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UNIT 1
What is Science and where does Biology fit in?
What is Science?
The word __________________ is derived from Latin and means “___________________”
An approach to understand the ________________________________
Scientific process includes making
aka the “_______________________________”
Scientists use two main approaches to learn about nature
_____________________________ science
______________________________ science
With hypothesis-based science, we pose and test hypotheses
Hypothesis-based science applies the five steps of the scientific method:
(1) ___________________________________ from others or results of earlier tests
This leads to the collection of ___________________________
Data are recorded observations or items of information; these fall into two categories
Types of Data
__________________________ data, or
___________________________ data, or
_________________________ Reasoning
_______________________ draws conclusions through the logical process of induction
________________ specific observations can lead to important __________________
For example, “the sun always rises in the east”
(2) _______________________ about unclear aspects of the observations: How? Why? When?
(3) _______________________ or tentative explanations of a phenomenon
(4) Predictions developed by the use of _____________________________________ (if...then)
(5) _______________ of predictions to determine if the predictions are supported or falsified.
A Case Study of Hypothesis-Based Science
Hypothesis: Mimicry helps protect nonpoisonous king snakes from predators where poisonous
coral snakes also live
The hypothesis predicts that predators learn to avoid the warning coloration of coral snakes
Controlled Experiment
The experiment has a ________________________ using brown artificial snakes for comparison
The _____________________________________ is artificial snakes with the red, black, and yellow
ring pattern of king snakes
Ideally, only the _______________________ of interest (the effect of coloration on the behavior
of predators) differs between the control and experimental groups
A controlled experiment means that control groups are used to ___________ the effects of
__________________________
A controlled experiment does not mean that all unwanted variables are kept _________________
What is the difference between a Hypothesis, Theory and Law?
Theories in Science
In the context of science, a ______________________ is
Broader in scope than a hypothesis
General, and can lead to new testable hypotheses
Supported by a large body of _______________________ in comparison to a hypothesis
What is biology?
Biology is the scientific study of ____________________
Life defies a simple, one-sentence definition
Life is recognized by what ___________________________________, therefore we describe life
according to seven characteristic
aka the properties of ______________________
Properties of Life
Importance of biological organization
New Properties Emerge at Each Level in the Biological _________________________
Life can be studied at different ______________, from molecules to the entire living _____________
The study of life can be divided into different levels of biological organization
Emergent Properties
___________________________________ result from the arrangement and interaction of
parts within a system
Emergent properties characterize ____________________________ entities as well
For example, a functioning bicycle emerges only when all of the necessary parts connect
in the correct way
Systems Biology
A system is
Systems biology constructs
The systems approach poses questions such as
How does a drug for blood pressure affect other organs?
How does increasing CO2 alter the biosphere?
The core theme of Biology is _______________________________
Evolution makes sense of everything we know about biology
Evolution explains patterns of ______________ and ___________________ in living organisms
Similar traits among organisms are explained by ___________________________________
Differences among organisms are explained by the accumulation of ___________________
The Three Domains of Life
Unity in the Diversity of Life
A striking unity underlies the diversity of life; for example
_______________ is the universal genetic language common to all organisms
All organisms are made up of _____________
What does Chemistry have to do with Biology?
A Chemical Connection to Biology
Biology is a ____________________________ science
Living organisms are ___________________ to basic laws of physics and chemistry
One example is the use of formic acid by ants to maintain “devil’s gardens,” stands of Duroia trees
The Chemical Basis of Life
Matter consists of chemical elements in pure form and in combinations called compounds
Matter
Elements
Compounds
The Elements of Life
About ___________% of the elements are ______________________________ elements
_____________________ elements are those required by an organism in minute quantities
The smallest unit of an element is an __________________.
Atoms are composed of subatomic particles
Where are they located in the atom?
How do you calculate the amount of subatomic particles in the atom?
Atomic number
Atomic mass
How can we determine the number of neutrons in an atom?
