Membrane Structure and Function

Active Transport

the movement of a substance across a biological membrane against its concentration or electrochemical gradient with the help of energy input and specific transport proteins

Amphipathic Molecule

a molecule that has both a hydrophilic region and a hydrophobic region

Aquaporin

a transport protein in the plasma membrane of a plant or animal cell that specifically facilitates the diffusion of water across the membrane (osmosis)

Concentration Gradient

an increase or decrease in he density of a chemical substance in an area; cells often maintain concentration gradients of ions across their membranes; when a gradient exists, the ions or other chemica

Cotransport

the coupling of the downhill diffusion of one substance to the uphill transport of another against its own concentration gradient

Diffusion

the spontaneous tendency of a substance to move down its concentration gradient from a more to a less concentrated gradient

Electrochemical Gradient

the diffusion gradient of an ion, representing a type of potential energy that accounts for both the concentration difference of the ion across a membrane and its tendency to move relative to the memb

Electrogenic Pump

an ion transport protein that generates voltage across a membrane

Endocytosis

the cellular uptake of macromolecules and particulate substances by localized regions of the plasma membrane that surround the substance and pinch off to form an intracellular vesicle

Exocytosis

the cellular secretion of macromolecules by the fusion of vesicles with the plasma membrane

Facilitated Diffusion

the spontaneous passage of molecules and ions, bound to specific carrier proteins, across a biological membrane down their concentration gradients

Flaccid

limp; a walled cell is this in surroundings where there is no tendency for water to enter

Fluid Mosaic Model

the currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of individually inserted protein molecules drifting laterally on a fluid bi-layer of phospholipid

Gated Channel

a protein channel in a cell membrane that opens or closes in response to a particular stimulus

Glycolipid

a lipid covalently attached to a carbohydrate

Glycoprotein

a protein covalently attached to a carbohydrate

Hypertonic

in comparing two solutions, referring to the one with higher solute concentration

Hypotonic

in comparing two solutions, referring to the one with a lower solute concentration

Integral Proteins

typically a transmembrane protein with hydrophobic regions that completely spans the hydrophobic interior of the membrane

Ion Channel

a single protein or protein complex that traverses the lipid bilayer of cell membranes and form a channel to facilitate the movement of ions through the membrane according to their electrochemical gra

Isotonic

having the same solute concentration as another solution

Ligand

a molecule that binds specifically to a receptor site of another molecule

Membrane Potential

the change difference between a cell's cytoplasm and the extracellular fluid, due to the differential disribution of ions; membrane potential affects the activities of excitable cells and the transmem

Osmoregulation

the regulation of solute and water concentrations in body fluids by organisms living in hyperosmotic, hypoosmotic, and terrestrial environments

Osmosis

the diffusion of water across a selectively permeable membrane

Passive Transport

the diffusion of a substance across a biological membrane

Peripheral Proteins

a protein appendage loosely bound to the surface of a membrane and not embedded in the lipid bilayer

Phagocytosis

a type of endocytosis involving large, particulate substances, accomplished mainly by macrophages, neutrophils, and dendritic cells

Pinocytosis

a type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes

Plasmolysis

a phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall when the cell loses water to a hypertonic environment

Proton Pump

an active transport mechanism in cell membranes that uses ATP to force hydrogen ions out of a cell, generating a membrane potential in the process

Receptor-Mediated Endocytosis

the movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a a cell to acquir

Selective Permeability

a property of biological membranes that allows some substances to cross more easily than others

Sodium-Potassium Pump

a special transport protein in the plasma membrane of animal cells that transports sodium out of the cell and potassium into the cell against their concentration gradients

Tonicity

the ability of a solution to cause a cell within it to gain or lose water

Transport Protein

a transmembrane protein that helps a certain substance or class of closely related substances to cross the membrane

Turgid

very firm; a walled cell becomes turgid if it has a greater solute concentration than its surroundings, resulting in entry of water

Cells and Organelles

Organelles

membrane-enclosed compartments (subcellular structures)

Cell Fractionation

taking cells apart and separating the major organelles from one another

Prokaryotic Cell

a type of cell which has its DNA concentrated at the nucleoid, which is not surrounded by a membrane

