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BIO101 Reviewer (Chapters 1-4)
CHAPTER 1 - Introduction to Biology
Biology - study of life
Properties of Living World Unity common traits rooted in the
phenomenon of biological evolution
Diversity- different types of environmentwhere diverse forms of
life have evolved
Characteristics of Living Organisms
Cells & Organization- organisms (organum, Latin) maintain
aninternal order separated from theenvironment- cell, simplest unit
of an organism (Cell
Theory)
Energy Use & Metabolism- cells acquire energy & use it
to maintaintheir internal order- cells use energy by catalyzing a
varietyof chemical reactions (metabolism) forbreakdown of nutrients
& synthesis ofcompounds
Response to Environmental Changes- needed to survive-
adaptations processes & structures byw/c organisms adjust to
short or long-termchanges
Regulation & Homeostasis- to stay the same, Greek- process
by w/c cells & organismsregulate their bodies to maintain
stableinternal conditions
Growth & Development- Growth - more or larger cells-
Development produces organisms w/ adefined set of
characteristics
Reproduction - needed to sustain life- DNA - genetic material;
blueprint of life
- genes contribute to the traits oforganisms- Molecular gene
expression
- DNA -> RNA-> Polypeptide (largelyresponsible for the
traits)
Biological Evolution- phenomenon that population oforganisms
change over the course ofmany generations
Different Levels of Organization
Atom - smallest component of an element- all matter is composed
of atoms
Molecules & Macromolecules
Organism - belonging to a particularspecies (related group of
organismssharing a distinct form & set of attributes)
Population - group of organisms of thesame species &
environment
Community - assemblage of populations
Ecosystem - interactions of community oforganisms w/ their
environment
Biosphere - all of the places on Earthwhere living organisms
exist
Two Mechanisms of Evolutionary Change
Vertical Descent w/ Mutation -progressions of changes in a
series ofancestors (lineage)- new species evolve from
pre-existing
species by the accumulation of mutations(changes in the genetic
material of anorganism)o Mutation - changes in the genetic
material of organismso Natural Selection - mutation is more
likely to increase in a population overmany generations
Horizontal Gene Transfer - geneticexchanges between different
species- Tree of Life - vertical evolution; Web ofLife - vertical
evolution andhorizontal gene transfer
Classification of Living Organisms Taxonomy- grouping of
species
3 Domains of Life- Bacteria & Archaea - prokaryotic- Eukarya
- eukaryotic; has a cell nucleus
- 4 kingdoms: Animalia (has anervous system; locomotion),
Plantae(photosynthesis), Fungi (has a cell wallbut cant carry out
photosynthesis) &Protista
Binomial - unique scientific name; GENUS(1st part) species (2nd
part)
Evolution - unifying concept in Biology Genome - complete
genetic make-up of
organism- acts as stable informational
unit, provides continuity from gen. to gen.& acts as
instrument of evolutionarychange
Biology as Scientific Discipline
Science - observation, identification,investigation &
theoretical explanation ofnatural phenomenon
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Hypothesis - proposed explanation fornatural phenomenon; based
on previousobservations & experiments
Theory - broad explanation of someaspect of the world w/ a large
body ofevidence
Knowledge - awareness & understandingof information
Curiosity - key phenomenon that sparksscientific inquiry2
Scientific Approaches
Discovery-based science - collection &analysis of data w/o
the need forpreconceived hypothesis
Hypothesis-testing - scientific method;used to test the validity
of a hypothesis
- observation, hypothesis,experimentation, analyzation of
data,accept/rejectCHAPTER 2 - Chemical Basis of Life I
Atoms
Biochemistry - study of atoms & molecules inthe context of