Do all carbon atoms have the same number of protons?
Do all carbon atoms have the same number of neutrons?
Isotopes
____________________________ isotopes decay spontaneously, giving off particles and energy
Some applications of radioactive isotopes in biological research are
Dating _____________________
Tracing ____________________ through metabolic processes
Diagnosing ___________________ disorders
Electron arrangement determines the chemical properties of an atom
Electrons in an atom are arranged in _____________________________, which may contain different
numbers of electrons
______________________ electrons are those in the ________________ shell, or valence shell
The chemical behavior of an atom is mostly determined by the ____________________electrons
Elements with a full valence shell are chemically _____________________
When is the valence shell full?
The formation and function of molecules depend on chemical bonding between atoms
Atoms with incomplete valence shells can ________________ or _________________ valence
electrons with certain other atoms
These interactions usually result in atoms staying close together, held by attractions called _____
_________________________ Bonds
Covalently bonded
Covalent bonds can be represented in various ways
For example
Electronegativity and covalent bonds
Electronegativity is an atom’s
The ____________ electronegative an atom, the ___________ strongly it pulls shared
electrons toward itself
For example Oxygen has a _____________ electronegativity
Unequal electron sharing creates polar molecules
Ionic Bonds
What is a Cation and an Anion?
A cation is a ______________________ charged ion
An anion is a ______________________ charged ion
Hydrogen bonds are
The attraction between slightly _________________ regions and slightly _________________
regions creates ___________________ bonds
Hydrogen bonding occurs in many biologically important compounds
Chemical reactions make and break chemical bonds
Chemical reactions are
The starting molecules of a chemical reaction are called _______________________
The final molecules of a chemical reaction are called ___________________________
All chemical reactions are reversible: products of the forward reaction become reactants for the
reverse reaction
Water and Life
The Molecule That Supports ___________ of Life
_____________ is the biological ______________________ on Earth
All living organisms require _____________________ more than any other substance
Most cells are surrounded by ____________, and cells themselves are about _______% water
The abundance of water is the main reason the Earth is ______________________
Four emergent properties of water contribute to Earth’s suitability for life
Four of water’s properties that facilitate an environment for life are
Cohesion of Water Molecules
Collectively, hydrogen bonds hold water molecules together, a phenomenon called ________
Cohesion helps the __________________ of water against ______________ in plants
________________________ is an attraction between different _________________,
for example, between water and plant cell walls
________________ ____________________ is a measure of how hard it is to break
the surface of a liquid
Surface tension is related to __________________________________
Moderation of Temperature by Water
It takes a ______________ amount of ______________ to change the temperature of water
The specific heat of water is ___ cal/g/ºC
Water ______________ changing its temperature because of its high specific heat
Water’s high specific heat can be ___________________ to hydrogen bonding
Heat is _______________________ when hydrogen bonds ______________
Heat is _______________________ when hydrogen bonds ______________
Water also moderates temperature by evaporative cooling
Floating of Ice on Liquid Water
Ice floats in liquid water because hydrogen bonds in ice are more “__________________,”
making ice less dense
Water reaches its greatest density at ___°C
Water: The Solvent of Life
A _____________________ is a homogeneous mixture of a liquid ___________________
and one or more dissolved ______________________
What is the difference between a solution, solvent, and solute?
An ___________________ solution is one in which ________________ is the solvent
Water is a versatile _______________ due to its _________________, which allows it to form
________________________ bonds easily
When an ionic compound is dissolved in water, each ion is surrounded by a sphere of
water molecules called a ____________________________
Water can also ____________________ compounds made of nonionic polar molecules
Even large polar molecules such as proteins can dissolve in water if they have ionic
and ____________________ region
Acidic and basic conditions affect living organisms
What is an acid and a base?
___________________ is a compound that _______________ H+ ions in solution
___________________ is a compound that _______________ H+ ions in solution
Therefore the pH scale measures the
How do you change the pH of a solution?
