Download Biology I Q1

STUDY PACK 1
Introduction To Biology
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Scientific method
o Observation
o Hypothesis: An educated guess for a phenomenon. Testable and makes a
prediction.
o Carefully designed and controlled experiments lead to acceptance or rejection of a
hypothesis.
o A hypothesis that fails to be disproven by multiple experiments becomes a theory.
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Law vs Theory: A theory explains while a law describes but doesn’t necessarily explain
why.
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Basic Attributes of Life
o Cellular organization: All life is composed of cell(s).
o Energy utilization: All life use energy in some form.
o Information processing: Organisms sense and integrate external signals in order
to adapt to environmental changes.
o Replication: Organisms can replicate themselves either sexually or asexually.
o Evolution: Organisms can adapt and change through generations.
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Cell Theory: All organisms are composed of cells and all cells come from preexisting
cells.
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Spontaneous Generation: A disproven scientific theory that asserted that living
creatures could arise from nonliving matter and that such processes were commonplace
and regular.
o Example: It was hypothesized that certain forms, such as fleas, could arise from
inanimate matter such as dust, or that maggots could arise from dead flesh.
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Pasteur’s Classic Experiment: An experiment that disproved the theory of spontaneous
generation and supported Cell Theory. Pasteur boiled a meat broth in a flask that had a
long neck that curved downward, like a goose. The idea was that the bend in the neck
prevented falling particles from reaching the broth, while still allowing the free flow of
air. The meat broth contained in the goose neck flask exhibited no bacterial growth while
the same meat broth in the open flask showed significant bacterial growth.
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Darwin’s Theory of Evolution: The basic idea of biological evolution is that
populations and species of organisms change over time.
o Evolution: "descent with modification," the idea that species change over time,
give rise to new species, and share a common ancestor.
o Natural selection
 Individuals in a population show variation in their characteristics.
 Some variation is heritable and can be passed from parent to offspring.
 Certain heritable traits increase an individual’s ability to survive or
reproduce.
 As a result, a population will change over time and through generations.
o Artificial selection
 An evolutionary process in which humans consciously select for or against
particular traits in organisms to forcibly induce evolution.
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Taxonomy: The practice of organizing organisms into groups or types.
o Linnaeus’ hierarchical system of classification: The groundwork of modern
taxonomy which classified species based on their observable traits and
characteristics.
o Modern taxonomy now classifies organisms based on evolutionary ancestry.

Tree of life: The tree of life expresses the idea that all life is related by common descent.
It represents Darwinian theory of derivative evolution.

Three Domains of Life
o Archaea: Prokaryotic organisms with no nuclear membrane. Distinct from
bacteria as their cellular membrane is composed of linked lipids.
 Methanogens
 Halophiles
o Eukaryote: Organisms with membrane bound nucleus.
 Animals
 Plants
 Fungi
o Bacteria: Prokaryotic organisms with no nuclear membrane with bacterial rRNA.
Distinct from Archaea as their cellular membrane are composed of ester linked
lipids and their cell wall contain peptidoglycan.
 Salmonella
 Cyanobacteria
Introduction To Biochemistry

Elements: Elements are the classification of different types of atoms. They are the
simplest substance and cannot be broken down by normal chemical reactions.

Atom: A particle of matter composed of protons and neutrons that form a nucleus, with
electrons bound to that nucleus.
o Proton: A subatomic particle that has a positive charge and that is found in the
nucleus of an atom. A proton has a mass of 1 amu.
o Neutron: A subatomic particle that has no charge and that is found in the nucleus
of an atom. A neutron has a mass of 1 amu.
o Electron: A subatomic particle that has a negative charge and a negligible mass
of .0005 amu. In simple terms, an electron has no mass.

Isotope: An atom of an element with a different number of neutrons. More neutrons than
normal.
o Can be used for carbon dating, a method of determining the age of an object using
the radioactive decay of certain isotopes.

Ion: An atom or group of atoms that has a positive or negative charge.
o Cation: A positively charged ion.
o Anion: A negatively charged ion.

Atomic Number: The number of protons in the nucleus of an atom, which determines
the chemical properties of an element and its place on the periodic table.

Atomic Mass: The number of protons and neutrons of an atom.