living organismsAtoms - smallest unit of matter; each specifictype
of atom occurs as an element
3 subatomic particles- Protons - (+) charge; found in the
atomicnucleus- Neutrons - no charge; found in theatomic nucleus-
Electrons - (-) charge; found at regions atvarious distances from
the nucleus
Orbitals - regions surrounding the nucleus
in w/c the probability of finding anelectron is high- can hold a
max. of 2 electrons- shapes: spherical (s-orbital) or
dumbbell(p-orbital)- occupy energy shells/levels (innermostshell of
atom - max. of 2 electrons; secondshell - 1 (2s) & 3 (2p)
orbitals; can hold 4pairs of electrons)
Valence electrons - electrons in the outershell; available to
combine w/ other atoms
Atomic No. - number of protons; = no. of
electrons Periodic table - rows ( indicate no. of
energy shells); columns (indicate no. ofvalence electrons)
Atomic Mass - atoms mass relative to themass of other atoms-
measured in daltons; 1 Da=1/12 the
Chemical Bonds & Molecules
Molecule - 2 or more atoms bondedtogether
Molecular formula - consists of thechemical symbols &
subscripts for all ofthe atoms present
Compound - molecule composed of 2 ormore diff. elements
Covalent bond - strong chemical bond;atoms share a pair of
electrons
Electronegativity - measure of anatoms ability to attract
electrons in abond from another atom
Polar covalent bonds - when 2 atomswith different
electronegativities form acovalent bonds, the shared electrons
aremore likely to be closer to the atom oflower
electronegativity
Polar molecules - molecules containingsignificant numbers of
polar bonds
Nonpolar molecules - moleculescomposed predominantly of
nonpolarbonds
Hydrogen bond - ability of one moleculeto loosely associate with
another moleculethrough a weak interaction
Ion - atom or molecule w/ net charge fromgaining or losing one
or more electrons
- cations (ions w/ + net charge); anions(ions w/ - net
charge)
Ionic bond - occurs when cation binds toan anion
Free radical - molecule containing anatom w/ a single, unpaired
electron in itsouter shell
- can be either charged or neutral
Chemical reaction - occurs when 1 ormore substances are changed
into othersubstances
- requires source of energy (heat);causes atoms & molecules
to vibrate &move (Brownian movement)- needs catalyst (substance
speedingup a chemical reaction- will eventually reach
equilibrium
Properties of Water Solute - substances dissolved in a
liquid
Solvent - liquid which substances aredissolved in
Solution - formed when solutes dissolvedin solvent
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Solute concentration - amount of solutedissolved in a unit
volume of solution
Molecular mass - sum of the atomicmasses of all atoms in the
molecule
Vaporization - water from liquid togaseous state
Colligative properties - temperature at w/c
a solution freezes or vaporizes- Heat of vaporization - heat
required tovaporize 1 mole of any substance- Heat of fusion - heat
required to cause asubstance to change from liquid to
solidstate
Anti-freeze molecules - produced by cold-blooded animals
Hydrolysis - process wherein water is usedto break apart another
molecule
Dehydration - removal of water moleculein a reaction &
formation of covalent bond
Features of water - participate in chem.reactions
- incompressible- has a very high heat capacity-
Hydrogen-bonding properties of water
(cohesion- molecules w/in a substancetend to noncovalently
attract each other;adhesion - ability of water to adhere toanother
surface)
- surface tension - measure of howdifficult it is to break the
interfacebetween liquid & air
Acids - molecules that release hydrogen
ions in solution- Strong acid - complete dissociation whenadded
to water (ex. HCl -> H + Cl)- Weak acid - some of the molecule
willstill remain when dissolved in water) (ex.H2CO3 -> H +
H2CO3)
Base - lowers H+ concentration; somerelease OH-
Solutions pH - concentration of H+- acidic solution (pH is below
7);
alkaline solution (pH is above 7); neutralsolution (pH is 7)
