

• Cells

  • The cell is the basic unit of life.

Organismal Level

• Tissues

• Organs

• Organ Systems

• Organism

Population Level

• The population of specific Species

• Community

Ecosystem Level

• Ecosystem

• Biosphere

  • Each level has emergency properties.

The Nature of Science

• Science aims to understand the natural world through observation and reasoning.

• Natural forces acting now have always acted.

  • The Fundamental nature of the universe has not changed since its inception.

The Scientific Process

Descriptive Science

• Observations lead to hypotheses.

• hypotheses are experimentally testable.

• Much of science is purely descriptive.

• classifying all life on earth: Sequencing of Human Genome

Logical Reasoning

• Two types

  • Deductive Reasoning

    • Applies to general Principles to predict specific results.

    • Deductive Reasoning is used to infer the species of a specimen from its characteristics.

  • Inductive Reasoning

    • Uses specific observations to construct general scientific principles.

Hypothesis-Driven Science makes and tests Predictions.

• Observation

• Hypothesis Formation

• Prediction

• Experimentation

• Conclusion

Hypothesis – possible explanation for an observation

• Must generate testable predictions.

• Tested by experiments.

• Hypotheses are either supported or rejected.

  • If rejected, can be modified or written anew.

  • Supported hypotheses are subject to replication, additional testing and being refined with new data.

Hypothesis testing

• State hypothesis- be precise.

• State Predictions/assumptions

  • If support them?

  • If false, then?

• Design study that tests those predictions

Experiment

• Tests hypothesis

• Consists of an experimental treatment and a control group

  • Experimental treatment, the variable of interest is altered to test a particular hypothesis.

  • Control group, the variable of interest is left unaltered.

    • Independent variable – manipulated.

    • Dependent- measured/observed.

Important to include…

• Control groups

• Conditions must be constant or equivalent (if possible)

• REPEAT!

Scientific theories

Theory

• Proposed explanation for a natural phenomenon: based on general principles.

• Body of interconnected concepts to explain facts: supported by scientific reasoning and experimental evidence.

  • Expresses the ideas of which we are most certain.

Cell Theory

• Cell is the smallest unit if life – Robert Hooke

• All Living thins are made of cells – Schwann and Schleiden

• Biogenesis life comes with pre-existing life – Rudolf Virchow (Rejection of theory of spontaneous generation

Philosophical Approaches to Science

• Reductionism

  • To break a complex process down to its simpler parts

• Systems biology

  • Examines the whole of a system as well as the workings of the parts.

• Models are used in science.

  • Models help us to organize thought.

  • Parts provided by reductionist approach.

  • Model shows how the parts fit together.

  • Suggest experiments to test the model.

Science as a social construct

Research results are published in scientific journals.

• Experiments and conclusions are reviewed by other scientists.

• Other scientists can use the publication to reproduce the experiment.

Challenges may exist with reproducibility of experiments.

• Misuse of statics, scientific fraud, and others

Example of scientific inquiry: Evolution

Charles Darwin

• Not the first to propose evolution.

  • Living things have changed over time.

• Darwin contribution was a mechanism.

  • Natural selection

• Darwin saw those characteristics of similar species varied from place to place.

  • Finches

    • 14 related species differ only slightly.

Thomas Malthus’s an Essay on the Principle of Population

• Populations of plants and animals increase geometrically.

• Humans can only increase their food supply arithmetically.

• Populations of species remain constant because death limits population numbers.

Selection

• Darwin saw that although every organism has the potential to produce more offspring, only a limited number do survive and reproduce themselves.

• Those with advantageous traits are more likely to survive and reproduce.

  • Frequency of such traits increases in the population.

  • Nature of the population changes

• Natural Selection

  • Darwin proposed that a natural process could select for certain advantageous traits.

    • Darwin read Wallace’s hypothesis of evolution by means of natural selection.

    • Darwin and Wallace combined ideas

  • Nature based.

• Artificial selection

  • Cosmetic

    • Ex: dog breading

Evidence supporting Darwin’s Theory

Fossil record

• Transitional forms have been found at predicted positions in time.

• Fossils show life on Earth back about 3.5 billion years ago.

Comparative Anatomy

• Vertebrate forelimbs all share the same basic array of bones.

• Homologous – same evolutionary origin but now differ in structure and function.

• Analogous – structures of different origin used for the same purpose (wings)

• Molecular Evidence

  • Compare genomes or proteins of different organisms.

  • Phylogenetic Trees – based on tracing origin of particular nucleotide changed to reconstruct an evolutionary history.

    • Tree of Life = phylogenetic tree

      • Vocab

        • Taxonomy – science of classification – naming

        • Taxon – Named Group

        • Phylogeny – Evolutionary history of a group(s) – Relationships

        • Phylum – Major branch on tree

        • K, P, C, O, F, G, S – not really works.

