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Define Matter
anything that takes up space and has mass
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Define Atoms
smallest chemical units of matter
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Atomic Structure
electrons
nucleus
neutrons
protons
- electrons: negatively charged subatomic particles circling a nucleus
- nucleus: structure containing neutrons and protons
- neutrons: uncharged particles
- Protons: positively charged particles
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Atomic Structure:
Element
Atomic Number
Atomic Mass
- Element: composed of a single type of atom
- Atomic Number: equal to the number of protons in the nucleus. change in number means change in element.
- Atomic mass: sum for the masses of protons, neutrons and electrons
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Isotopes
- Carbon-13 and carbon-14
- Atoms of a given element that differ in the number of neutrons in their nuclei
- carbon-13 is stable
- carbon-14 is unstable; release energy during radioactive decay
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What determines the atoms chemical behavior?
- Electrons. only electrons of atoms interact
- electrons occupy electron shells
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Valence electrons
electrons in the outermost chell that interact
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Valence
- combining capacity of an atom.
- -positive if it has electrons to give up
- -negative if it has electrons to give up
- -stable when outer electron shells contain eight electrons
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Chemical bonds
atoms combine by sharing or transferring valence electrons
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molecule
two or more atoms held together by chemical bonds
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compound
a molecule composed of more than one element
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electronegativity
- attraction of atom for electrons
- -the more electronegative an atom the greater the pull it's nucleur exerts on electrons
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4 types of Chemical Bonds
- Nonpolar covalent: equal sharing, not electronegative
- Polar Covalent: electronegative, unequal sharing. angeled
- Ionic Bond: no sharing. electrons are given up making the element an ion, completely positive, cation or completely negative, anion
- Hydrogen Bond: weak bond of water.
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Nonpolar covalent bonds
- shared electrons spend equal amounts of time around each nucleus
- atoms with similiar electronegativities
- no poles exist
- carbon atoms form four non polar covalent bonds with other atoms
- organic compounds contain carbon and hydrogen atoms
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Polar Covalent Bonds
- Unequal sharing of electrons due to signicantly different electronegativities
- Most important polar covalent bonds involve hydrogen -Allow for hydrogen bonding
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Ionic Bonds
- Occur when two atoms with vastly different electronegativities come together
- atoms have either positive (cation) or negative (anion) charges
- cations and anions attract eachother and form ionic bonds (no electrons shared)
- typically form crystalline ionic compounds known as salts
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Hydrogen Bonds
- Weak forces that combine with polar covalent bonds
- electrical attraction between partially charged H+ and full or partial negative charge on same or different molecule
- eaker than covalent bonds but essential for life
- many help to stabilize 3-D shapes or large molecules
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Chemical Reactions
- The breaking or making of chemical bonds
- involve reactants and products
- biochemistry involves chemical reactions of living things
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Define reactant
atoms, ions or molecules that exist at the begining of a reaction.
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Synthesis reactions (creating)
- Involve the formation of larger, more complex molecules
- reactant + reactant = product
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require energy (endothermic) - Most common type is dehydration synthesis -water molecule is formed
- all the synthesis reactions in an organism are called anabolism
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Decomposition Reactions
- Break bonds with larger molecules to form smaller atoms, ions, and molecules
- release energy(exothermic)
- Product = reactant + reactant
- most common type is hydrolysis
- ionic components of water are added to products
- all the decomposition reactions in an organism are called catabolism
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Exchange Reactions
–Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps
- –Involve atoms moving from one molecule to another
- Sum of all chemical reactions in an organism is called metabolism
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Water
- –Most abundant substance in organisms
- –Most of its special characteristics due to two polar covalent bonds
- –Cohesive molecules
- – surface tension
- –Excellent solvent
- –Remains liquid across wide range of temperatures
- –Can absorb significant amounts of energy without changing temperature
- –Participates in many chemical reactions
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Acids and Bases
- –Dissociated by water into component cations and anions
- –Acid – dissociates into one or more H+ and one or more anions
- –Base – binds with H+ when dissolved into water; some dissociate into cations and OH
- –Metabolism requires relatively constant balance of acids and bases
- –Concentration of H+ in solution expressed using the pH scale
- –Buffers prevent drastic changes in internal pH
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pH scale
- 0-6 is acidic increasing amts of H+
- 7 is neutral
- 8-14 is basic increasing amts of OH-
- change in # is an increase of base 10
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Salts
- –Compounds that dissociate in water into cations and anions other than H+ and OH–
- –Cations and anions of salts are electrolytes
- –Create electrical differences between inside and outside of cell
- –Transfer electrons from one location to another
- –Form important components of many enzymes
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Organic Macromolecules
- – large molecules used by all organisms
- Functional groups
- Lipids
- Carbohydrates
- Protiens
- nucleic acids
- –Monomers – basic building blocks of macromolecules
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Functional Groups
- –Contain carbon and hydrogen atoms
- –Atoms often appear in certain common arrangements – functional groups
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Lipids
- –Not composed of regular subunits, but are all hydrophobic because they are all carbon and hydrogen and all nonpolar.