Buffer - minimize fluctuations in the pH offluids; can raise or
lower pH as needed
CHAPTER 3 - Chemical Basis of Life IICarbon Atom & Study of
Organic Molecules
Carbon - provides atomic scaffold uponlife is built
Carbon-containing molecules - organicmolecules
Organic chemistry - science of studying
Characteristics of Carbon- ability to form 4 covalent bonds
w/
other atoms- carbon bonds may occur in linear, ring-
like or highly branched configurations- ability to form both
polar & nonpolarbonds(Hydrocarbons - molecules containing
C-Hbonds; nonpolar; insoluble in water)- carbon bonds are stable at
difftemperatures (shorter bond - stronger &more stable)
Functional groups - groups of atoms w/special chemical features
that arefunctionally important- (amino, carbonyl - ketone &
aldehyde,carboxyl, hydroxyl, methyl, phosphatesulphate &
sulfhydryl)
Isomers - carbon-containing moleculesexisting in multiple
forms
- 2 structures w/ an identicamolecular formula but different
structures& characteristics- 2 types:
Structural Isomers - same atomsdifferent bonding
relationship
Stereoisomers - identicabonding relationship; differs in
spatiapositioning(geometric isomers -
cis-transstereoisomers)(enantiomers - mirror images of each
other)Classes of Organic MoleculesLarge molecules - polymer;
linking of smallermolecules (monomer)Carbohydrates - composed of C,
H & O atomsCn(H20)n
- most of its C atoms are linked to a Hatom or Hydroxyl
groupSugars - small carbohydrates that taste sweetsource of energy
of living organisms
Monosaccharide - simplest sugars; mostcommon type: pentoses
(e.g. ribose &deoxyribose) and hexoses (e.gglucose)
Disaccharides - 2 sugars; (e.g. sucrose- composed of glucose
& fructosemaltose & lactose)- Glycosidic bond - bond
formedbetween 2 sugars
Polysaccharides - many sugars- e.g. (used to store energy)
starch -plant cells & glycogen - animal cells
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- Ester bond - hydroxyl group is linkedto carboxyl group by
removal of H20molecule (dehydration)
- Saturated fatty acid - C atoms in afatty acid are linked by a
singlecovalent bond
- Unsaturated fatty acid - C atoms in afatty acid are linked by
a double covalentbond
- Oils - fats high in unsaturatedfatty acids
Phospholipids - glycerol, 2 fatty acids &phosphate group
(linked to the 3rd
hydroxyl group of glycerol)- Amphipathic
Steroids - 4 fused rings of carbon atoms- Sterols - steroids w/
hydroxyl group;cholesterol
Waxes - lipids that are secreted by plants& animals onto
their surface
- contain 1 or more hydrocarbons &
long structures that resemble a fattyacid- nonpolar; repel
water
Proteins - first rank; composed of C, H, N &O atoms and
small amounts of other elements(S)- Amino acids - building blocks
of protein(structure: C atom + amino grp. + carboxylgrp. + H atom +
side chain)
- 20 amino acids - nonpolar (Glycine,Alanine, Valine, Leucine,
Isoleucine, Proline,Phenylalanine, Tyrosine, Tryptophan,
Cysteine& Methionine); Polar uncharged (Serine,
Threonine, Asparagine & Glutamine); Polarcharged (Aspartic
acid, Glutamic acid,Histidine, Lysine & Arginine)
- Peptide bond - bond formed betweena carboxyl & amino
group
- Polypeptide - resulting molecule whenamino acids are joined by
peptide bonds (endsof the resulting molecule: amino terminus -free
amino group; carboxyl terminus - freecarboxyl group)Protein
Structures at 4 Progressive Levels
Primary - linear amino acid sequence;
determined by genes Secondary - irregular or repeating
folding patterns; 2 types: helix & sheet
Tertiary - 3D shape of a singlepolypeptide; final structure of
afunctional protein for some
Quaternary - 2 or more polypeptides(protein subunits) each
adopting atertiar structure & then assemble w
- Electron Microscope - uses an electronbeam
(Types of Electron Microscope: TEM(Transmission Electron
Microscope) -beam of electrons is transmitted througha sample, has
the best resolution of anymicroscope; SEM (Scanning