Scientific Name

• Ex Latin name

  • Homo Sapiens

5 Concepts that unify biology.

Life is subject to chemical and physical laws.

• Living systems operate according to chemical and physical principles.

• Biological systems are the ultimate application of chemistry.

  • EX:

    • Movement of water in plants

    • Kidneys as an Osmotic machine

Structure determines function.

• Study structure to learn function.

• Know a function – look for that structure in other organisms.

  • EX:

    • Receptor on human cell for insulin known.

    • Find similar molecules in a worm.

    • Might be concluded that this molecule functions the same in the worm.

Living systems transform energy and matter.

• Constant supply of energy needed.

• Self- organizing properties at different levels

• Emergent properties from collections of molecules, cells, and individuals

  • EX

    • Spindle apparatus

Living systems depend on information transactions.

• Deoxyribonucleic Acid (DNA) consists of sequences of nucleotides.

• Genome – entire set of DNA instructions

• Continuity of life depends on faithful copying of DNA into daughter cells.

• Cells are information-processing systems.

  • Information in DNA is used to direct synthesis of cellular components.

    • Control of gene expression leads to different cells/tissue types.

  • Cells process environmental information.

Evolution explains the Unity and diversity of life.

• All organisms today descended from a simple creature 3.5 BYA.

• Some characteristics are preserved – Use of DNA

• Conserved characteristics have a fundamental role.

Chapter 2: The Nature of Molecules and the Properties of Water

All Matter is Composed of Atoms

• Matter has mass and occupies space

• All matter is composed of atoms

• Atoms are composed of subatomic particles

Atom Structure

• Atoms are composed of three types of subatomic particles

Protons

• Positively charged

• Located in the nucleus

Neutrons

• Neutral Particles

• Located in the Nucleus

Electrons

• Negatively charged

• Found in orbitals surrounding the nucleus

Atomic Number

• The number of protons equals the number of electrons

  • Atoms are electrically neutral

• Atomic number = Number of Protons

  • Every atom of a particular element has the same number of protons

• Element

  • Any substance that cannot be broken down into any other substance by ordinary chemical means.

Atomic Mass

• Mass or Weight?

  • Mass - Refers to the amount of substance

  • Weight - Refers to the gravity exerted on a substance

• Sum of protons and neutrons is the atom’s atomic mass

• Each proton an neutron has a mass of aproiximately 1 Dlaton

Electrons

• Negatively charged particles located in orbitals

• Neutral atoms have same number of electrons and protons

• Ions are charged particles - unbalanced

  • Cation- more protons than electrons = net positive charge

  • Anion - fewer proteins that electrons = net negative charge

Isotopes

• Atoms of a single element that possess different numbers of neutrons

• Radioactive isotopes are unstable and emit radiation as the nucleus breaks up

  • Half-life - time it takes for one-half of the atoms in a sample to decay

Electron Arrangement

• Key to the chemical behavior of an atom lies in the number and arrangement of its electrons in their orbitals

  • Bohr model - electrons in discrete orbits

• Modern physics defines orbital as area around a nucleus where an electron is most likey to be found

• No orbital can contain more than two electrons

Atomic energy levels

• Electrons have potential energy related to their position

  • Electrons farter from the nucleus have more energy

• Be careful not to confuse these two:

  • Energy levels - drawn as rings to indicate an electrons energy

  • Orbitals - have a variety of three-dimensional shapes; indicate an electrons most likely location

Redox

• During some chemical reactions, electrons can be transfered from one atom to another

  • Still retain the energy of their position in the atom

    • Oxidation - loss of electron

    • Reduction - gain of electron

Elements

• Periodic table displays elements according to valence electrons

  • Valence electrons - Number of electrons in outermost energy level

• Inert (nonreactive) elements have all eight elements

  • Octet rule - atoms tend to establish completely full outer energy levels

    • There are 90 naturally occurring elements

    • Only 12 elements are found in living organisms in substantial amounts

    • Four elements make up 96.3% of human body weight: C,H,O,N

    • Organic molecules contain primarily C,H,O,N

    • Some trace elements are very important

Chemical Bonds

• Molecules - groups of atoms held together in a stable association

• Compunds - molecules containf more than one type of element

• Atoms are held together in molecules or compounds by chemical bonds

Ionic Bonds

• Formed by the attraction of oppositely charged ions by electrostatic force

• Ions form when the atom has a grain or loss of electrons

  • Na atom loses an electron to become Na+

  • Cl atom gains an electron to become Cl-

  • Opposite charges attract so that Na+ and Cl- remain assosiated as an ionic compound

• Electrical attraction of water molecules can disrupt forces holding ions together

