Cells and Cell Chemistry (rev 9-11)

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Cells and Cell Chemistry (rev 9-11)

• All matter consists of elements
• Matter is anything that has mass and occupies
  space
• Element is a substance made of one kind of atom
• Periodic chart contains the 103 known elements,
  arranged by similar properties
• Atoms the smallest functional unit of an element
  that still retains the physical and chemical
  properties of the element

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• Elements of biological importance
• Carbon-C Oxygen-O
• Hydrogen-H Sodium-Na
• Nitrogen-N Calcium-Ca
• Chlorine-Cl Potassium-K
• Magnesium- Mg Phosphorous-P
• Sulfur-S Iron-Fe

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• Core of the atom is the cell nucleus.
• It consists of
• Protons (positive) charge, have mass (weight-1
  AMU)
• Neutrons have no charge (neutral particle), have
  mass (1 AMU)
• Protons and Neutrons are tightly bound together
• Electrons - (negative) charge, orbit the
  nucleus, have no discernable mass (lt0.001 AMU)
• Electrons are constantly moving so their actual
  location within their specific shell can not be
  determined
• Atoms and their parts are weighed by AMU-atomic
  mass units because they are so small.

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• All atoms are electrically neutral
• Have an equal number of protons and electrons
• Number of protons and electrons determines
  behavior of each atom
• The Periodic Table of the Elements identifies the
  11 composition of each atom.
  Na
• 22.990
• Letters in the middle the atoms chemical
  symbol
• Number on top the atomic number ( of protons)
• (and also the number of
  electronsWhy?)
• The number on the bottom is the atomic mass
• (use it to figure out the number of
  neutrons-How?)
• Subtract the atomic number ( of protons) from
  the atomic mass or subtract the top number from
  the bottom number.

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• Isotopes
• All atoms of a particular element have the same
  number of protons and electrons HOWEVER, they can
  have a different number of neutrons, therefore a
  different atomic mass (weight)
• These atoms are called isotopes.
• Isotopes tend to be unstable. They are called
  RADIOISOTOPES because they give off energy as
  radiation until they reach a stable state
• Some of this energy can damage the body
• Some of this can be used in medicine to tag and
  track molecules to determine their location in
  the body

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• Electrons have potential energy
• The term orbital describes the probable
  location of an electron within a shell
• The term shell refers to the energy level of
  electrons
• Each shell further away from the nucleus has a
  higher level of energy
• -- When an electron moves to a shell closer to
  the nucleus it loses energy
• --When an electron moves to a shell further away
  from the nucleus, it gains energy

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• Atoms are most stable when their outermost
  occupied electron shell is completely filled
• An atom with an unfilled outermost electron shell
  will try to interact with other atoms in order to
  fill this outermost shell
• Atoms try to share electrons with other atoms
• First shell can hold 2 electrons second can hold
  8 electrons few atoms have a third shell (can
  hold a maximum of 18 electrons)
• These interactions will typically cause the atoms
  to be bound to each other by a force called a
  chemical bond
• There are 3 principal types of chemical bonds
• Covalent
• Ionic
• Hydrogen

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• Covalent Bond
• Strong-rarely break apart
• Formed by the sharing of a pair or more of
  electrons with another atom (in order to fill the
  outermost shell)
• Sharing of 1 pair of electrons is a single bond
• Sharing of 2 pairs of electrons is a double bond
• Example Hydrogen gas, oxygen gas, water molecule

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• Ionic bond- bond between two oppositely charged
  atoms or molecules which was formed by the
  transfer of one or more electrons
• Atom with nearly full outer shell gains
  electrons gives the atom a net charge due to
  gain or loss of electrons
• charge for each electron lost
• - charge for each electron gained
• An electrically charged atom or molecule is
  called an ion. Examples Na, Cl-, Ca2
• Bond is of moderate strength

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• Hydrogen Bond
• Weak attraction which occurs between oppositely
  charged regions of polar molecules that contain
  covalently bonded hydrogen. We see this most
  often in a water molecule.
• Water is electrically neutral overall but still
  has partially charged ends (called poles). This
  type molecule is called a polar molecule.
• Since opposites attract, polar molecules arrange
  themselves to that the negative pole of one
  molecule is facing the positive pole of another
  molecule.
• Hydrogen bonds between liquid water molecules are
  so weak that they break and reform allowing water
  to flow.