- –Four groups: Fats, Phospholipids, Waxes, Steroids
- - Sterols maintain fluidity
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fats
- made by organisms via dehydraton synthesis that form esters between the 3 chains and an alcohol, glycerol.
- three fatty acid chains attached to a glycerol (triglycerides)
- saturated: each C molecule is bound to two H molecules
- unsaturate: one or more C atoms is attached to another C atom.
- Polyunsaturated: if several C atoms are bound.
- Abundant energy is stored in C-C covalent bonds.
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Phospholipids
- similiar to fats but two fatty acid chains and one phosphate.
- phosphate head is polar and hydrophilic.
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Waxes
- 1 long fatty acid chain and 1 long alcohol chain. completely water insoluable.
- mycobacterium tuberculosis surrounded by a waxy wall.
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Steroids
- 4 rings consisting of 5 or 6 C each, fused together and attached to various side chains.
- play many roles in human motabilism, some act as hormones.
- Fungi, plants and mycoplasm use sterol to mantain fluidity at low temperatures
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Carbohydrate definition and Functions 6
- –Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)n
- –Functions
- –Long-term storage of chemical energy
- –Ready energy source
- –Part of backbones of nucleic acids
- –Converted to amino acids
- –Form cell wall
- Involved in intracellular interactions between animal cells
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–Carbohydrate Types
- –Monosaccharides: simple sugars
- –Disaccharides: 2 monosaccharides are linked together via dehydration synthesis
- –Polysaccharides: polymers of 10s-1,000s of monosaccharides that are covalently linked via dehydration synthesis
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Protiens
- Polymers composed of monomers called amino acids
- –Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur
- –Functions: Structure, Enzymatic catalysis, Regulation, Transportation and Defense and offense
- Structures:primary, secondary, tertiary (3D shape), quanternary
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List the 5 functions of Protein
- Structure: cell walls. membranes, hair, skin, nails, muscles, flagella, cilia etc
- Enzymatic Catalysis: enhace the speed or liklihood of a chemical reaction
- Regulation: regulate cell function ie: hormones
- Transportation: channels and pumps
- Defense and offense: antibodies, complement, bacteriocins
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Describe the 4 structures of protein
- Primary:sequence of amino acids in a polypeptide chain
- Secondary: interaction between regions of the polypeptide resulting in a helix or pleated sheet, hydrogen bonding
- Tertiary: continued hydrogen bonding and covalent bonding. 3D shape
- Quaternary: more than one polypeptide chain
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Amino Acids
- –The monomers that make up proteins
- –Most organisms use only 21 amino acids in the synthesis of proteins
- –Side groups affect how amino acids interact with one another and how a protein interacts with other molecules
- –A covalent bond (peptide bond) is formed between amino acids by dehydration synthesis reaction
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Stereoisomers
molecules that are mirror images of eachother
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Nucleic Acids
- –DNA and RNA: the genetic material of organisms
- –RNA also acts as enzyme, binds amino acids, and helps form polypeptides
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Nucleic Acids: Nucleotides
- –Monomers that make up nucleic acids (DNA/ RNA)
- –Composed of three parts :
- Phosphate,
- Pentose sugar:deoxyribose or ribose
- One of five cyclic nitrogenous bases
- Adenine
- Guanine
- cytosine
- thymine or Uracil
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Nucleic Acid Structure
- –Three H bonds form between C and G
- –Two H bonds form between T and A in DNA or between U and A in RNA
- –DNA is double stranded in most cells and viruses
- –Two strands are complementary and antiparallel
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Nucleic Acid Function
- –DNA is genetic material of all organisms and of many viruses
- –Carries instructions for synthesis of RNA and proteins; controls synthesis of all molecules in an organism
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