Covalent Bonds

• Form when atoms share 2 or more valence ekectrons

• Results in no net charge, satisfies octet rule, no unpaired electrons

• Strength of covalent bond depends on the number of shared electrons

• Many biological compounds are composed of more than 2 atoms - may share electrons with more atoms

Electronegativity

• Atoms affinity for electrons

• Differences in elctroneagativity dictate how electrons are distributed in covalent bonds

  • Nonpolar covalent bonds - equal sharing of electrons

  • Polar covalent bonds - unequal sharing of electrons

Hydrogen bonds

• Electropositive hydrogen from one polar molecule is attracted to an electronegative atom that is often oxygen

  • Attraction produces hydrogen bonds

  • Each individual bond is weak and transitory

  • Cumulative effects are enormous

  • Responsible for many of waters important physical properties

Vande Waals Attraction

• Weak bond

• Non-directional attractive force called van der Waals forces

• Form when two atoms are very close to one another

  • Antibodies recognize the shape of an invading organism with this bond

Chemical reactions

• Chemical reactions involve the formation or breakin gof chemical bonds

• Atom sshift from one molecule to another without any change in number or identity of atoms

  • Reactants - original molecules

  • Products - molecules resulting from reaction

• Extent of chemical reaction influenced by:

  • Temperature

  • Concentration of reactants and products

  • Cataysts

• Many reactions are reversible

Water

• Life is inextricably tied to water

• Single most outstanding chemical property of water is its ability ot form hydrogen bonds

  • Weak chemical associations that form between the partially negative O atoms and the partially positive H atoms of two water molecules

Polarity of water

• Within a water molecule, the bonds between oxygen and hydrogen are highly polar

  • Oxygen is much more electronegative than hydrogen

• Partial electrical charges develop:

  • Oxygen is parialy negative δ+

  • Hydrogen is partially positive δ-

    • δ - PARTIAL

Properties of water

• Water has a high specific heat

  • A large amount of energy is required to change the temperature of water

• Water has a high heat of vaporization

  • The evaporation of water from a surface causes cooling of that surface

• Solid water is less dense than liquid water

  • Bodies of water freeze from top down

• Water is a good solvent

  • Water dissolves polar molecules and ions

• Water organizes nonpolar molecules

  • Hydrophobic - water-fearing

  • Hydrophilic - water-loving

  • Water causes hydrophobic molecules to aggregate or assume specific shapes

Acids and Bases

• Water can form ions

• Pure water

  • [H+] of 10^-7 mol/L

  • Considered to be neutral

  • Neither acidic nor basic

• pH is the negaitive logorithm of hydrogen ion concentration of solution

Acid

• Any substance that dissociated in water to increase the [H+] (and lowers the pH)

• The stronger an acid is, the more hydrogen ions it produces and the lower its pH

Base

• Substance that combines with H+ dissolved in water and thus lowers the [H+] (and raises the pH)

Buffers

• Substances that restits changes in pH

• Act by:

  • Releasing hydrogen ions when a base is added

  • Absorbing hydrogen ions when acid is added

• Overall effect of keeping [H+] relatively constant

Biological buffers

• Most Biological Buffers constit of a pari of molecules, one an acid and one a base

Chapter 3: The Chemical Building Blocks of Life

Carbon

• Framework of biological molecules constisr primarily of carbon boned to:

  • Carbon

  • O,S,N,P,or H

• Can form up to 4 covalent bonds

  • Hydrocarbons - Molecule only of carbon and hydrogen

    • Nonpolar

    • Functional groups add chemical properties

Isomers

• Molecules with the same molecular or empirical formula

  • Structural isomers

  • Stereoisomers - differ in how groups attached

    • Enantiomers

      • Mirror image molecules

      • Chiral

      • D-sugars and L-amino acids

Macromolecules

• Four general Classes

  • Carbohydrates

  • Proteins

  • Nucleic acids

  • Lipids (not polymers)

    • Polymer - Built by linking monomers

    • Monomer - Small similar chemical subunit

  • Dehydration synthesis

    • Formation of large molecules by the removal of water

    • Monomers are joined to form polymers

  • Breakdown of large molecules by the addition of water

  • Polymers are broken down into monomers

Carbohydrates

• Molecules with a 1:2:1 Ratio of carbon, hydrogen, oxygen

• Empirical formula (CH2O)

  • C–H covalent bonds hold much energy

    • Carbohydrates are good energy storage molecules

      • EX:

        • Sugars

        • Starch

        • Glucose

Monosaccharides

• Simplest carbohydrates

• 6 carbon sugars play important roles

• Glucose C6H12O6

• Fructose is a structural isomer of glucose

• Galactose is a stereoisomer of glucose

• Enzymes that act on different sugars can distinguish structural and stereoisomers of this basic six-carbon skeleton