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• A polar molecule is formed when electrons are
  unequally shared between two atoms.
• ThIs occurs because one atom has a stronger
  affinity for electrons than the other (yet not
  enough to pull the electrons away completely and
  form an ion) and the bonding electrons will spend
  a greater amount of time around the atom that has
  the stronger affinity for electrons.
• An example of this is the hydrogen-oxygen bond in
  water.

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Compounds

• Composed of molecules.
• A molecule forms when 2 or more atoms combine.
• Organic compounds contain the element carbon
• Inorganic compounds do not contain carbon

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Life depends on water

• Water is responsible for 60 of our body weight
• Water molecules are polar
• Water is liquid at body temperature
• Water can absorb and hold heat energy

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Two Biological Functions of Water

• Water is the biological solvent because it is a
  polar liquid at body temperature
• A solvent is a liquid in which other substances
  dissolve
• Solute is any dissolved substance.

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• Water helps regulate body temperature
• Water can absorb and hold heat with only a small
  increase in temperature. It prevents body
  temperature from rising suddenly.
• Water also holds heat when there is danger of too
  much heat loss (on a cold day for example).
• We can lose heat rapidly by evaporating water
  from our body surface.

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• So, water is the substance in which many chemical
  reactions take place.
• Water is the substance that carries solutes from
  one place to another.
• It also fills our intracellular and intercellular
  spaces.
• The term hydrophilic refers to polar molecules
  attracted to water and interact with it.
• The term hydrophobic refers to nonpolar molecules
  that are not attracted to water and therefore
  dont interact with it. (oil and water)

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The Importance of Hydrogen Ions

• Despite the covalent bonds between water
  molecules, the bonds can be broken into H and
  OH-.
• In pure water, there are only a few dissociated
  (broken apart) molecules
• Other sources of hydrogen ions in aqueous
  solutions
• Acids are any molecule that can donate a hydrogen
  ion (H --proton). Produce an acidic solution
  (which has a higher concentration of H than
  water)
• Bases are any molecule that can accept hydrogen
  ions. Produce a basic or alkaline solution (which
  has a lower H concentration than water).
• Acids and bases have opposite effects on the H
  concentration of solutions so they neutralize
  each other

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• How to indicate the acidity or alkalinity of a
  solution
• pH Scale measure of hydrogen ion concentration
  in a solution
• Scale goes from 0-14 pH of water is 7.0 or
  neutral
• Changes in pH of body fluids can affect how
  molecules are transported across the cell
  membrane and how rapidly certain chemical
  reactions occur. pH changes affect the bodys
  homeostasis.

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• Buffers minimize pH change
• Buffers are essential to maintain homeostasis of
  pH in body fluids
• Carbonic acid (H2CO3) and bicarbonate (HCO3-) act
  as one of the bodys most important buffer pairs.
  They pick up H when fluids are too acidic and
  release them when fluids are too basic.

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Organic Molecules of Living Organisms

• Organic molecules are molecules that contain
  carbon and other elements held together by
  covalent bonds.
• Carbon is the building block of all organic
  molecules.
• Comprises 18 of body weight
• Forms four covalent bonds with other molecules
• Can form single or double bonds
• Can build micro- or macromolecules

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• Living organisms synthesize 4 classes of organic
  molecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

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• Living organisms use carbohydrates for energy
  plants also use them for structural support
• Monosaccharides are the simplest carbohydrate
• Glucose, fructose, ribose and deoxyribose are 4
  of the most important monosaccharides in humans
• Oligosaccharides short chains of monosaccharides
  linked together.
• Disaccharides consist of 2 linked
  monosaccharides
• examples sucrose (table sugar), fructose,
  lactose
• Some oligosaccharides are bonded to cell membrane
  proteins called glycoproteins
• Glycoproteins participate in linking adjacent
  cells together and in cell-cell recognition and
  communication