Chemical Bonds: Atoms bond because they want to attain a stable valence electron
configuration (2, 8, 8/18, etc), so they do so by bonding with other atoms and either
donating or borrowing an electron.
o Ionic bond: Formed when one or more electrons are transferred from one atom to
another.
o Hydrogen bond: Attraction between a slightly positive hydrogen atom and a
negatively charged atom.
o Covalent bond: A chemical bond that involves sharing a pair of electrons
between atoms in a molecule
 Polar bond: A covalent bond between atoms in which the electrons are
shared unequally.
 Non-polar bond: A covalent bond in which electrons are shared equally
by both atoms.
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Kinetic Energy: The energy an object has due to its motion
Potential Energy: Stored energy that results from the position or shape of an object
o What electrons have more potential energy?
 Electrons further from the nucleus of an atom have more potential energy.
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Valence Electrons: Electrons that are found in the outermost shell of an atom, these
electrons can form bonds.
Electron Shells
o 1st Shell: 2 electrons
o 2nd Shell: 8 electrons
o 3rd Shell: 8 electrons (18 if there exists a 4th shell)
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How can you predict the number of bonds an atom will form?
o Given an atomic number of a neutral charge atom, you know how many proteins
there are, thus you can infer the number of electrons it possesses. With that
information, you can graph its electron shells and determine the number of
electrons missing from its valence shell.
o For an atom with an atomic number of 6, there are 6 protons and thus 6 electrons.
6 electrons fills the 2 electron requirement for the first shell, and 4 electrons of the
valence shell. Thus, this atom can form up to 4 bonds to satisfy the octet rule.
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Hydrophilic molecules: Attracted to water (polar).
Hydrophobic molecules: Hate water, generally nonpolar and relatively insoluble in
aqueous solutions.
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Acid: A substance that increases the hydrogen ion concentration of a solution.
Base: A substance that decreases the hydrogen ion concentration in a solution.
Buffer: A compound that prevents sharp, sudden changes in pH.
pH Scale: Measurement system used to indicate the concentration of hydrogen ions (H+)
in solutions; ranges from 0 to 14
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Reactant: The substance that undergoes change during a reaction.
Product: The resulting substance of a chemical reaction.

Hydrolysis: Splitting of a chemical bond by the addition of water, with the H+ going to
one molecule and the OH- going to the other.
Dehydration Synthesis: A chemical reaction in which two molecules covalently bond to
each other with the removal of a water molecule.
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What must happen in order for a chemical reaction to occur?
o The reactants must be brought together.
o There must be enough energy to overcome the initial activation threshold to
permit the reaction to occur.
What affects the rate of a chemical reaction?
o Surface area, temperature, concentration, and the presence of catalysts and
inhibitors
Functional Groups
o A specific grouping of atoms within molecules that have their own characteristic
properties regardless of other atoms present in the molecule.
o These functional groups exhibit consistent function regardless of the parent
molecule they are attached to.
Introduction To Biological Macromolecules
 Four main classes of biological macromolecules
Macromolecule
Monomers
Polarity
Functions
Carbohydrates
Monosaccharides
Polar
Provides cells
with short-term
energy (broken
down into ATP)
Lipids
Fatty acids
Non-Polar
Provides longterm energy
storage
Proteins
Nucleic Acids
Amino acids
Nucleotides
Depends:
Membrane
proteins
present as
nonpolar
Cytoplasmic
proteins
present as
polar
Polar
Biological
membranes are
made of lipids
Catalyzes
chemical
reactions
Examples
Glucose
Sucrose
Starch
Cellulose
Phospholipids
Fats
Steroids
Enzymes
Antibodies
Hormones
Keratin
Signals
Cellular
identifiers
Structural
Stores and
processes
genetic
information
DNA
RNA
Protein
synthesis

Monomer: A simple compound whose molecules can join together to form polymers.

Polymer: Molecules composed of many monomers; makes up macromolecules.

How are monomers added to polymers?
o Monomers are added to polymers through enzyme catalytic reactions. This is
called polymerization.
 Monosaccharides can join together through glycosidic bonds.
 Amino acids become polypeptides through peptide bonds.
o Addition polymerization is a type of polymerization in which monomers link
together to form a chain between carbon to carbon bonds.

How are monomers removed from polymers?
o Depolymerization is when polymers revert to their monomeric constituents. This
can happen through enzyme catalyst reactions or when a polymer reaches its
ceiling temperature.
o Examples:
 The digestion of food through enzymes.
 Polymers are exposed to high temperatures which break their chemical
bonds.

