LS 204 Chapt. 4 Chemistry

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LS 204 Chapt. 4 Chemistry

• Biology is the study of living things, which
  involves chemical reactions (metabolism)
• Organisms are composed of macromolecules,
  molecules and atoms, which is Chemistry
• Knowledge of Chemistry is essential to
  understand Biology

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Biological Hierarchy of Organisms

• Classification system to organize Fig. 4.1
• Study biology to learn about all forms of life
  including yourself
•  Level Subdisciplines
• Biosphere ecology
• Ecosystem ecology
• Community ecology
• Population population genetics, evolution,
  paleontology
• Organism anatomy physiology
• Organ system anatomy physiology
• Organ anatomy physiology
• Tissue cell biology, microbiology, molecular
  genetics
• Cell cell biology, microbiology, molecular
  genetics
• Organelle cell biology, microbiology, molecular
  genetics
• Macromolecule/ molecule chemistry, biochemistry
• Atom chemistry

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Hierarchy of lifesee Fig. 4.1
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Goals Chapter 4 Chemistry

• Compare and contrast different states of matter
• Describe atomic structure
• Demonstrate use of the Periodic Table of Elements
• Explain ionic, covalent, and hydrogen bonding
• Describe polar molecules their unique
  characteristics
• Discuss organic molecules, chemical reactions

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Your starting point

• The most basic unit of a chemical substance is
  ___
• Matter is defined as anything that _____
• What are the three states of matter? _____
• What are the 3 most common subatomic particles?
• Which subatomic particles interact during
  chemical reactions?
• What is the molecular formula for water?
• What are 3 common types of chemical bonds?
• What happens in anabolic reactions?
• What is meant by organic molecules?
• Are proteins organic or inorganic?

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What is matter?

• Matter is stuff which has mass (or weight) and
  takes up space.
• Mass is actual physical amount, whereas weight
  includes force of gravity.
• Three states of matter solid, liquid, gas.
• Example for water ice water steam/ vapor

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• Elements
• The most basic chemical substances.
• Ex. iron, oxygen, carbon, helium.
• Some elements are pure some function combined
  with others.
• Living organisms require about 20 elements
• 95 of body is carbon, hydrogen, oxygen, nitrogen
  (C, H, O, N).
• 70 of the body is molecule water (H2O)
• Table 4.3 shows symbols for different elements
• (C carbon Na sodium (natrium))

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2. Atomic structure

• Atom smallest complete
• unit of an element.
• Molecule 2 or more atoms
• joined together
• (water H2O)
• Macromolecule is bigger,
• more complex
• (a protein, carbohydrate)

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Atomic structure

• Atoms contain subatomic particles
• proton, neutron, electron are most
  important.
• Nucleus middle of atom and contains
• protons (p, positively charged)
• neutrons (n, neutral).
• Electrons (e-) are very tiny, negatively
  charged move around the nucleus. Fig. 4.2
• An atom is electrically neutral
• the number of electrons number of
  protons.

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Electrons

• Electrons are negatively charged
• Electrons move in orbitals, multiple paths with
  different energy levels (shells)
• 1st shell can have only 2 e- and is closest to
  nucleus.
• 2nd shell can have 8 e-
• 3rd shell also can have 8 e-
• (gets more complex)

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Atomic number

• Atomic number is unique for each element number
  of protons (and number of electrons)
• Ex. H 1 C 6, O 8
• Question Nitrogen has atomic number of 7 how
  many protons?
• how many electrons?

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Atomic weight or mass

• Atomic weight and mass almost same weight of 1
  atom.
• 1 atomic mass unit (1 u) the mass or weight of
  1 proton
• (1 neutron weighs the same),
• Weight of an electron is so tiny as to not be
  counted.
• Therefore, the atomic weight of an element
• number of protons plus number of neutrons.
• All atoms of an element have the same atomic
  number (ex. C 6).
• Different isotopes can have different numbers of
  neutrons, and atomic weights Regular C C12
  weight of 12 (has 6 neutrons)
• radioactive C14 has
  weight of 14 (8 neutrons)

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3. Periodic table of elements (Fig. 4.3)