Disaccharides

• Two monosaccharides linked together by dehydration synthesis

• Used for sugar transport or energy storage

  • Ex:

    • Sucrose

    • Lactose

    • Maltose

Polysaccharides

• Long chains of monosaccharides

  • Linked through dehydration synthesis

• Energy Storage

  • Plants use starch

  • Animals use glycogen

• Structural support

  • Plants use cellulose

  • Arthropods and fungi use chitin

Proteins

• Functions include

  • Enzyme Catalysis

  • Defense

  • Transport

  • Support

  • Motion

  • Regulation

  • Storage

Amino Acids

• Proteins are polymers

  • Composed of 1 or more long unbranched chains

  • Each chain is a polypeptide

• Amino acids are monomers

• Amino acid structure

  • Central carbon atom

  • Amino group

  • Carboxyl group

  • Single hydrogen

  • Variable R group

R Groups

• Determine the chemistry of amino acid

  • Nonpolar – leucine

  • Polar Uncharged – Theronine

  • Charged – Glutamic Acid

  • Aromatic – phenyalaline

  • Unique – Proline and cysteine

    • Amino acids joined by dehydration synthesis - Peptide bond

Protein Structure

• The shape of a protein determines its function

Primary and Secondary

• Primary - sequence of amino acids

• Secondary - Interaction of groups in the peptide backbone

  • α helix

  • β sheet

Tertiary and Quaternary

• Tertiary - final folded shape of globular protein

  • Stabilized by a number of forces

  • Final level of structure for proteins constituting of only a single polypeptide chain

• Quaternary Structure - Arrangement of individual chains (subunits) in a protein with two or more polypeptide chains

Additional Structural characteristics

Motifs

• Common elements of secondary structure seen in many polypeptides

• Useful in determining the function of unknown proteins

Domains

• Functional Units within a larger structure

• Most proteins are made of multiple domains that perform different parts of the protein's function

Chaperones

• Once thought newly made proteins foled spontaneously

• Chaperon proteins help proteins fold correctly

• Studies show that defective chaperone proteins can result in other proteins failing to fold properly

Denaturation

• Protein loses structure and function

• Due to environmental conditions

  • pH

  • Temperature

  • Ionic concentration of solution

Nucleic acids

• Polymer – Nucleic acids

• Monomers – nucleotides

  • Sugar + phosphate + nitrogenous base

  • Sugar is deoxyribose in DNA or ribose in RNA

  • Nitrogenous bases include

    • Purines: adenine and guanine

    • Pyrimidenes: thymine, cytosine, uracil

  • Nucleotides connected by the phosphodiester bonds

DNA vs RNA

DNA

• forms a double helix, uses deoxyribose, and uses thymine among nitrogenous bases

• ENcodes information for amino acid sequence of proteins

  • Sequence of bases

• Double helix - 2 polynucleotide strands connected by hydrogen bonds

  • Base pairing rules

    • A – T (or U if RNA)

    • C – G

RNA

• Usually single-stranded, uses ribose, and uses uracil in place of thymine

• Similar to DNA but…

  • Contains ribose instead of deoxyribose

  • Contains uracil instead of thymine

• Usually a single polynucleotide strand

• RNA uses information DNA to specify sequence of amino acids in proteins

  • mRNA

  • tRNA

  • rRNA

    • Other varieties as well

Other Nucleotides

• ATP - adenosine triphosphate

  • Primary energy currency of the cell

• NAD+ and FAD-

  • Electron carriers for many cellular reactions

Fat types

• Steroids

• Phospholipids

• Triglycerides

Lipids

• Hydrophobic lipids form fats and membranes

• Loosley defined group of molecules with one main chemical characteristic

  • Insoluble in water

• High proportion of nonpolar C–H bonds causes the molecule to be hydrophobic

  • EXAMPLES OF LIPIDS

    • Fats

    • Oils

    • Waxes

    • Some vitamins

Fats

Triglycerides

• Composed of 1 glycerol and 3 fatty acids

Fatty acids

• Need not be identical

• Chain length varies

• Saturated - no double bonds between carbon atoms

• Unsaturated - 1 or more double bonds

• Trans fats produced industrially

Phospholipids

• Composed of:

  • Glycerol

  • 2 fatty acids - nonpolar tails

  • A phosphate group - polar “head”

• Form all biological membranes

  • Micelles - lipid molecules orient with polar (hydrophilic) heads toward water and nonpolar hydrophobic tails away from water

  • Phospholipid Bilayer - more complicated structure where 2 layers form

    • Hydrophobic heads point outwards

    • Hydrophobic tails point inward toward each other

Other kinds of lipids

• A terpenes are found in biological pigments, such as chlorophyll and retinal

• Steroids play important roles in membranes and as hormones involved in chemical signaling