Diffusion: Movement of molecules from an area of higher concentration to an area of
lower concentration.
Osmosis: Diffusion of water through a selectively permeable membrane.
Facilitated diffusion: Movement of specific molecules across cell membranes through
protein channels.
Hypertonic solution: A solution in which the concentration of solutes is greater than that
of the cell that resides in the solution.
Hypotonic solution: A solution in which the concentration of solutes is less than that of
the cell that resides in the solution.
Isotonic solution: A solution whose solute concentration is equal to the solute
concentration inside a cell.
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Macromolecules: Proteins

Amino acid: The building blocks of proteins. A compound with an amino group on one
end and a carboxyl group on the other end.
o There are 20 different types of amino acids differentiated by the R-group.

Protein: Macromolecule that contains carbon, hydrogen, oxygen, and nitrogen; needed
by the body for growth and repair. Composed of one or more polypeptides.

Peptide bond: The covalent bond that forms between the carboxyl group of one amino
acid and the amino group of another amino acid.

Polypeptide: A polymer chain of many amino acids linked together by peptide bonds.

Four levels of protein structure
o Primary: The sequence of amino acids. Proteins are constructed from a set of 20
amino acids.
o Secondary: The formation of α-helixes and β-pleated folds. Both fold types are
secured by hydrogen bonds.
o Tertiary: Overall 3D shape of a polypeptide formed by interactions between
amino acid side groups. Stabilized by bonds between R-groups or between Rgroups and the peptide’s backbone.
o Quaternary: Shape produced by combinations of multiple polypeptides.
Stabilized by bonds between R-groups of different peptides.

Side Groups: In proteins, side groups/chains are attached to the alpha-carbon atoms of
the amide backbone and are responsible for determining charge and polarity of the amino
acid. Also called the R-Group.

Enzyme: A type of protein that acts as a biological catalyst.
o Enzymes work by reducing the activation energy required by a reaction, thereby
increasing the rate of reaction.
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Substrate: The reactant being catalyzed by an enzyme.
Enzyme product: The resulting molecules of a substrate catalyzed by an enzyme.

Fischer Lock and Key Model: The substrate fits into enzyme precisely like key into a
lock.

Induced Fit Model: Enzymes conform to the substrate when binding to optimize the
physical interface.

Enzyme active site: The region of an enzyme where substrate molecules bind and
undergo a chemical reaction. Contains catalytic groups of amino acids that promote
formation and/or degradation of bonds.

Enzyme regulation
o Cofactors: Many enzymes are only active when bound to non-protein helper
molecules known as cofactors.
o Feedback inhibition: Many enzymes are inhibited by the end product of the
pathway they control. For example, the enzymes that produce ATP from glucose
will slow down as more ATP is plentiful.
o Competitive inhibition: An inhibitor that attaches to the enzyme’s active site.
o Noncompetitive inhibition: An inhibitor that shuts down an enzyme but doesn’t
block its active site, instead binding to the enzyme’s allosteric site.

What factors influence enzyme activity?
o Temperature
o pH
o Substrate concentration
o Inhibitors

Denaturation: A structural change in a protein that results in a loss of its biological
properties.
o Denaturation can be caused by excessive heat, chemical action, or agitation that
results in the unfolding or breaking of polypeptide bonds. Hydrogen bonds being
weaker can be broken more easily.

Nucleotide: A building block of DNA, consisting of a five-carbon sugar covalently
bonded to a nitrogenous base and a phosphate group.
o Composition: Sugar, phosphate, nitrogen base

Phosphodiester bond: The type of bond that links the nucleotides in DNA or RNA to
form their backbones. Joins the phosphate group of one nucleotide to the hydroxyl group
on the sugar of another nucleotide.
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Nucleic acid: Nucleic acids are used to create, encode, and store information. Composed
of nucleotides. The two main classes of nucleic acids are DNA and RNA. If the sugar is
ribose, the polymer is RNA; if the sugar is deoxyribose, the polymer is DNA.
Macromolecules: Nucleic Acids
Comparison
Function
Structural
Sugar
Base Pairs
Propagation