Nucleoid

the area not enclosed by a membrane where the DNA is concentrated, in a prokaryotic cell

Eukaryotic Cell

a type of cell which has a true nucleus, and many organelles

Cytoplasm

the entire space between the nucleus and the plasma membrane

Plasma Membrane

the selective barrier which allows the sufficient passage of oxygen, nutrients, and wastes to service the entire volume of the cell at the boundary of the cell

Flagellum

locomotion organelle present in some animal cells; composed of membrane-enclosed microtubules

Centrosome

region where the cell's microtubules are initiated; in an animal cell, contains a pair of centrioles

Cytoskeleton

reinforces cell's shape, functions in cell movement; components made of protein (microfilaments, intermediate filaments, microtubules)

Microvilli

projections that increase the cell's surface area

Peroxisome

organelle with various specialized metabolic functions; produces hydrogen peroxide

Mitochondrion

organelle where cellular respiration occurs and most ATP is produced

Lysosome

digestive organelle where macromolecules are hydrolyzed

Golgi Apparatus

organelle active in synthesis, modification, sorting, and secretion of cell products

Ribosomes

nonmembranous organelles that make proteins, free in cytoplasm or bound to rough ER nuclear envelope

Chromatin

material consisting of DNA and proteins; visible as individual chromosomes in a dividing cell

Nucleolus

nonmembranous organelle involved in production of ribosomes; a nucleus has one or more nucleoli

Nuclear Envelope

double membrane enclosing the nucleus; perforated by pores, contiguous with ER

Cell Wall

outer layer that maintains cell's shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein

Plasmodesmata

channels through the cell walls that connect the cytoplasm of adjacent cells

Chloroplast

photosynthetic organelle, converts energy of sunlight to chemical energy stored in sugar molecules

Central Vacuole

prominent organelle in older plant cells, functions include storage, breakdown of waste products, hydrolysis of macromolecules; enlargement of vacuole is a major mechanism of plant growth

Endoplasmic Reticulum

network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough(ribosome-studded) and smooth regions

Vesicles

sacs made of membrane

Glycoproteins

proteins that have carbohydrates covalently bonded to them

Transport Vesicles

vesicles in transit from one part of the cell to another

Phagocytosis

the process of engulfing smaller organisms or food particles

Food Vacuoles

vacuoles which store food

Contractile Vacuoles

they pump out excess water due to osmosis

Cristae

infoldings of the inner membrane in 

mitochondria

Mitochondrial Matrix

the space in between the cristae

Thylakoids

membranous system in the form of interconnected sacs in chloroplast

Granum/Grana

each stack in the choloroplast

Stroma

the fluid outside the thylakoids

Centrioles

composed of nine sets of triplet microtubules arranged in a ring

Integral Proteins

proteins which penetrate the hydrophobic core of the lipid bilayer

Peripheral Proteins

proteins that are not embedded in the lipid bilayer, but are loosely bound to the surface

Glycoproteins

carbohydrates covalently bonded to protein

Glycolipid

carbohydrates covalently bonded to lipid

The Structure and Function of Large Biological Mol

Gene

a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses)

Nucleic Acids

A polymer (polynucleotide) consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities. The two types are DNA and RNA.

Deoxyribonucleic Acid (DNA)

A double-stranded, helical nucleic acid molecule consisting of nucleotide monomers with a deoxyribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and thymine (T); capable o

Ribonucleic Acid (RNA)

A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in pro

Polynucleotides

A polymer consisting of many nucleotide monomers in a chain; nucleotides can be those of DNA or RNA.

Nucleotides

The building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group.

Pyrimidine

One of two types of nitrogenous bases found in nucleotides, charaterized by a six-membered ring. Cytosine (C), Uracil (U), and Thymine (T)

Purines

One of two types of nitrogenous bases found in necleotide, characterized by a six-membered ring fused to a five-membered ring. Adenine (A) and Guanine (G)

Ribose

The sugar component of RNA necleotides.

Deoxyribose

The sugar component of DNA necleotides, having one fewer hydroxyl group than ribose, the sugar component of RNA nucleotides.

Double Helix

The form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis ito a spiral shape.

Antiparallel

The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.