• Focus on the first 3 rows, main elements for
  biology.
• (handout has names of elements in
  addition to abbreviations)
• Table is a specific arrangement which helps
  understand chemical properties of atoms.
• H (1 proton), Helium (He) has 2 protons and 2
  neutrons.
• Fig. 4.3 Oxygen has atomic number of 8 -gt 2
  electrons in 1st shell, 6 in outer shell.
• Rows periods, represent the different shells
  
• 1st (2 e-), 2nd (8 e-), 3rd (8 e-).
• Columns groups elements that share the same
  number of e- in the outermost shell, (and
  properties)

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Hierarchy of life
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4. Chemical interactions

• Electrons in atoms outermost shell determine the
  reactivity of the element.
• Chemical bonding two or more atoms join
  together to form molecules.
• Valency shell is the outermost e- shell
• If shell is full, the atom is stable or inert
• (He has 2, Ne has 8, Ar has 8).
• These atoms do not usually enter into
  chemical reactions.
• If outer shell is not full, atom wants to make
  that shell full gains or loses or shares
  electrons with other atoms.

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Ionic bonding

• ions have permanently gained or lost an e- they
  are not electrically neutral.
• Na is sodium that has lost the 1 e- in its
  outermost shell.
• Cl- is chlorine that has gained 1 e- to add to
  the 7 it had for a full outermost shell.
• Two ions bond together to form NaCl salt.

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Covalent bonding is sharing electrons.

• H2 hydrogen gas (H-H)
• each has 1 e- in outer shell, and wants 2
• sharing, each nucleus of 1 p has 2 e- part of
  the time.
• O2 oxygen gas (OO)
• each atom wants 2 e- to fill its outer shell (has
  6)
• by sharing 2 e-, they each have full outer
  shell this double sharing is called a double
  bond.
• H2O water (H-O-H) O wants two e-, and shares 1
  e- each with 2 different H atoms.

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Hydrogen bonding is weak bonds

• Sharing between an H in 1 molecule and atom in
  another
• important for biological molecules and
  macromolecules.
• O does not share fairly in H2O it is big and
  tends to keep the e- near its nucleus.
• The O is more negative (d-) and the H is more
  positive (d). Polarity (Fig. 4.9).
• Water molecules line up
• with the little of one water
• with the little of another.

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• hydrophilic polar solutions
• (water) water-loving
• hydrophobic nonpolar solutions
• (oil, hydrocarbons). water-hating

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Molecules and compounds.

• Molecule two or more atoms binding together
• If two of the same element (O) -gt a molecule of
  O2.
• If different elements H and O a compound and a
  new name (ex. H2O is water).
• Molecular formula tells what atoms and how many
  are in a molecule CO2 carbon dioxide
• Structural formula is diagram of how atoms are
  joined which ones together (Fig. 4.10).
• Important for understanding properties of complex
  molecules example of 3 sugars different
  properties.
• C6H12O6 for glucose, fructose, galactose

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Structural formulas of sugars
C6H12O6 for glucose, fructose, galactose
glucose
galactose
fructose
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5. Chemical reactions

• Breaking and remaking covalent bonds is the basis
  of metabolism.
• Organic compounds contain C and H (and others)
• Carbon-based life form Most macromolecules of
  animals, plants.
• Carbohydrates (CHO), proteins (also have S and
  N), lipids, nucleic acids (have N, P).
• Inorganic compounds do not have both C and H ex.
  CO2, HCl Fe(OH)3

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5. Chemical reactions

• Energy from breaking down macromolecules of food
  and use it to make new molecules.
• Enzymes do the reactions
• Chemical equations reactants -gt products
• some reactions are reversible.
• Anabolic reactions synthesis molecules -gt
  macromolecules
• Catabolic reactions decomposition breakdown,
  digestion of macromolecules.
• Exchange reactions swap pieces
• AB CD -gt AC BD example.

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Review questions

• Which subatomic particles are always in the
  nucleus?
• Which subatomic particles are not included in
  atomic mass?
• What is the difference between ionic and covalent
  bond?
• For oxygen, write the number of protons ___ and
  electrons ____
• How many electrons in the outer shell of iodine?