DNA
(Deoxyribonucleic Acid)
Long-term storage of genetic
information.
Transmission of genetic
information to make cells.
Double stranded helix
Deoxyribose sugar and
phosphate backbone
A-T (Adenine – Thymine)
G-C (Guanine – Cytosine)
DNA is self-replicating
Base Pairs are connected through hydrogen bonds
RNA
(Ribonucleic Acid)
mRNA is used to transfer
code from the nucleus to the
ribosomes to instruct them to
generate proteins.
Single stranded helix
Ribose sugar and phosphate
backbone
A-U (Adenine – Uracil)
G-C (Guanine – Cytosine)
RNA is synthesized from
DNA
Macromolecules: Carbohydrates
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Monosaccharides: Monosaccharides, also called simple sugars are the most basic form
of carbohydrates. They can be combined to create more complex carbohydrates. They
cannot be broken down by hydrolysis into simpler forms.
o Pentose Sugars: A 5 carbon monosaccharide simple sugar.
 Ribose (RNA), deoxyribose (DNA)
o Hexose Sugars: A six carbon monosaccharide.
 Glucose, fructose, galactose
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Disaccharides: Carbohydrates that are made up of two monosaccharides.
o Examples: Sucrose, lactose, maltose.
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Polysaccharides: Carbohydrates that are made up of more than two monosaccharides.
o Starch: A storage polysaccharide in plants consisting of combined glucose
monosaccharides.
o Glycogen: A storage polysaccharide found in animals, fungi, and bacteria.
Glycogen is composed of glucose monosaccharides.
o Cellulose: A polysaccharide consisting of glucose monomers that reinforces
plant-cell walls.
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Carbohydrates: Carbohydrates are saccharides, serving as the fuel of choice for the
mitochondrial processes of energy production.
o Metabolic role of carbohydrates
 Many cells consume glucose through glycolysis to release energy in the
form of ATP and NADH. Starch and glycogen store energy.
o Structural role of carbohydrates
 Many plant cell walls are composed of polysaccharides such as cellulose
that creates structural support to cells and helps regulate the effects of
hypertonicity or hypotonicity in cells.
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Glycosidic linkage: A covalent bond formed between two monosaccharides by a
dehydration reaction.

Reducing Sugar: Any carbohydrate that is capable of reducing other substances.
Reducing sugars have a free ketone or aldehyde group in their chemical composition. All
monosaccharides are reducing sugars, some disaccharides or polysaccharides can also act
as reducing sugars. Reducing sugars give away electrons, thereby reducing substances
while the sugar itself will become oxidized.
Macromolecules: Lipids

Fatty acid: Building Blocks of Lipids, either saturated or unsaturated.
o Saturated fatty acids: Only single bonds between adjacent carbon atoms.
o Unsaturated fatty acids: At least one double or triple bond between adjacent
carbon atoms.
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Lipid: Energy-rich organic compounds, such as fats, oils, and waxes, that are made of
carbon, hydrogen, and oxygen.

Triglycerides: A type of lipid. Excess calories are stored as triglycerides for later use.
o Composed of a glycerol molecule with three fatty acid chains.
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Phospholipid: A lipid that contains phosphorus and that is a structural component in cell
membranes.
o Composition: Hydrophilic head composed of a phosphate group. and two
hydrophobic tails composed of fatty acid chains.
o Phospholipids assemble into bilayers spontaneously when introduced into
aqueous environments.
 Their assembly is driven by their hydrophobic properties, and they arrange
themselves in a manner that minimizes the surface area exposed to water.
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Phospholipid bilayer selective permeability
o Gases like O2, CO2, and N2 are permeable because of their small size. Non-polar
molecules can pass through the bilayer. Polar molecules require transportation
proteins to pass through the bilayer.
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Membrane Permeability: Passive Transport
o Membrane transport that does not require energy to pass through. Passive
transport relies on the second law of thermodynamics and Fick's first law,
molecules move through kinetic energy from an area of high concentration to low
concentration through entropy.
 Examples: Simple diffusion, osmosis, facilitated diffusion.
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Membrane Permeability: Active Transport
o Membrane transport that requires cellular energy. Primary active transport uses
adenosine triphosphate (ATP) and secondary active transport uses electrochemical
gradient.
 Examples: Primary active transport, secondary active transport,
endocytosis
Origins of Life

How old is Earth?
o 4.5 billion years old

How old are the earliest forms of life on Earth?
o At least 3 billon years old

Where on Earth do we think life began?
o The bottom of the ocean.
o The depths of water provided protection of UV radiation as the ozone layer had
not yet formed in Earth’s atmosphere.
o Hydrothermal vents on the ocean floor release alkaline fluids which could supply
the energy needed to build organic molecules.
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Miller Urey Experiment
o An experiment that combined gases to simulate early prebiotic atmospheric
conditions: water, methane, ammonia, and hydrogen.
o The mixture was then electrified to simulate lightning.
o The result was that amino acids were formed, proving that organic molecules
could be generated from inorganic molecules.
o This experiment provided support to evolutionary science.

RNA world hypothesis
o A hypothetical stage in the evolutionary history of life on Earth in which selfreplicating RNA molecules proliferated before the evolution of DNA and
proteins.
o Basically it means that RNA preceded DNA and that RNA based life were the
first to exist as opposed to DNA based life.