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Biochemistry-Review of the Basics

OL. Biochemistry-Review of the Basics. Smallest unit of matter Ex. Carbon atoms, Oxygen atoms etc. Substances made up of ONLY a single type of atom Ex. A bar of 100% pure gold would ONLY contain gold atoms Organized based on reactivity on the Periodic Table

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Biochemistry-Review of the Basics

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  1. OL Biochemistry-Review of the Basics • Smallest unit of matter • Ex. Carbon atoms, Oxygen atoms etc. • Substances made up of ONLY a single type of atom • Ex. A bar of 100% pure gold would ONLY contain gold atoms • Organized based on reactivity on the Periodic Table • Elements important to Biology – C. HOPKINS CaFe • Any combination of atoms of the SAME element • Ex. O2, H2, N2, • Any combination of atoms of 2 or more elements • Ex. CO2, H2O, PO4- • Atoms contain 3 subatomic particles • Protons- + charge- found in nucleus • Neutrons- 0 charge- found in nucleus • Electrons- - charge- orbit nucleus • 1st orbit- holds 2 electrons, 2nd and 3rd orbit- hold 8 electrons each • All atoms react so that their electron orbits will become full Atoms Elements Molecule Compound Atomic Structure Electron Orbits

  2. OL Biochemistry-Ions & Isotopes • Sometimes atoms may gain or lose protons or neutrons • This makes them behave differently • When an atom gains or loses an electron it is called an ion • Electrons are negatively charged, so gaining an electron makes the atom MORE negative, while losing one makes it MORE positive • Ex. Ca2+ is a calcium atom that has LOST 2 electrons • An important ion in our bodies is HCO3- which prevents our blood from becoming too acidic • Some atoms may gain neutrons (loss does not usually occur)‏ • Since neutrons have weight, this changes the atomic weight, making them heavier • Ex, 14C is an isotope of carbon with 2 extra neutrons • Isotopes play important roles in radioactive dating and medicine • When an atom gains or loses a proton it becomes a new element #'s change Electrons Neutrons Protons

  3. OL Biochemistry-Bonding • All atoms want complete electron shells and will bond with others to get them • This is because complete shells put atoms at a low energy state • When atoms share electron pairs to complete their shells that is a Covalent Bond • Sharing only 1 pair is known as a single bond • 2 pairs can be shared (double bond), as well as 3 (triple bond)‏ • Ex. CO2, N2, O2 all use covalent bonds • Atoms may also take or donate electrons to • complete their shells • This creates ions • Ex. NaCl • When 2 or more atoms bond a chemical reaction takes place • Reactants- what you start with • Products- what you end with • Coefficients- how much you have Chemical Bonds Covalent Bonds Ionic bonds Chemical reactions

  4. OL Biochemistry-Bonding • Making or breaking bonds requires energy • Energy is defined as the ability to do work • 2 types of energy • Potential- energy that is stored, not being used • Ex. a boulder at the top of a hill • Kinetic- energy that is doing work actively • Ex. a boulder rolling down a hill • In chemical reactions the energy is usually provided in the form of heat • Exothermic reactions result in products with less potential energy than the reactants • As a result energy (heat) is released from the system • These reactions are able to happen spontaneously • Endothermic reactions result in products with more potential energy than the reactants • As a result, energy (heat) must be added to the system(and thereby removed from the surroundings)‏ • These reactions do not happen spontaneously Energy in reactions Exothermic Rx's Endothermic Rx's

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  6. The 4 major molecules that make up all organisms are carbon-based Has 4 valence electrons and therefore can form 4 covalent bonds Multiple bonds allows for ring, chain, & branched chain shapes Single, double, triple bonds able to be formed Latin for “Many parts”- long molecules of repeating subunits Subunits called Monomers- “single part” A.k.a. Biomolecules/Macromolecules 4 classes of polymers found in living things Carbohydrates Polymer- polysaccharide; monomer-monosacharride Contain C,H, &O only Ring structures Function in structure and energy storage Animals -Plants Structure: Chitin Cellulose Storage: Glycogen Starch OL Biochemistry- Polymers Overview Carbon Polymers