Enzymatic Proteins

Function: selective acceleration of chemical reactions. Digestive enzymes catalyze the hydrolysis of the polymers in food.

Structural Proteins

Function: support. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin provide a fibrous framework in animal connective tissues. Keratin is the prote

Storage Proteins

Function: storage of amino acids. Ovalumin is the protein of egg white, used as an amino acid source for the developing embryo. Casein, the protein of milk, is the major source of amino acids for baby

Transport Proteins

Function: transport of other substances. Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules ac

Hormonal Proteins

Function: coordination of an organism's activities. Insulin, a hormone secreted by the pancreas, helps regulate the concentration of sugar in teh blood of vertebrates.

Receptor Proteins

Function: response of cell to chemical stimuli. Receptors build into the membrane of a nerve cell detect chemical signals released by other nerve cells.

Contractile and Motor Proteins

Function: movement. Actin and myosin are responsible for the contraction of muscles. Other proteins are responsible for the undulations of organelles called cilia and flagella.

Defensive Proteins

Function: protection against disease. Antibodies combat bacteria and viruses.

How to Make an Amino Acid Polymer

When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule

Frederick Sanger

The pioneer in determining the amino acid sequence of proteins.

Roger Kornberg

Awarded the Nobel Prize in Chemistry for using X-ray crystallography to determine the 3-D shape of RNA polymerase II, which binds to the DNA double helix and synthesizes RNA.

Carbon and the Molecular Diversity of LIfe

Organic Chemistry

The study of carbon compounds.

Vitalism

The belief in a life force outside the jurisdiction of physical and chemical laws, provided the foundation for the new discipline of organic chemistry.

Mechanism

The view that physical and chemical laws govern all natural phenomena.

Tetravalence

One facet of carbon's versatility that makes large, complex molecules possible. It acts as an intersection point from which a molecule can branch off in as many as four directions.

Hydrocarbon

An organic molecule consisting only of carbon and hydrogen. It is a hydrophobic compound because the great majority of it's bonds aer relatively non-polar carbon-to-hydrogen linkages.

Isomers

Compounds that have the same number of atoms of the same elements but different structures and hence different properties.Three different types.

Structural Isomers

Differ in the covalent arrangement of their atoms.

Geometric Isomers

Have the same covalent partnerships, but they differ in their spatial arrangement.The differences arise from the inflexibility of double bonds, which do not permit rotation.

Enantiomers

One of two compounds that are mirror images of each other. They are important in the pharmaceutical industry because two different ones of a drug may not be equally effective. Examples: Ibuprofen and

Functional Group

A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.

Hydroxyl

Is polar as a result of the electrons spending more time near the electronegative oxygen atom. Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

Carbonyl

A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. These two groups are also found in sugars, giving rise to two major groups of sug

Ketones

A carbonyl group within a carbon skeleton.

Aldehydes

A carbonyl group at the end of a carbon skeleton.

Carboxyl

Has acidic properties because the covalent bond between oxygen and hydrogen is so polar. Found in cells in the ionized form with a charge of 1- and called a carboxylate.

Amino

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Ionized, with a charge of 1+, under cellular conditions. Glycine is made up of both an amino group and car

Sulfhydryl

Two sulfhydryl groups can react, forming a covalent bond. This "cross-linking" helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of

Phosphate

Contibutes negative charge to the molecule of which it is a part (2- when at the end of a molecule, as above; 1- when located internally in a chain of phosphates). Has the potential to react with wate

Methyl

Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function.

ATP (adenosine triphosphate)

an adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells.

Friedrich Wohler

Attempted to make an "inorganic" salt, ammonium cyanate, by mixing solutions of amonium ions (NH4+) and cyanate ions (CNO−), but instead he made urea, an organic compound present in the urine of anima

Stanley Miller

Set up a closed system to simulate the conditions on early earth to see if organic molecules would form.

Jons Jakob Berzelius

Made the distinction between organic compounds, those thought to arise only in living organisms, and inorganic compounds, those found only in the nonliving world.

Carbon

Has 6 electrons, 4 of which are valence electrons. Completes valence shell by forming covalent bonds with other atoms.