Let’s say you have a well stocked kitchen and no antacids, what would you consume if you
were suffering from heartburn?
Buffers
The internal pH of most living cells must remain close to pH 7
_______________ are substances that minimize changes in concentrations of H+ and OH– in a
solution
Most buffers consist of an _______________________ pair that reversibly combines with ___
Carbon and the Molecular Diversity of Life
Carbon: The Backbone of Life
Living organisms consist mostly of carbon-based compounds (___________________)
Carbon is ___________________ in its ability to form large, complex, and diverse molecules
Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all
composed of ________________________ compounds
The Formation of Bonds with Carbon
With ______ valence electrons, carbon can form four covalent bonds with a variety of atoms
This ______________ makes large, complex molecules possible
The electron configuration of carbon gives it covalent compatibility with many different elements
The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are
the “___________________________” that governs the architecture of living molecules
Molecular Diversity Arising from Carbon Skeleton Variation
__________________________ chains form the skeletons of most organic molecules
Carbon chains vary in _____________________ and ____________________
Hydrocarbons
A few chemical groups are key to the functioning of biological molecules
Distinctive properties of organic molecules depend on the carbon skeleton and on the
molecular components __________________________ to it
A number of characteristic groups can _____________________ the hydrogens attached to
skeletons of organic molecules
The Chemical Groups Most Important in the Processes of Life
_________________________ groups are the components of organic molecules that are most
commonly involved in ________________________ reactions
The ________________ and ____________________ of functional groups give each
molecule its unique properties
The seven functional groups that are most important in the chemistry of life:
The Structure and Function of Large Biological Molecules
Cells make a huge number of large molecules from a small set of small molecules
Four main classes of biological macromolecules
Cells __________________ the most of their large molecules by joining smaller organic
___________________ into chains called ____________________
Monomers are usually linked by ____________________________ reactions
A _________________ molecule is ____________________
Polymers are _______________ down to monomers by the reverse process, _____________
A _________________ molecule is ____________________
Now let’s look at the four major organic molecules needed for life.
CARBOHYDRATES
Carbohydrates serve as ________________ and ___________________ material
What are the different types of carbohydrates?
______________________
Monosaccharides (single sugars) are carbohydrate ___________________
Monosaccharides have molecular formulas that usually have a ratio of 1:2:1 (C:H:O)
___________________ (C6H12O6) is the most common monosaccharide
______________________
A disaccharide is formed when a dehydration reaction joins ______ monosaccharides
This covalent bond is called a _________________________
The monosaccharide and disaccharide are primarily used for ______________ purposes
______________________
Polysaccharides, the ______________ of sugars, have storage and structural roles
The structure and function of a polysaccharide are determined by its sugar
________________ and the ______________________ of glycosidic linkages
________________________________________
__________________, a storage polysaccharide of _______________ consists
entirely of glucose monomers
Plants _____________ surplus starch as granules within chloroplast and other plastids
The simplest form of starch is ____________________
_____________________ is a storage polysaccharide in ___________________
Humans and other vertebrates store glycogen mainly in liver and muscle cells
________________________________________
The polysaccharide ___________________ is a major component of the tough wall of
plant cells
Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
LIPIDS
Fats/Lipids
Lipids are diverse compounds consisting mainly of carbon and hydrogen atoms
Linked by _____________________ covalent bonds
____________________________ (water-fearing)
___________, also called ___________________ or ______________________, are
lipids whose main function is energy _____________________
Polymers of ________________________________ (usually three molecules)
and one ______________________________ molecule
What is the difference between fats and oils?