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• Polysaccharides a complex carbohydrate formed
  when thousands of monosaccharides are joined
  together in long chains and branches
• Extra long chains energy is stored in the bonds
  of the polysaccharide molecule
• Glycogen most important polysaccharide made in
  animals stores energy
• Starch most important in plants stores energy
• Cellulose Undigestible polysaccharide made in
  plants for structural support
• Undigested cellulose in the food we eat is called
  fiber

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Lipids

• Are relatively insoluble in water
• Most Important Subclasses of Lipids
• Triglycerides energy storage molecules
• Glycerol and 3 fatty acids make up triglyceride
  can be saturated or unsaturated
• Saturated fats are usually solid at room
  temperature
• Unsaturated fats are usually liquids at room
  temperature
• Are stored in adipose tissue

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• Phospholipids
• Are the primary structural component of cell
  membranes
• Have a phosphate group (PO4-) at one end this
  negative charge makes the phospholipid a polar
  molecule and thus one end of it is soluable in
  water. The other end is neutral and is not
  soluble in water

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• Steroids
• Are classified as lipids because they are
  relatively insoluble in water
• Cholesterol is a steroid
• We all need a certain amount of cholesterol
  because it
• is an important part of the cell membrane
• is used in making estrogen and testosterone

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Proteins are macromolecules constructed from
long strings of amino acids

• A string of 3-100 amino acids is called a
  polypeptide
• When a polypeptide is longer than 100 amino acids
  it is called a protein

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• The body has many different proteins each serves
  different functions.
• Structural support --Muscle contraction
• Part of the cell membrane --Enzymes
• Protein shape can be changed in the presence of
  polar molecules.
• The ability to change shape is essential to the
  functions of certain proteins.
• Protein structure can be damaged by high
  temperatures or changes in pH.
• Denaturation refers to permanent disruption of
  protein structure which causes a loss of function
  i.e. boiling an egg

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• Enzymes
• are proteins that function as a biological
  catalyst (a substance that speeds up the rate of
  a chemical reaction without itself being changed
  or consumed by the reaction)
• they speed up a reaction that would have happened
  anyway but it would have taken longer
• They serve as catalysts because, as proteins,
  they can change shape. This allows them to bind
  to other molecules and orient them so they can
  work with each other.
• The functional (or changeable) shape of an enzyme
  is dependent on
• temperature of reaction medium
• pH
• ion concentration
• presence of inhibitors

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Other organic molecules

• Nucleic Acids
• DNA deoxyribonecleic acid
• RNA ribonucleic acid
• Functions
• DNA directs everything the cell does including
  the instructions for producing RNA.
• RNA is a closely related macromolecule and
  carries out the instructions of DNA including how
  to produce proteins.
• Structure
• Composed of Nucleotides consist of a phosphate
  group, a sugar, and a nitrogenous base
• DNA structure is a double helix two associated
  strands of nucleic acids
• RNA is a single-stranded molecule

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Structure of DNA and RNA

• DNA double-stranded helix
• Sugar deoxyribose
• Nitrogenous bases adenine, thymine, cytosine,
  guanine (the protein code is actually contained
  in the sequencing of nucleotides)
• Pairing adenine-thymine and cytosine-guanine
• RNA single-stranded helix
• Sugar ribose
• Nitrogenous bases adenine, uracil, cytosine,
  guanine
• Pairing adenine-uracil, cytosine-guanine

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• Adenosine Triphosphate (ATP)
• Nucleotide
• Made up of adenine ribose (which is a 5 carbon
  sugar). Together these are called adenosine.
  There is also a 3 phosphate group called
  triphosphate.
• Is a universal energy source for cells
• The bonds between the phosphate groups contain a
  lot of potential energy