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General Biology
BI 102, Fall 2014
CRN 22608
Instructor: Bill Thomas (Instructor website under Thomas, William)
Email: [email protected]
Learning Objectives – Week 1 • Properties of life
• The 3 domains of life – Archaea, Bacteria, Eukarya
• Biological Themes – Evolution, Flow of Energy, Cooperation, Structure Determines Function,
Homeostasis
• Scientific process
• Unifying Theories of Biology – Cell Theory, Gene Theory, Theory of Heredity, Theory of Evolution
• Atoms: Structure and properties
• Electron shells and orbitals
• How are ions formed?
• The types of bonds: ionic, covalent, hydrogen bonds (and van der Waals forces)
• Biological importance of the special properties of water
• Become familiar with the terms “hydrophilic” and “hydrophobic” and understand their biological
importance
• Understand the basics of the pH scale
• Logarithmic
• Lower Higher = Acidic Basic
• Learn the four main types of biological macromolecules and their components
• What is a monomer?
• Two reactions: dehydration synthesis and hydrolysis
• Which requires energy input? Which releases energy?
• Understand the basics of protein structure (primary, secondary, etc.)
• See how the structure of a macromolecule determines its function
First-day business • Introductions
• Syllabus
• Read safety instructions in lab packet for Thursday
• McGraw Hill Connect resources
http://connect.mheducation.com/class/w-thomas-bi-102-lbcc-fall-14-1
LearnSmart: Objective: Familiarize yourself with material we will be covering in class
Homework: Weekly Activity
LearnSmart and online homework together make up 10% of your grade—don’t
forget about them!
Course Objectives
• Hands-on lab experience
DNA extraction, genetics, electrophoresis!
• Gaining a better understanding of biological systems
Cell structure and function
Genetics and heredity
Evolutionary processes
• Understanding the scientific method
Scientific inquiry
• Impact of cell biology on your life
Photo : Frank Wojciechowski
The Domains of Life
• Historically, life was grouped into three kingdoms.
• Modern taxonomy divides life into three domains
textbookofbacteriology.net
The six kingdoms of life
What is Life?
• What qualifies something as “living” versus “non-living?”
• Consider these points complexity
movement
response to stimulation
• A life-defining property must be exclusive to living things
Are these properties
unique to living things?
Properties of Life
• 1. Cellular organization
all living things are comprised of at least one cell
• 2. Metabolism
all living things process energy which is used to power other processes
• 3. Homeostasis
all living things maintain relatively stable internal environments to optimize conditions for metabolism and other processes
Properties of Life
• 4. Growth and reproduction
all organisms have the capacity
for growth and reproduction
• 5. Heredity
all organisms pass genetic
information to future generations
from parents to offspring
Does this possess the
properties of life?
The Organization of Life
• Living things function and interact with
each other on many levels
• The organization of life is a hierarchy of
levels of increasing size
cellular
organismal
populational
Figure 1.4 Levels of organization:
cellular level
Alternative example:
1. Atoms (C, H, N, O, S)
2. Molecule (amino acid)
3. Macromolecule (protein;
e.g., actin)
4. Organelle (Cytoskeleton)
This level of organization is where
we will spend most of our time!
Figure 1.4 Levels of organization:
organismal level
Figure 1.4 Levels of organization:
populational level
On which of these three levels
(cellular, organism, population)
do you think evolution takes
place?
