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Unit 1: Chemistry and Cells
Chapter 2: The Chemical Context of Life
2
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The Elements of Life
 Essential elements: a chemical element required for an organism to
survive, grow, and reproduce
...
2 An element’s properties depend on the structure of its atoms
 atom: the smallest unit of matter that retains the properties of an element
Subatomic particles
 Neutrons: a subatomic particle having no electrical charge with a mass
of about 1
...
One or more electrons move around
the nucleus
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3 The formation and function of molecules depends on chemical bonding between
atoms
 chemical bonds: result of interaction, hold atoms together 
Covalent Bonds

 covalent bond: when two atoms share a pair of valence electrons 
molecule: consists of two or more atoms held together by covalent bonds 
single bond: (H-H)  double bond: (H=H) electronegativity: the attraction
of a particular atom for shared electrons  nonpolar covalent bond: if one
element is more electronegative, it pulls the shared electrons closer to itself,
creating a polar covalent bond 
Ionic Bonds
 Ion: charged atom cation: a positively charged atom  anion:
negatively charged atom  ionic bond: holds atoms together due to attraction
of opposite charges  ionic compounds: 3D crystalline lattice arrangement
held together by electrical attractions
...

Vans der Waals Interactions
 van der Waals interactions: all atoms and molecules are
attracted to each other when in close contact 
Molecular Shape and Function
 A molecule’s characteristic size and shape affect how it interacts with
other molecules
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2
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Matter is conserved in chemical reactions
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2
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Cohesion of Water Molecules
 cohesion creates a more structurally close organized liquid 
adhesion:  surface tension:
Moderation of Temperature by Water
Temperature and Heat
 kinetic energy:  thermal energy:  temperature:  heat:
 calorie:  kilocalorie:  joule: 
Water’ High Specific Heat
 specific heat 
Evaporative Cooling
 heat of vaporization:  evaporative cooling: 
Floating of Lice on Liquid Water
Water: The Solvent of Life
 solution:  solvent:
Hydrophilic and Hydrophobic Substances
Solute Concentration in Aqueous Solutions
Acids and Bases

The pH Scale
Buffers
Acidification: A Threat to our Oceans

Chapter 3: Carbon and the Molecular Diversity of Life
What is an
organic
compound?

 organic compound: compound containing carbon 
3
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Each carbon atom acts an intersection point from which a molecule can
branch off in as many as four directions
...


 The electron configuration of carbon gives it covalent compatibility
with many different elements
...
Thus, the two double bonds in CO2 have the same number of shared
electrons as four single bonds
...

Molecular Diversity Arising from Variation in Carbon Skeletons
 Hydrocarbons: consist of only carbon and hydrogen hydrocarbons
are the major components of petroleum (fossil fuel)  neither petroleum nor
fat dissolve in water both are hydrophobic compounds because the great
majority of their bonds are relatively non-polar carbon to hydrogen linkages
...



The Chemical Groups Most Important to Life

ATP: An Important Source of Energy for Cellular Processes
 adenosine triphosphate (ATP): consists of the organic molecule
adenosine to which three phosphate groups are attached  adenosine attached

to a string of three phosphate groups = ATP  when three phosphates are
present, one phosphate may split off as a result of a reaction with water
...
2 Macromolecules are polymers, built from monomers
 polymer: chainlike molecules formed from the linking together of monomers
 monomers: identical small molecules 
The Synthesis and Breakdown of Polymers
 Enzymes catalyze both dehydration reactions and hydrolysis 
dehydration reaction: one monomer provides a hydroxyl group and the other
contributes a hydrogen to release a water molecules
...
3 Carbohydrates serves as fuel and building material
 Carbohydrates:
Sugars
 Monosaccharides: have the general formula of CH2O  the number
(n) of these units forming a sugar varies from three to seven, with hexoses
(C6H12O6), trioses, and pentose being the most common
...
Sugar molecules
that are not used in this way are generally incorporated as monomers into
disaccharides or polysaccharides  disaccharide: two linked monosaccharides
 glyosidic linkage: links two monosaccharides to create a disaccharide 

What is a
function of a
lipid?