ElectronMicroscope) - utilizes electron beam toproduce a 3D image
of the surface of thesample)
Overview of Cell StructureCell structure - relies on 4 critical
phenomena:matter, energy, organization & information
Prokaryotes - have a simple structure;lack a membrane- enclosed
nucleus; 2
categories: Bacteria & ArchaeaStructure of typical bacterial
cell:- Plasma Membrane - important barrierbetween cell & its
external environment- Cytoplasm - region of the cell containedw/in
the p lasma membrane
- structures in the bacterial cytoplasm(nucleoid - region where
DNA islocated; ribosomes - involved in proteinsynthesis)- Cell Wall
- supports & protects theplasma membrane; porous
- Glycocalyx - outer gelatinous covering ofbacteria; traps
water; (capsule -very thick glycocalyx)- Appendages - pili (allows
prokaryotes toattach to surfaces); flagella (allowsprokaryotes to
swim)- Proteins important in the architectureinside the cytoplasm
of bacterialcells (FtsZ - cell division;
MreB - cell polarity; CreS - cell shape)
Eukaryotes - include protists, fungi, plants& animals
- its DNA is housed in a nucleus
(organelle - membrane-boundcompartment w/ a specific structure
&function)
- exhibits compartmentalization (manyorganelles separating the
cell to
different regionsGeneral Structure of Animal/Plant Cell
PLANT CELLS LACK lysosomes, centrioles& flagella
ANIMAL CELLS LACK cell wall, centralvacuole &
chloroplasts
The Cytosol
- region outside the organelles but inside theplasma
membrane
Nucleic Acids - storage, expression &transmission of genetic
information
- nucleotide (monomer); composed of aphosphate group, 5-C sugar
& a single/doublering of carbon of C & N atoms (base)-
phosphoester bond - phosphate group of 1nucleotide is linked to the
sugar of adjacentmolecule2 classes:
DNA (Deoxyribonucleic acid) - storesgenetic info
- contains deoxyribose sugar- 4 bases: purine bases (adenine
&
guanine) & pyrimidine bases (cytosine& thymine); (A-T
& G-C pairing)- Double helix (2 strands of
nucleotidescoiled)
RNA (Ribonucleic acid) - decodinginformation into instructions
for linkingamino acids to form a polypeptide chain
- contains ribose sugar - Single-
stranded- 4 bases: adenine, guanine, cytosine &uracil- forms
of RNA : mRNA (messengerRNA) & tRNA (transfer RNA) -
convertinformation contained in DNA intoformation of new
polypeptide
CHAPTER 4 - General Features of CellsCell Theory - Matthias
Schleiden, TheodorSchwann & Rudolf Virchow (every celoriginates
from another cell)Cell Biology - study of individual cells and
their
interactions w/ each other
Endosymbiosis - process by which a neworganism originates from
the fusion of twoexisting organismsMicroscopy
Microscope - magnification tool enablingthe study of structure
& function of cells
Robert Hooke - studied cork; coined theterm cell
Zacharias Jansen - invented 1st compoundmicroscope
Max Knoll & Ernst Ruska - invented the1st electron
microscope
Anton van Leeuwenhoek - inventedsimple microscope; discovered
bloodcells & first to see sperm cells of animals
3 important parameters in microscopy :Magnification - ratio
between size of animage produced by microscope & actualsize;
Resolution - measure of clarity of anobject; Contrast - ability to
visualize a
(polypeptide - unit of structure; protein - unitof function)
- requires ribosome & 2 RNA molecules(ribosome - site for
polypeptide synthesis;mRNA - provides info; tRNA - carry
aminoacids, bind it to mRNA)* once entire polypeptide is made, it
isreleased from the ribosome
Cytoskeleton - network of 3 differenttypes of protein
filaments:
- Microtubules - hollow tubule;important in cell shape &
organization;formed in the centrosome ormicrotubule-organizing
center(centrioles - pair of structures
perpendicular to each other found w/inthe centrosome)-
Intermediate filaments - twistedfilament; function as
tension-bearingfibers that maintain cell shape &rigidity- Actin
filaments - spiral filament;microfilaments; important in