  7. A.k.a Fats Polymer- triglycerides; monomers- glycerol and fatty acids Contains C,H,O only 2 types Saturated- no double bonds in carbon chain Unsaturated- double bonds in carbon chain Monounsaturated- only 1 dbl bond Poly unsaturated- 2 or more dbl bonds Function in energy storage Polymer- polypeptides; monomer- amino acid Contains C,H,O, & N Diverse functions Enzymes-speed up chemical reactions 4 levels of structure Primary “beads on a string”, secondary a helix or b pleated sheet Tertiary “globular”, and quaternary of 2 or more a.a. chains combined OL Biochemistry-Polymers Lipids Proteins

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  9. Polymer- DNA/RNA; monomers- nucleotides Contains C,H,O,N, & P Holds heritable instructions for making proteins Nucleotides made up of 3 parts 5- Carbon Sugar- either deoxyribose or ribose Phosphate group (PO4)‏ Nitrogenous base 5 types Adenine Tyrosine Cystiene Guanine Uracil OL Biochemistry-Polymers Nucleic Acids

  10. Proteins that speed up chemical reactions Do this by lower the energy needed to break bonds- the activation energy (Ea) Rx's involve breaking bonds and rearranging them into products Takes energy to begin (Ea ), even if the reaction is exothermic Provide a place for reactants to meet This “active site” stresses bonds- lowers Ea Enzymes are specific for the molecules they work on (the substrates)- like a lock and key Competitive-wrong substrate in active site Non-competitive- molecule binds to an allosteric site which causes an shape change in the enzyme so the substrate can't bind Enzymes work best at an ideal temp and pH The speed of the reaction also depends on the amount of enzyme or substrate present OL Biochemistry- Enzymes Definition How enzymes work Inhibition Speed of Rx

  11. Water is unique because polar covalent bondingcauses the formation of hydrogen bonds Oxygen is very electronegative Electronegativity is the attraction an element has to electrons As a result pulls electrons from hydrogen, whichcauses partial charges O becomes slightly more negative H becomes slightly more positive Bond is still covalent but now has “poles”- hence a polar covalent bond This results in Hydrogen-bonds bonds between the oxygen of one H2O and the hydrogen of another Remember opposites attract Indvidually weak but collectively strong Hydrogen bonds lead to all of the unique properties of water OL Biochemistry- Properties of Water Overview Polar Covalent Bonds

  12. Specific Heat = the energy to raise 1g of anything by 1oC For water this amount of energy = 1 calorie H-bonds are collectively strong so water can absorb much energy (heat) w/o a big temp change Leads to high boiling point- keeps earth cool b/c bodies of water absorb a lot of heat without significant temperature change Cohesion- the ability of molecules to bond with themselves Water can H-bond with other water molecules Leads to surface tension across bodies of water Adhesion- the ability of molecules to bond with other molecules Water can H-bond with any other slightly charged molecule Leads to water “climbing” up the tubes in trees against gravity Density- how much mass something has compared to its size Ice floats b/c as water freezes H-bonds solidify in a crystalline pattern Leads to air pockets between molecules and therefore less density This allows for only the top layer of lakes/streams to freeze, protecting the life below Bonds to and dissolves any charged thing-helps dissolve medicines & nutrients OL Biochemistry- Properties of Water High Specific Heat Cohesion/ Adhesion Less dense as a solid Good Solvent

  13. How acidic or basic a chemical is is measured by the pH scale A logarithmic scale (multiples of 10) that ranges from 0-14 0 is most acidic 7 is neutral 14 is most basic (alkaline) Because the scale is logarithmic, a pH of 6 would be 10 times more acidic than a pH of 7. Conversely, a pH of 7 is 10 times more basic than a pH of 6. 5 would be 100 times more acidic than 7, 4 1000x and so on Acidity is measured in how many H+ ions are formed when a chemical mixes with water Acids form more H+ ions than Bases The more H+ ions formed, the stronger then acid. Ex. pH 12 forms 10x more H+ ions than pH 13 and is therefore 10x more acidic OL Biochemistry- pH Overview pH Scale Definitions & Logic