Polysaccharides
 Polysaccharides: are storage or structural macromolecules
...

 glycogen: a highly branded polymer of glucose as an animal energy
storage unit
Structural Polysaccharides:
 Cellulose: the major component of plant cell walls, differs
from starch and glycogen by the configuration of the ring form of
glucose and the resulting geometry of the glycoside bonds
...
4 Lipids are a diverse group of hydrophobic molecules
 lipids: do not form polymers, mix poorly with water
Fats
 fat: composed of fatty acids attached to the glycerol  saturated fatty
acid: have no double bonds in their carbon chains  unsaturated fatty acid:
fatty acids with double bonds  fats are excellent energy storage molecules,
containing twice the energy of carbohydrates such as starch
...
 ^Ideal for cell walls
...

What can a
protein do?

3
...
Plants have storage proteins in their seeds
...

Transport Proteins:
Function: Transport of substances
Ex: Hemoglobin, the iron-containing protein of vertebrate blood,
transports oxygen from the lungs to other parts of the body
...

Hormonal Proteins:
Function: Coordination of an Organism’s activities
Ex: Insulin, a hormone secreted by the pancreas, causes other
tissues to take up glucose, thus regulating blood sugar
concentration
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Contractile and motor proteins
Function: Movement
Ex: Motor proteins are responsible for the undulations of cilia and
flagella
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Structural proteins
Function: Support
Ex: Keratin is the protein of hair, horns, feathers, and other skin
appendages
...
Collagen and elastin proteins
provide a fibrous framework in animal connective tissues
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
Protein Structure and Function
 A protein has a unique 3-d structure created by folding one or more
polypeptide chains
...

Depending on the sequence of amino acids, various types of bonds form
between parts of the chain as protein is synthesized in the cell
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Globular proteins are roughly spherical  fibrous proteins are long fibers
 Primary Structure: the genetically coded sequence of amino acids
within a protein
...
A ἀ helix is a coil produced by hydrogen bonding
between every fourth amino acid
...
The following chemical interactions help produce the stable and unique
shape of a protein:  Hydrophobic interactions between nonpolar side groups
clumped in the center of the molecule fuel to their repulsion by water, vans der
Waals interactions among those nonpolar side chains, and ionic bonds between
negatively and positively charged side chains
...
The individual polypeptide subunits are held together in
a precise structural arrangement to form a function protein
...

What determines Protein Structure?
 The bonds and interaction that maintain that 3-d shape of a protein
may be disrupted by changes in pH, salt concentration, or temperature, causing
a protein to unravel
...
 With X-ray crystallography biochemists have
identified the structure of thousands of proteins
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
3
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 Nucleic Acids: are polymers made of nucleotide monomers
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to the next and is
replicated when a cell divides
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The Components of Nucleic Acids
 Polynucleotides are polymers of nucleotides: monomers that consist of
pentose (5carbon sugar) bonded to a phosphate group and nitrogen base 

Nitrogenous bases are either pyrimidines or purines, consist of one of two
nitrogen containing rings
...
 In a nucleotide, the base
attaches to 1 carbon and a phosphate group attaches to the 5 carbon of the
sugar
...

 Adenine  thymine; Guanine Cytosine  RNA molecules are
usually single polynucleotides 
DNA and Proteins as Tape Measures of Evolution
 Genes form the hereditary link between generations  closely related
members of the same species share many common DNA sequences
...
1 Biologist use microscopes and the tools of biochemistry to study cells
Microscopy
 microscopes invented in 1590  cell wall was first seen by Robert
Hooke in 1674 
 Light Microscope (LM): visible light is passed through the specimen
and then through glass lenses
...

 The three important parameters of microscopy: magnification,
resolution, and contrast  Magnification: the ratio of an object’s image size to
its real size
...
 Contrast: the difference in brightness between light and
dark areas of an image  methods for increasing contrast include staining or
labeling cell components 
 organelles: the membrane enclosed structures within eukaryotic cells
 Electron Microscope (EM): focuses a beam of electrons through a specimen
or onto its surface  Resolution is inversely related to the wavelength of the
radiation a microscope uses for imaging and electron beams have much shorter
wavelengths than visible light 
 Transmission electron microscope (TEM): aims an electron beam
through a very thin section of a specimen – the specimen has been stained with
atoms of heavy weights, which attaches to certain cell structures  the image
displays a pattern of transmitted electrons  uses electromagnets as lenses to
bend the paths of the electrons 
 Scanning Electron Microscope: controlled by electromagnetic
“lenses”, an electron beam scans the surface of the sample, usually coated with
a thin film of gold  the beam excites electrons on the surface and these
secondary electrons are detected by a device that translates the pattern of
electrons into an electronic signal to a video screen
...
2 Eukaryotic Cells have internal membrane that compartmentalize their functions
 two types of cells: eukaryotic and prokaryotic 
Comparing Eukaryotic and Prokaryotic Cells
How are they the same?