celstrength and shape
Motor proteins - use ATP as source ofenergy to promote
movement
- consists of 3 domains: head (site of
ATP bonding & hydrolysis; causesmovement & bend in the
hinge), hinge& tail (attached to other proteins)- axoneme -
arrangement containingmicrotubules, motor protein dynein
&linking proteins
Nucleus & Endomembrane SystemEndomembrane system - larger
network ofmembranes enclosing thenucleusVesicles - small
membrane-enclosed sphereswhere other organelles of the system
passmaterials to each other
Nuclear envelope - doule-membranestructure enclosing the
nucleus
Nuclear pores - provide passageway forthe movement of molecules
in & out ofthe cell
Chromosomes - inside the nucleus;composed of genetic material
& proteins
Chromatin - complex formed by DNA &such protein
Nuclear matrix - inside the nucleus;filamentous network of
proteins;
Nucleus - organization, protection &expression of genetic
material
Nucleolus - re ion in the nucleus; where
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- Has an inner & outer membrane tooseparated by an
intermembrane space
- thylakoid membrane - 3
rd
membranewhere light energy is captured; formsmany fluid-filled
tubules that tend to stackon top of each other to form a
structurecalled granum(thylakoid lumen - enclosed by thethylakoid
membrane ; facilitates process ofphotosynthesis)- stroma -
compartment of chloroplastinside the inner membrane but outside
thethylakoid membrane- specialized version of plant organellesknown
as plastids (chromoplasts - 2nd type
of plastid; synthesize & store yelloworange & red
pigments; leucoplasts - 3r
type of plastid; lacks pigment moleculesAmyloplast - leucoplast
that synthesize &store starch)
Peroxisomes - discovered by Christian deDuve
- consist of a single membrane thatencloses a fluid-filled
lumen- catalyze certain chemical reactions, thosethat breakdown
molecules by removing Hor adding O
- usually contain enzymes involved inmetabolism of fats &
amino acids(catalase - enzyme in peroxisome thatbreaks down
hydrogen peroxide to makewater and oxygen gas)(glyoxisomes -
contain enzymes needed toconvert fats to sugars)
- Rough ER - initial synthesis & sortingof proteins
- glycosylation - attachment ofcarbohydrate to proteins &
lipids- studded w/ ribosomes
- Smooth ER - metabolic diverseprocesses; accumulation of
calcium ions;synthesis & modification of lipids
Golgi Apparatus - discovered by CamilloGolgi
- composed of a stack of flattenedmembranes- 3 overlapping
functions: secretion,processing & protein sorting- packages
diff. types of proteins into
secretory vesicles- proteolysis - cut proteins into
smallerpolypeptides; enzymes- proteases
Lysosomes - found in animal cells; lyse ordegrade
macromolecules
- Acid hyrdolases - found in lysosomes;enzymes that use water
molecules tobreak a covalent bond- autophagy - eating of ones
self;cellular material is enclosed in a doublemembrane
(autophagosome)
Vacuole - empty space; transport
substances or store materials; fordegradation
- central vacuole - found in matureplant cells; (tonoplast -
membrane ofcentral vacuole) stores large amount ofwater, enzymes
& inorganic ions; performsspace-filling function(turgor
pressure - pressure exerted on cellwall by the large size of the
vacuole; helpsmaintain structure of plants & forexpansion of
its cell wall - for growth)- contractile vacuoles - found in
freshwater
organisms; expands as water enters thecell- phagocytic or food
vacuoles - wheresome protists engulf their food
Plasma Membrane - vital in cell signalling;vital role in animals
- cell adhesion
Semiautonomous Organelles- can grow and divide to
reproducethemselves; depend on other parts of the cellfor their
internal components
Mitochondria - thread granule; has anouter & inner membrane
(highly folded toform projections called cristae;mitochondrial
matrix - compartment insideinner membrane) separated by
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