  14. The pH Scale Don’t draw

  15. GT Biochemistry-Review of the Basics • Smallest unit of matter • ONLY 1 type of atom • C. HOPKINS CaFe • 2+ atoms of SAME element • 2+ atoms of DIFF elements • 3 subatomic particles • Protons- + - nucleus- 1amu • Neutrons- 0 – nucleus- 1amu • Electrons- - - orbits- Ø mass • 1st - 2 • 2Nd - 8 • 3rd - 8 • Atoms want orbits full • Electrons → ions; + lost, - gained ( Ca2+ )‏ • Neutrons → isotopes (14C)‏ • V. useful Atoms Elements Molecule Compound Atomic Structure Electron Orbits When #'s 

  16. GT Biochemistry-Bonding • All want complete electron shells-bond to get them • Complete shells=low energy state • Share electrons • 1 pair = single bond, 2=double, 3=triple • Take or donate electrons • Creates ions • Bonds require a chemical reaction • = heat (ability to work)‏ • Potential (in bonds) vs. Kinetic (released)‏ • Energy of products < reactants • Spontaneous- releases heat • Energy of products > reactants • Non-spontaneous- consumes heat Chemical Bonds Covalent Bonds Ionic bonds Chemical Rx's Energy in reactions Exothermic Rx's Endothermic Rx's

  17. All org's C-based (organic)‏ 4 poss. bonds Rings, chains, branched chains Single, double, triple bonds “Many parts” Monomer subunits A.k.a. Biomolecules/Macromolecules 4 classes Carbohydrates (polysaccharides)- monomer (monosachharides)‏ C.H.O only- fnx in structure/energy Plants- cellulose/starch Animals- chitin/glycogen Fats/Lipids (triglycerides)- monomer (fatty acids/glycerol)‏ CHO only- fnx in energy Saturated- Ø dbl bonds Unsaturated- >/= 1 dbl bond GT Biochemistry- Polymers Overview Carbon Polymers

  18. Proteins: polymer (polypeptides)- monomer (amino acids)‏ C,H,O, N, P, S 20 a.a's Most diverse fnx's-made via DNA Enzymes-speed Rx's 4 levels of structure 1o- “Beads on a string”- Peptide bonds 2o-  helix or  pleated sheet 3o- “globular” 4o- >/+ 1 polypeptide (Not all)‏ Nucleic Acids: polymer (DNA/RNA)- monomer (nucleotides) C,N,O, N, P Genetic info- makes proteins Nucleotide parts Sugar Phosphate N-Base (A,T,G,C,U)‏ GT Biochemistry- Polymers Polymers

  19. Proteins-facilitate Rx's Lower Ea Sum of Rx's in org Rx's break bonds and rearrange Takes E to begin (Ea ), even if Rx exotherm. Place for reactants Stresses bonds- lowers Ea Specific- lock and key Competitive-wrong key in active site Non-competitive-allosteric site → shape  Negative- product blocks active site Positive- product is coenzyme/cofactor Depends on: Temp -Amnt substrate pH -Amnt enzyme GT Biochemistry- Enzymes Definition Metabolism How enzymes work Inhibition Regulation Speed of Rx

  20. Water unique b/c polar covalent bonding O v. electronegative Pulls e-'s unequally → Partial charges Results in H-bonds → unique properties High specific heat → High boiling pt S.H. = E to raise 1g by 1oC = 1 Calorie High heat of vaporization → evap cooling HoV = E to vaporize 1g Cohesion/Adhesion → Surface tension & Rise against gravity Less dense as a solid → Insulation of lakes/streams Good solvent → medicine GT Biochemistry- Properties of Water Overview Polar Covalent Bonds Properties

  21. Acidity/Alkalinity- pH scale measures Logarithmic scale -0-14 0 most acidic 7 neutral 14 most basic (alkaline) Acidity measured by H+ ions formed w/water Acids form more H+ The more H+ ions formed, the stronger then acid. OL Biochemistry- pH Overview pH Scale Definitions & Logic

  22. The pH Scale Don’t draw

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