Steroid

A type of lipid characterized by a carbon skeleton consisting of four rings with various chemical groups attached. Examples: female (estradiol) and male (testosterone) sex hormones.

Chemistry of Life

Matter

Anything that takes up space and has mass; is made up of elements.

Element

Any substance that cannot be broken down to other substances by chemical reactions.

Compound

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

Emergent Property of a Compound

A compound has characteristics different from those of its elements. Example: The metal sodium combines with the poisonous gas chlorine, forming the edible compound sodium chloride, or table salt.

Four Most Common Elements in Living Matter

Carbon (C), Oxygen (O), Hydrogen (H), and Nitrogen (N)

Trace Element

An element indispensable for life but required in extremely minute amounts.

Atom

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

Subatomic Particles

Atoms are composed of these even smaller parts.

Neutron

A subatomic particle having no electrical charge, found in the nucleus of an atom.

Proton

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

Electron

A subatomic particle with a single negative electrical charge that moves around the nucleus of an atom.

Atomic Nucleus

An atom's dense central core, containing protons and neutrons.

Dalton

A measure of mass for atoms and subatomic particles; the same as the atomic mass unit, or amu.

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.

Mass Number

The sum of the number of protons and neutrons in an atom's nucleus.

How to Calculate the Number of Neutrons

Atomic mass (subscript) - Atomic Number (superscript)

Atomic Mass

An approximation of the total mass of neutrons and protons of an atom.

Isotope

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

Radioactive Isotope

An isotope (an atomic form of a chemical element) that is unstable; the necleus decays spontaneously, giving off detectable particles and energy.

Energy

the capacity to cause change, especially to do work (to move matter against an opposing force).

Potential Energy

The energy that matter posesses as a result of its location or spatial arrangement (structure). Example: Water in a reservoir on a hill has more of it because of its altitude.

Electron Shell

An energy level of electrons at a characteristic average distance from the nucleus of an atom. Example: Sunlight excites them in the surface of a car to higher energy levels.

Valence Electron

An electron in the outermost electron shell.

Valence Shell

The outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom.

Orbital

The three-dimensional space where an electron is found 90% of the time.

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.

Covalent Bond

A type of strong chemical bond in which two atoms share one or more pairs of valence electrons.

Molecule

Two or more atoms held together by covalent bonds.

Single Bond

A single covalent bond; the sharing of a pair of valence electrons by two atoms.

Structural Formula

A type of molecular notation in which the constituent atoms are joined by lines representing covalent bonds. H--H

Molecular Formula

A type of molecular notation representing the quantity of constituent atoms, but not the nature of the bonds that join them. H2

Double Bond

A double covalent bond; the sharing of two pairs of valence electrons by two atoms.

Valence

The bonding capacity of a given atom; usually equals the number of unpaired electrons required to complete the atoms's outermost shell.

Electronegativity

The attraction of a given atom for the electrons of a covalent bond.

Nonpolar Covalent Bond

A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity.

Polar Covalent Bond

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

Ion

A 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.

Ionic Bond

A chemical bond resulting from the attraction between oppositely charged ions.

Ionic Compound

A compound resulting from the formation of an ionic bond; also called a salt.

Salt

A compound resulting from the formation of an ionic bond; also called an ionic compound.

Hydrogen Bond

a type of weak chemical bond that is 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 ano

van der Waals Interactions

Weak attractions between molecules or parts of molecules that result from localized charge fluctuations.

Chemical Reaction

The making and breaking of chemical bonds, leading to changes in the composition of matter.

Reactant

A starting material in a chemical reaction.

Product

A material resulting from a chemical reaction.

Chemical Equilibrium

in a chemical reaction, the state in which the rate of the forward reaction equals the rate of the reverse reaction, so that the relative concentrations of the reactants and products do not change wit

Introduction to the Study of Life

Evolution

Descent with modification; the idea that living species are descendants of ancestral species that were different from the present-day ones; also defined more narrowly as the change in the genetic comp

Biology

The scientific study of life.