What is the difference between saturated and unsaturated fats
Fatty acids vary in length (number of carbons) and in the number and locations
of double bonds
______________________ fatty acids have the maximum number of
hydrogen atom possible and no double bonds
_______________________ fatty acids have one or more double bond
The major function of fats is ____________________________
Humans and other mammals store their fat in _______________________
Adipose tissue also ______________ vital organs and _________________ the body
Phospholipids
In a ________________________, two fatty acids and a phosphate group are attached
to _____________________
The two fatty acid tails are _________________________, but the phosphate group
and its attachments from a _______________________________ head
When phospholipids are added to water, they self-assemble into a _______________,
with the hydrophobic tails pointing towards the ___________________
The structure of phospholipids results in a bilayer arrangement found in _______________
Phospholipids are the ________________________ component of all cell membranes
Steroids
__________________ are lipid characterized by a carbon skeleton consisting of four
fused rings
______________________, and important steroid, is a component in animal cell membranes
Although cholesterol is essential in animals, high levels in the blood may contribute to
______________________
PROTEINS
Proteins include a diversity of structures, resulting in a wide range of ___________________
Proteins account for more than _____% of the dry mass of most cells
Proteins functions include
A protein is a polymer constructed from _______________________ monomers
Amino acids are organic molecules with _____________ and _______________ groups
Amino acids differ in their properties due to differing side chains, called ____ groups
Amino Acid Polymers
Amino acids are linked by ________________________ bonds
A polypeptide is a ___________________ of amino acids
Polypeptides range in length from a few to more than a thousand monomers
Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end
(____________________) and an amino end (_____________________)
Protein Structure and Function
A functional protein consists of one or more polypeptides precisely twisted, folded, and
coiled into a unique shape
The sequence of amino acids determines a protein’s ______________________ structure
A protein’s ______________________ determines its ________________________
A protein's shape depends on four levels of structure
NUCLEIC ACIDS
Nucleic acids _________________, ___________________, and help __________________
hereditary information
The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a _______
Genes are made of ________, a nucleic acid made of monomers called __________________
There are two types of nucleic acid-DNA and RNA
DNA vs RNA
DNA is a ______________________
DNA uses a nitrogenous bases _____________________________
DNA is composed of _______________________________ sugar
Specific sequences of DNA make up genes that program the amino acid sequences of proteins
RNA is ___________________________________
RNA uses a nitrogenous bases ___________________________
RNA is composed of ______________________________ sugar
RNA copies the genes and carries the code to a ribosome so that it can be translated to a protein
Why should we care about the cell?
Why is it important to know about cells?
Cell theory
1.
[Schleiden & Schwann]
2
[Virchow]
There are two kinds of cells
_____________________ & ___________________________
Only organisms of the domains ___________________ and _________________ consist of
prokaryotic cells
Protists, fungi, animals, and plants all consist of _________________ cells
Comparing Prokaryotic and Eukaryotic Cells
Basic features of all cells
Prokaryotic cells are characterized by having
No _____________________
DNA in an unbound region called the ________________________
No membrane-bound __________________________
__________________________ bound by the plasma membrane
Eukaryotic cells are characterized by having
DNA in a ___________________ that is bounded by a _______________________________
Membrane-bound ___________________________
Cytoplasm in the region between the plasma membrane and nucleus
Eukaryotic cells are generally much _______________________ than prokaryotic cells
Eukaryotic cells are partitioned into functional compartments
Distinguished by a true _____________________________
Contain both membranous and nonmembranous ________________________
So let’s look at an animal and plant cell
Animal cells
Are bounded by the ____________________________________ alone
Lack a ______________________________
Contain ________________________ and _______________________________
Often have ________________________________
Plant cells
Are bounded by both a plasma membrane and a rigid cellulose ___________________
Have a _____________________________ and _____________________________
Usually ___________________ centrioles, lysosomes, and flagella
Cell Structures
Nucleus, Cytoplasm (Cytosol and organelles) and Cell/Plasma Membrane
Nucleus
The nucleus is the cell's _______________________________ control center
The nucleus contains the cell's ___________________
