Properties that distinguish living organisms from the non-living, inorganic world

·         Order

·         Regulation, homeostasis

·         Energy processing

·         Evolutionary adaptation

·         Growth and development

·         Response to the environment

·         Reproduction

 What, fundamentally, do we mean by this thing called science?

·         “to know”

·         Way of trying to learn how the physical world works

·         Reality based

·         Systematized, methods

·         Search for explanation and information

The Scientific Method

The process of scientific inquiry

1)      observations

2)      questions

3)      formulate testable hypothesis

4)      make a prediction (if…then)

5)      test prediction (further observations and experiments)

6)      results (either support or falsify hypothesis)

      can never provide final absolute proof

A well designed scientific experiment has...

·         Adequate controls, investigates a single variable at a time, large sample sizes, and is replicated, or the experiment is repeated to be sure the results are reproducible from trial to trial.

                                                 Proton

·         Subatomic particle with a single, positive, electrical charge found in the nucleus of an atom.

·         # of protons = characteristic of an element, same as # of electrons

·         Mass à heavy, about 1.7 x 10^-24

·         Charge à +1 (electrically charged)

Neutron

·         Subatomic particle having no electrical charge found in the nucleus of an atom.

·         Mass à heavy, 1.7 x 10^ -24

·         Charge à 0 (electrically neutral)

Electron

·         Subatomic particle with single negative electrical charge. One or more electrons move around the nucleus of an atom.

·         # of electrons = # of protons

·         Mass = light, 1/2000 that of a neutron or proton

·         Charge = -1 (electrically charged)

Element

·         Simplest kind of matter that can exist, any substance that cannot be broken down to any other substance by chemical reactions.

Ex. Oxygen, Carbon, Iron

Mass Number

Sum of the number of protons and neutrons in an atom’s nucleus. 

Atomic Number

The number of protons in the nucleus of an atom, unique for each element and designated by a subscript to the left of the elemental symbol.  

Isotopes

·         One of several atomic forms of an element, each with the same number of protons but a different number of neutrons, thus differing in atomic mass.

·         Unstable = gives off energy as radioactivity.

Electron Shells

·         correspond to energy levels

·         the outermost, or valence shell, determines the tendency of an element to form chemical    bonds.

·         An energy level of electrons at a characteristic average distance from the nucleus of an atom.

Compound

 a substance consisting of two or more different elements combined in a fixed ratio. 

Molecule

2 or more atoms held together by covalent bonds.

Atom

the smallest unit of matter that retains the properties of an element. 

Nucleus

(1) an atom’s central core, containing protons and neutrons. (2) the chromosome-containing organelle of a eukaryotic cell. (3) a cluster of neutrons.

Ion

  an atom or group of atoms that has gained or lost one or more electrons, thus acquiring a charge.

Cation

a positively charged ion

Anion

a negatively charged ion

Chemical Bond

An attraction between two atoms, resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms. The bonded atoms gain complete outer electron shells.  

Polar Covalent Bond

A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

·         (LOOK FOR O & N!)

·         HYDROPHILIC

Non Polar Covalent Bond

electrons are shared equally between two atoms of similar electronegativity.

·         HYDROPHOBIC

Hydrogen Bond

weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.

Covalent Bond

a sharing arrangement

Ionic Bond

resulting from the attraction between oppositely charge ions.

·         WEAK in water, water soluble.

Cohesion 

the binding together of like molecules often by hydrogen bonds.the way in which water beads up on a waxy surface.  

properties of water

high capacity for temperature moderation(due to high specific heat)

high capacity for evaporative cooling

ice floats b/c water is less dense as a solid

The properties of water as a solvent

good solvent for POLAR solutes

"universal solvent" 

BAD solvent for NONPOLAR solutes such as oils

water molecules have greater attraction for each other

Acid

compound that adds hydrogen ions when dissolved in water (H+) increses ion concentration of a solution.