Some Properties of Life

Order to structure. Regulation of body temperature by adjusting heat exchange with the surrounding air. Evolutionary adaptions that evolve over many generations which allow the reproductive success of

Emergent Properties

New properties that arise with each step upward in the hierarchy of life, owing to the arrangement and interactions of parts as complexity increases. Example: the importance of arrangement in the dist

Reductionism

The minimalization of complex systems to simpler components that are more manageable to study. Example: by studying the molecular structure of DNA that had by extracted from cells, James Watson and Fr

Levels of Biological Organization

1. The Biosphere - Earth, 2. Ecosystems - Ontario, 3. Communities - In forest ecosystem, trees, plants, animals, mushrooms, fungi, and microorganisms, 4. Population - sugar maple trees and white-taile

Biosphere

The entire portion of Earth inhabited by life; the sum of all the planet's ecosytems. It includes most regions of land, most bodies of water, and the atmosphere to an altitude of serveral kilometers.

Ecosystems

All the organism in a given area as well as the abiotic factors with which they interact; one or more communities and the physical environment around them.

Communities

All the organisms that inhabit a particular area; an assemblage of populations of different species living close enough together for potential interaction.

Population

A localized group of individuals of the same species that can interbreed, producing fertile offspring.

Organism

Individual living things

Organ and Organ System

A specialized center of body function composed of several different types of tissues. A group of these work together in performing vital body functions.

Tissue

An integrated group of cells with a common function, structure, or both.

Cell

Life's fundamental unit of structure and function.

Organelle

Any of serveral membrane-enclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells.

Molecules

A chemical structure consisting of two or more atoms.

System

A combination of components that function together.

Systems Biology

An approach to studying biology that aims to model the dynamic behavior of whole biological systems.

Eukaryotic Cell

A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with these type of cells include protists, plants, fungi, and animals.

Prokaryotic Cell

A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles. DNA is not sperated from the rest of the cell by enclosure in a necleus. Organisms with these cells include bacteria

DNA (deoxyribonucleic acid)

A nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses.

Gene

A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA or RNA in some viruses.

Genome

The entire "library" of genetic instructions that an organism inherits.

Bioinformatics

The use of computers, software, and mathmatical models to process and integrate biological information from large data sets.

Negative Feedback

An accumulation of an end product of a process slows that process.

Positive Feedback

An end product speeds up its production.

Taxonomy

The branch of biology that names and classifies species, formalizes this ordering of species into groups of increasing breadth.

Domain Bacteria

Any of the prokaryotic microorganisms that are genetically distinct from archaea and eukarya, and inhabits all kinds of environments.

Domain Archaea

Any of the prokaryotic microorganisms that are genetically distinct from bacteria and eukaryotes, and often inhabiting extreme environmental conditions.

Domain Eukarya

Any of the eukaryotic organisms that are genetically distinct from bacteria and archaea, includes three kingdoms of multicellular eukaryotes: kingdoms Plantae, Fungi, and Animalia.

Charles Darwin's Theory of Evolution

First, contemporary species arose from a succession of ancestors. This evolutionary history of species is called "descent with modification." Second, the evolutionary mechanism for descent with modifi

Inquiry

A search for information and explanation, often focused by specific questions.

Two Main Types of Scientific Inquiry

Discover science and Hypothesis-based science

Discovery Science

Describes natural structures and processes as accurately as possible through careful observation and analysis of data.

Data

recorded observations

Inductive Reasoning

A type of logic in which generalizations are based on a large number of specific observations.

Hypothesis

A tentative answer to a well-framed question - an explaination on trial. Leads to predictions that can be tested by making additional observations or by performing experiments.

Deductive Reasoning

A type of logic in which specific results are predicted from a general premise.

Scientific Method

A systematic approach to solving a problem by discovering knowledge, investigating a phenomenon, verifying and integrating previous knowledge. It follows a series of steps that evaluates the veracity

The fundamental steps of the scientific method are:

(1) Identifying the problem to solve, (2) Formulating a tentative answer or hypothesis, (3) Testing the hypothesis, (4) Gathering and analyzing data, (5) Making conclusions

Controlled Experiment

An experiment in which an experimental group is compared with a control group that varies only in the factor being tested.

Theory

An explanation that is broad in scope, generates new hypotheses, and is supported by a large body of evidence.

Model

A repesentation of a theory or process.

Technology

The application of scientific knowledge for a specific purpose, often involving industry or commerce but also including uses in basic research.