Controls cellular activities by directing ______________________ synthesis
The nucleus is separated from the cytoplasm by the ______________________ envelope
______________________ in the envelope control flow of materials in and out
Ribosomes are synthesized in the ___________________________
Cytoplasm is composed of ___________________ and __________________________
Cytosol
Organelles
___________________________ and ________________________________
___________________________ make proteins for use in the cell and export
Two types ___________________ and _____________________ ribosomes
The __________________________ system regulates protein traffic and performs
metabolic functions in the cell
Components of the endomembrane system
These components are either continuous or connected via transfer by _____________
The ___________________________________________
Broken into two parts
_______________________ lacks attached ribosomes
_______________________ lipids
Processes materials such as toxins and drugs in liver cells
_______________________
Has bound ribosomes, which secrete ____________________________
(proteins covalently bonded to carbohydrates)
Distributes _________________________, proteins surrounded by membranes
Is a membrane ___________________ for the cell
The ___________________________________: Shipping and Receiving Center
The Golgi apparatus consists of flattened membranous sacs called _______________
Functions of the Golgi apparatus
_________________________ products of the ER
__________________________ certain macromolecules
________________ and ______________________ materials into transport vesicles
___________________________: Digestive Compartments
A ____________________________ is a membranous sac of hydrolytic enzymes that can
digest macromolecules
Lysosomal enzymes can ____________________ proteins, fats, polysaccharides, and
nucleic acids
A lysosome ____________________ with the food vacuole and digests the molecules
Lysosomes also use enzymes to ___________________ the cell’s own organelles and
macromolecules, a process called ________________________
_____________________________: Diverse Maintenance Compartments
A plant cell or fungal cell may have one or several __________________________,
derived from endoplasmic reticulum and Golgi apparatus
_____________________________ are formed by phagocytosis
__________________________ vacuoles, found in many freshwater protists, pump excess
water out of cells
__________________ vacuoles, found in many mature plant cells,hold organic
compounds and water
The Endomembrane System: A Review
The endomembrane system is a complex and dynamic player in the cell’s compartmental
organization
Energy-converting organelles
Mitochondria ________________ chemical energy from ____________________
Mitochondria are found in nearly all eukaryotic cells
Made of __________ membranes
Carry out __________________________________________
Convert the chemical energy in food to _______________ for cellular work
Chloroplasts convert ___________________ energy to ___________________ energy
Chloroplasts are found in plants and some protists
Are the site of ________________________________
Have a complex membranous structure for capturing
Mitochondria and chloroplasts evolved by _________________________________
Proposes that the mitochondria and chloroplast were formerly small prokaryotes that
began living in larger cells
____________________________: Oxidation
Peroxisomes are
Peroxisomes produce __________________________ and convert it to water
Peroxisomes perform _________________________ with many different functions
How peroxisomes are related to other organelles is still unknown
The cytoskeleton is a network of fibers that organizes structures and activities in the cell
The cytoskeleton is a network of fibers extending throughout the _____________________
It _______________________ the cell’s structures and activities, anchoring many organelles
It is composed of three types of molecular structures
Microtubules
_______________________________ are hollow rods about 25 nm in diameter and about
200 nm to 25 microns long
Functions of microtubules
___________________ the cell
Guiding ________________________ of organelles
_____________________________ chromosomes during cell division
Centrosomes and Centrioles
In many cells, microtubules grow out from a ________________ near the nucleus
The centrosome is a “__________________________________________”
In animal cells, the centrosome has a pair of _______________________, each
with nine triplets of microtubules arranged in a ring
Cilia and Flagella
Microtubules control the beating of __________ and ___________________,
locomotor appendages of some cells
Cilia and flagella differ in their _________________________ patterns
Microfilaments (Actin Filaments)
________________________________ are solid rods about 7 nm in diameter, built as
a twisted double chain of ________________________ subunits
Function in
Maintenance of cell _____________________________
_________________________ in cell shape
_____________________________ contraction
Cytoplasmic ____________________________
Cell ___________________________ (as in psuedopodia)
Cell ___________________________ (cleavage furrow formation)