The Organization of Life
• At higher levels of the living hierarchy, new properties become apparent that were absent at the lower levels
• These emergent properties result from the interaction of diverse but simpler components
• Many higher order processes that are hallmarks of life are emergent properties
metabolism
consciousness
Biological Themes: Evolution
Evolution is genetic change in a
species over time
The mechanism for evolution is
natural selection
The diversity of life is explained by
evolutionary processes
Biological Themes: Flow of Energy
All living things require energy
Energy from the sun flows through the living world
Organisms acquire energy differently
How much energy is available determines how many and what kinds of organisms can live together in an ecosystem
biology.tutorvista.com
Biological Themes: Cooperation
As energy and other resources are
limiting, many organisms have
evolved cooperation as a means of
survival
Symbiosis describes when two
species live in direct contact
Biological Themes: Structure Function
Structure Determines Function
Evolution favors structures that
function in an adaptive manner
Many structures are specialized for a
particular function
tiger.towson.edu
naturedocumentaries.com
Biological Themes: Homeostasis
Homeostasis is a physiological condition of “steady-state”
The internal environment of organisms is relatively stable
Organisms act to control their internal environments so that the complex processes of metabolism function efficiently
Scientific Investigation
Scientists systematically
conduct experiments to
evaluate hypotheses about
observed phenomena
• You’ve probably used the
scientific method without
realizing it!
Copyright © 2011 Pearson Education, Inc.
What’s missing from
this experimental
design?
Fig.1.5 The scientific process
Stages of a Scientific Investigation
The scientific process has six stages
1. Observation
science begins with careful observation of natural phenomena
2. Hypothesis scientists make an educated guess that might be true
often scientists formulate multiple ideas about a phenomenon; these are called alternative hypotheses
Stages of a Scientific Investigation
3. Predictions
if a hypothesis is correct, then specific
consequences can be expected
4. Testing
scientists conduct experiments to attempt to
verify predictions made by hypotheses
• 5. Controls
experiments usually employ a parallel design • scientists use a control to assess the influence of
potential factors, called variables
• conditions stay the same in the control in comparison to the variable condition
• 6. Conclusion
a hypothesis that has been tested and not rejected is tentatively accepted
Stages of a Scientific Investigation
The
Experiments
of Francesco
Redi
Copyright © 2011 Pearson Education, Inc.
Scientific Method in Action
Theory and Certainty
• The term “theory” means different things
to different audiences
To scientists
• A theory represents certainty and is a unifying
explanation for a broad range of observations
To the general public
• A theory implies a lack of knowledge or guess
Theory and Certainty
• Scientists’ acceptance of theory is
provisional
the possibility always remains that future
evidence will cause a theory to be revised
• The process of science is not just trial-
and-error but involves judgment and
intuition
Four Theories Unify Biology as a
Science
• 1. The Cell Theory
• 2. The Gene Theory
• 3. The Theory of Heredity
• 4. The Theory of Evolution
The Cell Theory
• All organisms are composed of
at least one cell
• The cell is the most basic unit
of life
• All cells come from pre-
existing cells
The Gene Theory
• Genetic information is encoded in
molecules of deoxyribonucleic acid
(DNA)
• Genes encode specific proteins
• The proteins encoded by an organism’s
genes determine what it will be like in
terms of form and function
The Theory of Heredity
Genes are passed down generations
as discrete units
Mendel’s theory of heredity
gave rise to the field of genetics
Chromosomal theory of
inheritance located Mendelian
genes on chromosomes
The Theory of Evolution
• All living organisms are related to one another in a common tree of descent
The six kingdoms of life are grouped into three domains
• Theory of evolution explains the unity and diversity of life
The Theory of Evolution
• Charles Darwin attributed evolution to natural selection
Organisms best able to respond to
the challenges of living will leave
more offspring, thus their traits
become more common in the
population
• Scientists have been able to identify
changes in individual genes that are
responsible for differences among
individuals
Figure 1.13 The theory of evolution
Figure 2.2 Basic structure of an atom
Atoms - Properties • An atom is characterized by the
number of protons it has or by its overall mass
atomic number
• the number of protons in the nucleus
• Why not the number electrons?