Base

reduces hydrogen ion concentration of a solution

pH scale

0 = Very Acidic

7= Neutral

14 = Basic

Buffer

a substance that consists of acid and base forms in a solution that minimizes changes in pH when extraneous acids or bases are added to the solution 

Structural Isomers

have same molecular formula but differ in the covalent arrangements of their atoms

geometric isomers 

one of several compounds that have the same molecular formula and covalent arrangement but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds. 

Enantiomers

one of two compounds that are mirror images of each other.

functional groups

reactive groups of atoms that confer certain chemical properties. 

Hyrdroxyl Group

  a.       Structure: (-OH) a hydrogen atom is bonded to an oxygen atom.

b.      Compound: Alcohols (usually names ending in –ol)

c.       Functional Properties:

                                                              i.      Is polar as a result of the electrons spending more time near the electronegative oxygen atom.

                                                            ii.      Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

Carbonyl

a.       Structure: (=CO) carbon atom double bonded to a oxygen atom.

b.      Compound: Ketones – if carbonyl group is within a carbon skeleton.

Aldehydes – if at the end of carbon skeleton.

c.       Functional Properties:

                                                              i.      A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

                                                            ii.      These two groups are also found in sugars, giving rise to 2 major groups of sugars, aldoses and ketoses.

a.       Structure: (-COOH) oxygen atom double bonded to a carbon atom that is also bonded to an –OH group.

b.      Compound: Carboxylic acids, or organic acids

c.       Functional Properties:

                                                              i.      Has acidic properties (is a source of hydrogen ions) because covalent bond between oxygen and hydrogen is so polar.

                                                            ii.      Found in cells in the ionized form with a charge of 1 – and called a carboxylate ion.

a.       Structure: (-NH2) nitrogen atom bonded to two hydrogen atoms.

b.      Compound: Amines

c.       Functional Properties:

                                                              i.      Acts as a base; can pick up an H+ from the surrounding solution (water in living organisms).

                                                            ii.      Ionized, with a charge of 1+, under cellular conditions.

Sulfhydryl

a.       Structure: (-SH or HS-) sulfur atom bonded to hydrogen atom.

b.      Compound: Thoils

c.       Functional Properties:

                                                              i.      Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.

                                                            ii.      Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair.

a.       Structure: (P) phosphorus atom is bonded to 4 oxygen atoms; 1 oxygen is bonded to the carbon skeleton; 2 oxygens carry negative charges.

b.      Compound: Organic phosphates

c.       Functional Properties:

                                                              i.      Contributes negative charge to the molecule of which it is a part.

                                                            ii.      Has the potential to react with water, releasing energy.

Polymer

A long molecule consisting of many similar or identical building blocks linked by covalent bonds.

Condensation Reaction > Dehydration Reaction

A reaction in which two molecules are covalently bonded to each other through loss of a water molecule

Hydrolysis Reaction

Chemical process that splits molecules by the addition of water, functioning in disassembly of polymers and monomers.

Carbohydrates

o   Sugars or polymers of sugars

o   Transport or store energy

o   Structure

o   Hydrophilic – water soluble, polar

Monosaccharides

o   Glucose, fructose, diverse (many isomers)

Disaccharides

o   Aka sugars, sucrose = table sugar, lactose = milk sugar

Polysaccharides 

Lipids

·         Extremely hydrophobic b/c predominantly hydrocarbon

Fats/ Oils

o   a fat (or oil) molecule is made by bonding three fatty acids to a molecule of

glycerol.

o   Saturated fatty acids – saturated with hydrogen.

o   Unsaturated fatty acids – has one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton.

o   The level of saturation of its component fatty acids affects the physical properties of a fat.

Phospholipids

o   Make up cell membranes.

o   Only has 2 fatty acids attached to glycerol

o   Has hydrophilic (polar) head and two hydrophobic (nonpolar) tails

§  When added to water they self assemble into double layered bilayers that shield their hydrophobic portions from water.

Steroids

o   Includes cholesterol (important in animal membrane structure) and many hormones.

Enzymatic Protein

  Selective acceleration of chemical reactions

Structural Protein

Provides Support

Storage Protein

Storage of amino acids

Transport protein

transport of other substances

Hormonal Protein

coordination of an organism's activities 

Receptor Protein

response of cell to chemical stimuli

Defensive Protein

protection againse disease

Peptide Bond

the covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction. 