 All cells are bound by a plasma membrane, which encloses a
semifluid called cytosol
...
3 The eukaryotic cell’s genetic instructions are housed in the nucleus and
carried out by ribosomes
The Nucleus: the Information Central
 the nucleus is surrounded by the nuclear envelope, a double
membrane perforated by pores – the inner membrane is lined by the
nuclear lamina most of the cell’s DNA is located in the nucleus,
where it is organized into units called chromosomes, some are made
up of chromatin
 nucleolus: a dense structure visible in the no dividing
nucleus, synthesizes ribosomal RNA (rRNA) and combines it with
protein to assemble ribosomal subunits 
Ribosome: Protein Factories
 ribosomes: composed of protein and ribosomal RNA – most
of the proteins produced from free ribosomes are used with the
cytosol – protein produced by bound ribosomes attached to the
endoplasmic reticulum or nuclear envelope will usually be packaged
into organelles or exported from the cell 
4
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 Proteins intended for secretion are manufactured by membranebound ribosomes and then threaded into the lumen of the rough ER  many
are covalently bounded to small carbohydrates to form glycoproteins
...
5 Mitochondria and Chloroplasts change energy from one form to another
The Evolutionary Origins of Mitochondria and Chloroplasts
Mitochondria: Chemical Energy Conversion
Chloroplasts: Capture of Light Energy
Peroxisomes: Oxidation
4
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7 Extracellular components and connections between cells help coordinate cellular
activities
Cell Walls of Plants
The Extracellular Matric (ECM) of Animal Cells
Cell Junctions
Plasmodesmata in Plant Cells
Tight Junction, Desmosomes, and Gap Junctions in Animal Cells
The Cell: A living unit greater than the Sum of its Parts

Chapter 5: Membrane Transport and Cell Signaling
 Selective permeable: membrane allows some substance to cross more easily that others 
5
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
Membrane is held together by hydrophobic interactions, which are much weaker than covalent bonds 
Extreme environments pose a challenge for life, resulting in evolutionary adaptions that include differences
in membrane lipid composition
...
Because
 Fluid …
...

 Mosaic … it is made up of many different parts (integral proteins, peripheral proteins, glycoproteins)
 Lipid Bilayer … of its phospholipid component that can fold in itself creating a double layer (bilayer)
when placed in a polar surrounding, like water
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 Some bacteria and Archea that thrive in
temperatures > 90 degrees C, their membranes have unusual lipids that help prevent excessive fluidity
...



Six Major Functions of performed
by Protein:
1
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Protein that spans
the membrane may
provide a
hydrophilic channel
across the
membrane that is
selective for a
particular solute
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Transport proteins
that shuttles a
substance across
the membrane by
changing shape  some of these proteins hydrolyze ATP as an energy source to
actively pump substance across the membrane
2
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A protein built into the membrane may be an enzyme with its active site exposed
to substances
3
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Microfilaments or other elements of the cytoskeleton may be non - covalently
bound to membrane proteins, a function that helps maintain cell shape and
stabilizes the location of certain membrane proteins
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Proteins that bind to ECM molecules can coordinate extracellular and intracellular
changes
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Cell-cell recognition
a
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This type of cell-cell is usually short livded
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Intercellular Joining
a
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This type of binging is longer lasting
6
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A membrane protein (receptor) may have a binding site with a specific shape that
fits the shape fo the chemical messenger (ex: hormone) The external messenger
(signaling molecule) may cause the protein to change shape, allowing it to relay the
message to the inside of the cell, usually by binding to a cytoplasmic protein
...