Intermediate Filaments
_______________________________________ range in diameter from 8–12
nanometers, larger than microfilaments but smaller than microtubules
They __________________________ cell shape and fix organelles in place
Intermediate filaments are more permanent cytoskeleton fixtures than the other two classes
Membrane Structure and Function
Life at the Edge
The plasma membrane is the boundary that separates the living cell from its surroundings
The plasma membrane exhibits __________________________________, allowing
some substances to cross it more easily than others
Cellular membranes are fluid _______________________ of lipids and proteins
______________________ are the most abundant lipid in the plasma membrane
Phospholipids are __________________________ molecules, containing hydrophobic and
hydrophilic regions
The fluid mosaic model states that a membrane is a fluid structure with a “mosaic” of
various proteins embedded in it
Membrane Proteins and Their Functions
A membrane is a collage of different proteins, often grouped together, embedded in the
fluid matrix of the lipid ____________________________
Proteins determine most of the membrane’s specific _____________________________
______________________ proteins are bound to the surface of the membrane
______________________ proteins penetrate the hydrophobic core
Six major functions of membrane proteins
The Role of Membrane Carbohydrates in Cell-Cell Recognition
Cells recognize each other by _________________ to surface molecules, often containing
carbohydrates, on the extracellular surface of the plasma membrane
Membrane carbohydrates may be covalently bonded to lipids (forming ___________________)
or more commonly to proteins (forming _________________________)
Carbohydrates on the external side of the plasma membrane vary among species,
individuals, and even cell types in an individual
Membrane structure results in ______________________________________
A cell must ________________________ materials with its surroundings, a process
controlled by the ________________________
Plasma membranes are selectively permeable, ____________________________ the
cell’s molecular traffic
The Permeability of the Lipid Bilayer
_____________________________ (nonpolar) molecules, such as hydrocarbons, can
dissolve in the lipid bilayer and pass through the membrane rapidly
Polar molecules, such as sugars, ____________________ cross the membrane easily
Passive transport is
____________________ is a process in which particles spread out evenly in an available space
Particles move from an area of ________________ concentrated particles to an area
where they are _________________ concentrated
This means that particles diffuse down their _________________________________
Do the particles ever stop moving?
Diffusion across a cell membrane does not require energy, so it is called _______________
Osmosis is the
Water moves across membranes in response to solute concentration inside and outside of
the cell by a process called ___________________________
Water balance between cells and their surroundings is _________________ to organisms
_________________________ is a term that describes the ability of a solution to cause a cell
to gain or lose water
Tonicity is dependent on the concentration of a ___________________________
solute on both sides of the membrane
Tonicity
______________________ indicates that the concentration of a solute is the same on
both sides
______________________ indicates that the concentration of solute is higher
outside the cell
______________________ indicates a higher concentration of solute inside the cell
Osmoregulation
Many organisms are able to maintain water balance within their cells by a process
called ___________________________________
This process __________________ excessive uptake or excessive loss of water
Transport proteins may facilitate diffusion across membranes
Many substances that are necessary for _____________________ of the cell do not freely
diffuse across the membrane
They require the help of specific transport proteins called _______________________
These proteins assist in ______________________________, a type of passive
transport that does not require ________________________
Cells expend energy in the active transport of a solute against its concentration gradient
Cells have a mechanism for moving a solute _______________ its concentration gradient
It requires _________________________
The mechanism alters the shape of the membrane protein through
_____________________________ using ATP
Active transport allows cells to maintain concentration gradients that differ from their
surroundings
The ________________________________ pump is one type of active transport system
_____________________ and _______________________ transport large molecules across
membranes
A cell uses two mechanisms for moving large molecules across membranes
_______________________ is used to export bulky molecules, such as proteins or
polysaccharides
_______________________ is used to import substances useful to the livelihood of
the cell
In both cases, material to be transported is packaged within a vesicle that fuses with the
membrane
There are _____________________ kinds of endocytosis