·         unique sequence of amino acids

if the pH, salt concentration, temperature, or other aspects of its environment are altered, the protein may unravel and lose its native shape. Mis-shapen proteins = biologically inactive.

protein molecules that assist in the proper folding of other proteins. They keep the new polypeptide segregated from “bad influences” in the cytoplasmic environment while it folds spontaneously.  

·         Polymers of nucleotides and are involved in the storage and transfer of genetic information in cells

·         Two types of Nucleic Acids:

1.)    DNA

2.)    RNA

o   enable living organisms to reproduce their complex components from one generation to the next

·         The Importance of Ratio of Surface Area to Volume

o   For each square micrometer of membrane, only a limited amount of a particular substance can cross per second.

                                  Prokaryotic Cells

o   Lacking a membrane-enclosed nucleus and membrane enclosed organelles.

o   Bacteria and archaea.

                                       Eukaryotic Cells

o   Cell WITH a membrane-enclosed nucleus and membrane-enclosed organelles.

o   Protists, plants, fungi, and animals.

                           In animal cells but NOT in plant cells…

1.)    Lysosmomes

2.)    Centrosomes with centrioles

3.)    Flagella (but present in some plant sperm)

·         In plant cells but NOT in animal cells…

1.)    Chloroplasts

2.)    Central vacuole

3.)    Cell wall

Membrane enclosing the cell. Acts as selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the entire cell.

Network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough and smooth regions.

-    Smooth ER: lacking ribosomes; synthesis of lipids, metabolism of carbohydrates, detox of drugs and poisons.

-    Rough ER: studded with ribosomes; makes secretory proteins; membrane factory for the cell; makes its own membrane phospholipids.

where products of the ER are modified and stored and then sent to other destinations; consists of flattened membranous sacs.

                                     Endomembrane System

o   Includes…nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, various vacuoles, and the plasma membrane.

o   Synthesis of proteins and their transport into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of proteins.

·         How does a food vacuole form?

o   Phagocytosis, fuses with lysosome whose enzymes digest the food.

·         Energy Processing in Mitochondria

o   Site of cellular respiration, process that generates ATP by extracting energy from sugars, fats and other fuels with help of oxygen.

·         Energy Processing in Chloroplasts

·         Functions of the Cytoskeleton

o   Structure, movement (flagella, cilia, muscle contraction), vesicle transport, changes in cell size and shape.

1.)    Tight Junction: water tight (ex. Skin, intestinal tract).

2.)    Desmasome: (anchoring junctions)

3.)    Gap Junction: (Communicating Junctions) cytoplasmic connections, planarian lab.

The main lipid component of biological membranes that forms the cell surface membrane and consists of a hydrophobic inner core region sandwiched between two regions of hydrophilicity.

Functions of Membrane Proteins

1.      Transport

2.      Enzymatic activity

3.      Signal transduction

4.      Cell-cell recognition

5.      Intercellular joining

6.      Attachment to cytoskeleton and extracellular matrix

Fluid Mosaic Model

The membrane is a fluid structure with a “mosaic” of various proteins embedded in or attached to a double layer (bilayer) of phospholipids.

Diffusion (Passive Transport)

Spontaneous movement of a substance down its concentration gradient, from high to low concentration.

Facilitated Diffusion à spontaneous passage of molecules or ions across a biological membrane with the assistance of specific transmembrane transport proteins.

Channel proteins

Function by having a hydrophilic channel that certain molecules or atomic ions use as a tunnel through the membrane.

Carrier Proteins

Hold onto their passengers and change shape in a way that shuttles them across the membrane.

The diffusion of water across a selectively permeable membrane. From lower to higher concentration.

Transport vesicles migrate to the plasma membrane, fuse with it, and release their contents.

Endocytosis

Molecules enter cells within vesicles that pinch inward from the plasma membrane.

1.      Phagocytosis

2.      Pinocytosis

3.      Receptor mediated endocytosis