mass number
• the number of protons plus neutrons in the nucleus
• electrons have negligible mass www.chemistry.wustl.edu
Table 2.1
“Organic”
Electrons
• Electrons determine the chemical behavior of atoms
These subatomic components are the parts of the atom that come close
enough to each other in nature to interact
• Electrons are associated with energy
Electrons have energy of position, called potential energy
Electrons occupy energy levels, or electron shells, of an atom, which
are actually complex, three-dimensional volumes of space called
orbitals
• orbitals are where electrons are most likely to be found
Electron Shells & Energy
• As electrons move to a
lower energy level, closer
to the nucleus, energy is
released
• Moving electrons to
energy levels farther out
from the nucleus requires
energy
Figure 2.3 The electrons of
atoms possess potential energy
Electron Shells & Orbitals
• Electron shells have specific numbers of orbitals that may be filled
with electrons
atoms that have incomplete electron orbitals tend to be more reactive
atoms will lose, gain, or share electrons in order to fill completely their
outermost electron shell
these actions are the basis of chemical bonding
Ions
Ions – atoms that have gained or lost one or more electrons
Isotopes
Isotopes – atoms that have the same number of protons but different
numbers of neutrons
most elements in nature exist as mixtures of different isotopes
Isotopes & Radioactivity
• Some isotopes are unstable and break up into particles with lower
atomic numbers
this process is known as radioactive decay
• Radioactive isotopes have multiple uses
dating fossils
medical procedures
Figure 2.7 Using a
tracer to identify cancer
Molecular bonds
A molecule is a group of atoms held together by energy in the form of a chemical bond
• There are 3 principal types of chemical bonds 1. Ionic
2. Covalent
3. Hydrogen
• van der Waals forces are a kind of weak chemical attraction (not a bond) that come into play when atoms are very close to each other
Ionic compounds
• Ionic bonds involve the
attraction of opposite electrical
charges
• Molecules comprised of these
bonds are often most stable as
crystals
Fig. 2.8(a) The formation of
ionic bonds in table salt
Molecules – Covalent bonds
Covalent bonds form between two atoms when they share
electrons
The number of electrons shared varies depending on how many
the atom needs to fill its outermost electron shell
Covalent bonds are stronger than ionic bonds because they are
directional
Single
covalent
bond
Double
covalent
bond
Oxygen gas (O2)
Methane gas (CH4)
C H H
H
H
O O O
–
H H
H
H
–
–
–
– –
– –
–
–
– –
–
–
– –
–
– –
– –
–
O –
–
–
–
C
Polar molecules
• Some atoms may be better at attracting the shared electrons of a covalent bond
This creates tiny partial negative and positive charges within the molecule, now called a polar molecule
Polar covalent bonds form when the shared electrons of a covalent bond spend more time in the vicinity of a particular atom
What is this important polar
molecule?
Hydrogen bonding
Hydrogen bonds are weak electrical attractions between the positive
end of one polar molecule and the negative end of another
each atom with a partial charge acts like a magnet to bond weakly to
another polar atom with an opposite charge
the additive effects of many hydrogen bonding interactions can add
collective strength to the bonds
Example?
Electrons – Big Picture
• Electrons can be “energized”; this energy can be used
by cells to do work
• The number of electrons and the way they are shared by
atoms give molecules biologically important properties:
Charge: the charge on an ion restricts its movement in a cellular
environment, can be used in transport
Polarity: polar molecules interact with ions and other polar
molecules, are repelled by nonpolar molecules
Nonpolarity: nonpolar molecules repel polar and charged
molecules, “hide” from water
Polarity of Water
Water can form hydrogen bonds
Hydrogen bonding confers on water many different special properties
Unique Properties of Water
Why is this
important?