Synthesis and Sidedness of Membranes
 The asymmetric arrangement of proteins, lipids, and their associated carbohydrates in
the plasma membrane is determined as the membrane is being built by the endoplasmic reticulum
(ER) and Golgi apparatus
...
2 Membrane Structure results in selective permeability
 The plasma membrane permits a regular exchange of nutrients, waste products, oxygen, and
inorganic ions
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
5
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 Water
diffuses down its own concentration gradient, which is affected by the solute concentration
...
 An animal cell will neither gain nor lose water in an isotonic environment
...
 If placed in a hypotonic
solution, the cell will gain water, swell, and possible lyse (burst)
...
Water
moving into the cell cause the cell to
swell against the cell wall creating
turgor pressure  turgid cells
provide mechanical support for nonwoody plants
...
In a
hypertonic medium, a plant cell
undergoes plasmolysis – the plasma
membrane pulls away from the cell
wall as water exits 

Facilitated Diffusion
 Facilitated diffusion involves the diffusion of polar molecules and ions across a
membrane with the aid of transport proteins (either channel proteins or carrier proteins)  Many
ion channels are gated channels which open and close in response to electrical or chemical stimuli
...
4 Active Transport uses energy to move solutes against their gradients
The need for energy in Active Transport
 Active transport: to pump a solute across a membrane against its gradient requires work;
the cell must expend energy  is essential if a cell is to maintain internal concentration of small
molecules that differ from their concentration outside of the cell  ATP may be transferred to a
carrier protein, inducing it to change its shape and translocate the bound solute across the
membrane
...

How Ion pumps maintain membrane potential
 cells have a membrane
potential, a voltage across the plasma
membrane due to the unequal
distribution of ions on either side 
this electrical potrntial energy results
from the separation of opposites
charges: the cytoplasm of a cell is
negatively charged relative to the
extracellular fluid
...

Both the membrane potential and the
concentration gradient affects the
diffusion of an ion; thus an ion
diffuses down its electrochemical
gradient
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A proton pump that transports H out of the cell generates voltage across
membrane in plants, fungi, and bacteria
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5 Bulk Transport across the plasma membrane occurs by exocytosis
Exocytosis
 the cell secretes biological molecules by fusion of vesicles with the plasma membrane 
exocytosis  Golgi Appartus makes transport vesicle  TV moves along microtublues  vesicle
fuses with cell membrane  contents spill to ouside of the cell 
Endocytosis
 Endocytosis: the cell takes in molecules and particulate matter by forming new vesicles
from the plasma membrane 
Three types of Endocytosis
1
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Pinocytosis: cell continually “gulps” droplets of extracellular fluid into tiny vesicles

3
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5
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Sutherland investigated how the animal hormone epinephrine (adrenaline)
stimulates the breakdown of the storage polysaccharide glycogen within liver cells and skeletal
muscle cells  Epinephrine does not interact directly with the enzyme responsible for glycogen
breakdown; an intermediate step or series of steps must be occurring inside the cell
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Reception: the target cell’s detection of a signaling molecule coming from outside the cell
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2
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The third stage of cell signaling, the transduced signal trigger a specific cellular response
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 the cell-signaling process helps ensure that crucial activities like these occur in the right
cells, at the right time, and in proper coordination with the activities of other cells the organism
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 Most ligands
are large and water-soluble, and they bind to receptors in the plasma membrane 
Receptors in the Plasma Membrane
 G protein-couple receptor (GPCR): a cell-surface transmembrane receptor that works
with the aid of a G protein  Binding of the appropriate signaling molecule to a G protein-couple
receptor activates the receptor which then binds to and activates a specific G protein located on the
cytoplasmic side of the membrane  G protein: a protein that binds the energy-rich molecule
GTP (similar to ATP) 
 ligand-gated ion channel: a membrane receptor that has a region that can act as a “gate;
for ions when the receptor assumes a certain shape  when a signaling molecules binds as a ligand
to the receptor protein, the gate opens or closes, allowing or blocking the diffusion of specific ions
(ex: Na, Ca) through a channel in the protein  these proteins bind the ligand at a specific site on
their extracellular side
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
Intracellular Receptors
 Hydrophobic chemical messengers and small signaling molecules such as the nitric
oxide may cross a cell’s plasma membrane and bind to receptors in target cells that function as
transcription factors that regulate gene expression 
Transduction by Cascade of molecular Interactions
 The relay molecules enable a small number of extracellular signals to be amplified to
produce a large cellular response
...

Protein Phosphorylation and Dephosphorylation
 Protein kinases are enzymes that transfer phosphate groups from ATP to proteins
...
 Hundreds of
different kinds of protein kinases regulate the activity of a cell’s proteins 

Small Molecules and Ions as
Second Messengers
 Second Messengers: small,
water-soluble molecules or ions
that rapidly relay the signal from
the membrane-receptor-bound
“first messenger” into a cell’s
interior
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The cAMP often
activates protein kinases A, which phosphorylates other proteins
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 ST may lead to the activation of transcription factors, which regulate the expression of specific
genes

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