Evaporative
cooling
Hydrophilic vs. Hydrophobic
• High polarity
In solution, water molecules tend to form the maximum number of hydrogen bonds
• hydrophilic molecules are attracted to water and dissolve easily in it
– these molecules are also polar and can form hydrogen bonds
• hydrophobic molecules are repelled by water and do not dissolve
– these molecules are nonpolar and do not form hydrogen bonds
Figure 2.14 How salt dissolves in water
Water Ionizes
• The covalent bond within a water molecule sometimes breaks spontaneously
• This produces a positive hydrogen ion (H+) and a negatively charged hydroxide ion (OH-)
H2O OH- + H+
Water Hydroxide Hydrogen
Figure 2.15 The pH scale
• The amount of ionized
hydrogen from water in a
solution can be measured
as pH
• The pH scale is
logarithmic, which means
that a pH scale difference of
1 unit actually represents a
10-fold change in hydrogen
ion concentration
Acids & Bases
• Pure water has a pH of 7 there are equal amounts of [H+] relative to [OH-]
• Acid – any substance that dissociates in water and increases the [H+] acidic solutions have pH values below 7
• Base – any substance that combines with [H+] when dissolved in water basic solutions have pH values above 7
Biological pH
• The pH in most living cells and their environments is fairly close to 7 proteins involved in metabolism are sensitive to any
pH changes
• Organisms use buffers to minimize pH disturbances
a buffer is a chemical substance that takes up
or releases hydrogen ions
Blood is an example of a biological buffer
Organic Molecules
Carbon is the basis of all organic molecules
Carbon core has attached
groups of atoms called functional groups
• The functional groups confer specific chemical properties on the organic molecules
Macromolecules
Macromolecules are actually assembled from many similar small components, called monomers
the assembled chain of monomers is known as a polymer
• There are four types of macromolecules: 1. Proteins
2. Nucleic acids
3. Carbohydrates
4. Lipids
Fig. 3.3 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
N
H
C
H H
C
O P
O
–O
O– O
O C C
N C
N
C H
H
H
H H H H
P
P
P
P
P
P P
P
P
P
P
P
P
P
P
G
C
G
C
T
A
A
A
A
T
T
H H
H H
H
O
H O H H H H H H H H H H
H O C C C C C C C C C C C C
H H H H H H H H H H H
Polymer: Starch
Polymer: Fat molecule
(d) Lipid (b) Nucleic acid
Monomer:
Nucleotide
(a) Protein
Monomer:
Amino acid
Alanine
Ala
Val Ser Val
Ala
Monomer:
Monosaccharide
(c) Carbohydrate
Polymer: Polypeptide
Polymer: DNA strand
Monomer:
Fatty acid
OH
OH OH
HO
CH2OH
OH
NH2
CH2
OH
CH3
Which of these monomers is polar? What does that mean for the
polymer/macromolecule?
Dehydration synthesis
All macromolecules are assembled the same way
A covalent bond is formed between two subunits by
removing a hydroxyl group (OH) from one subunit and a hydrogen (H) from another subunit
Because this amounts to the removal of a molecule of water (H2O), this process is called dehydration synthesis
Figure 3.4(a) Dehydration synthesis
Figure 3.4(b) Hydrolysis
Which process releases energy: dehydration synthesis or hydrolysis?
Proteins
Complex macromolecules that are polymers of many subunits called amino acids
Figure 3.3(a) Polymers are built from monomers: protein
Amino acids
Small molecules with a simple basic structure, a carbon atom to which three groups are added
• an amino group (-NH2)
• a carboxyl group (-COOH)
• a functional group (R)
20 different
R groups
Figure 3.6(b) The formation of a peptide bond
Protein structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Tertiary
structure
Secondary
structure
β-pleated sheet
Primary
structure
Amino
acids
α-helix
Quaternary
structure
Protein structure: Primary
Primary structure –
the sequence of amino
acids in the polypeptide
chain
• This determines all
other levels of protein
structure
Figure 3.7 Levels of protein
structure: primary structure
Primary
structure
Amino
acids
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Protein structure: Secondary
Secondary structure – the
initial folding of the amino acid
chains
• Occurs because regions of
the polypeptide that are non-
polar are forced together
• The folded structure may
resemble coils, helices, or
sheets
Figure 3.7 Levels of protein
structure: secondary structure
Secondary
structure
β-pleated sheet
α-helix
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Protein structure: Tertiary
Tertiary structure – the final 3-D shape of the protein
• The final twists and folds that lead to this shape are the result of polarity differences in regions of the polypeptide
Figure 3.7 Levels of protein
structure: tertiary structure
Tertiary
structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Protein structure: Quaternary
Quaternary structure
– the spatial
arrangement of
component
polypeptides in
proteins comprised of
more than one
polypeptide chain
Figure 3.7 Levels of protein
structure: quaternary structure
Quaternary
structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 3.8 Protein denaturation
Heat
pH
Inactive
Figure 3.9 Protein structure
determines function
Nucleic Acids
Nucleic acids are very long polymers that
store information
comprised of monomers called nucleotides
Figure 3.3(b) Polymers are built from monomers: nucleic acid
Figure 3.10
The structure
of a nucleotide
Each nucleotide has 3 parts
1. a five-carbon sugar
2. a phosphate group
3. an organic nitrogen-
containing base
• There are five different types of
nucleotides
• information is encoded in
the nucleic acid by
different sequences of
these nucleotides
Dehydration reaction
DNA & RNA
There are two types of nucleic acids
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
• RNA is similar to DNA except that
it uses uracil instead of thymine
it is comprised of just one strand
it has a ribose sugar (instead of deoxyribose)
Figure 3.11 How DNA structure
differs from RNA
The Double Helix
The structure of DNA is a
double helix because
there are only two base pairs
possible
• Adenine (A) pairs with
thymine (T)
• Cytosine (C) pairs with
Guanine (G)
the bonds holding together a
base pair are hydrogen
bonds
a sugar-phosphate backbone
comprised of phosphodiester
bonds gives support
Structure of DNA
The hydrogen bonds of the base pairs can be broken
to unzip the DNA so that information can be copied
• each strand of DNA is a mirror image so the DNA contains
two copies of the information
Having two copies means that the information can be
accurately copied and passed to the next generation
Carbohydrates
Carbohydrates are used for energy or as
structural molecules
a carbohydrate is any molecule that contains the
elements C, H, and O in a 1:2:1 ratio
the sizes of carbohydrates varies
• simple carbohydrates – made up of one or two monomers
• complex carbohydrates – long polymers
Figure 3.3(c)
Polymers are built
from monomers:
carbohydrate
Figure 3.14 The structure of glucose
Mono- & Disaccharides
• Simple carbohydrates are
small
monosaccharides consist of
only one monomer subunit
• an example is the sugar
glucose (C6H12O6)
disaccharides consist of two
monosaccharides
• an example is the sugar
sucrose, which is formed by
joining together two
monosaccharides, glucose
and fructose
Polysaccharides
Complex carbohydrates are
long polymer chains
because they contain many
C-H bonds, these
carbohydrates are good for
storing energy
• these bond types are the
ones most often broken by
organisms to obtain energy
the long chains are called
polysaccharides
Carbohydrate storage
• Plants and animals store energy in
polysaccharide chains formed from
glucose
plants form starch
animals form glycogen
• Some polysaccharides serve structural
functions and are resistant to digestion by
enzymes
cellulose is found in the cell walls of
plants
chitin is found in the exoskeletons of
many invertebrates and in the cell walls of
fungi
Lipids
Lipids – fats and other molecules that are not soluble in water
lipids are nonpolar molecules
lipids include fats, phospholipids, and many other molecules
Figure 3.3(d) Polymers are built from monomers: lipid
Fats Used for long-term energy
storage
fats have two subunits
1. fatty acids
2. glycerol
fatty acids are chains of C
and H atoms
Glycerol contains three
carbons and forms the
backbone to which three
fatty acids are attached
Glycerol
Fatty acids How is the energy released?
Figure 3.17 Saturated and
unsaturated fats
What
forces are
at work
here?
Lipid membranes
• Biological membranes use lipids
phospholipids make up the two layers of the membrane
cholesterol (a steroid) is embedded within the membrane
• Lipids also include oils, other steroids, rubber, waxes,
and pigments
Figure 3.16 Lipids
are a key
component of
biological
membranes
What properties of
phospholipids
make them work as
a membrane?
Steroids
Lipids that have rings in their
structure
• Structural components of
membranes (cholesterol)
• Signaling molecules
(testosterone, estrogen)
Testosterone