Transcript Biochemistry-Review of the Basics

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Biochemistry-Review of the Basics
Atoms

Smallest unit of matter

Elements

Molecule

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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Elements important to Biology – C. HOPKINS CaFe
Any combination of atoms of the SAME element

Compound
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Electron
Orbits
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Ex. O2, H2, N2,
Any combination of atoms of 2 or more elements
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Atomic
Structure
Ex. Carbon atoms, Oxygen atoms etc.
Ex. CO2, H2O, PO4-
Atoms contain 3 subatomic particles

Protons- + charge- found in nucleus

Neutrons- 0 charge- found in nucleus

Electrons- - charge- orbit nucleus
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1st orbit- holds 2 electrons, 2nd and 3rd orbit- hold 8 electrons each
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All atoms react so that their electron orbits will become full
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#'s change
Biochemistry-Ions & Isotopes
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Sometimes atoms may gain or lose protons or neutrons
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Electrons
Neutrons
Protons
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This makes them behave differently
When an atom gains or loses an electron it is called an ion
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Electrons are negatively charged, so gaining an electron makes the
atom MORE negative, while losing one makes it MORE positive
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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)
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Since neutrons have weight, this changes the atomic weight,
making them heavier
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Ex, 14C is an isotope of carbon with 2 extra neutrons
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Isotopes play important roles in radioactive dating and medicine
When an atom gains or loses a proton it becomes a new element
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Chemical
Bonds
Biochemistry-Bonding
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All atoms want complete electron shells and will bond with others to get
them
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Covalent
Bonds
Ionic bonds
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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
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Sharing only 1 pair is known as a single bond
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2 pairs can be shared (double bond), as well as 3 (triple bond)
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Ex. CO2, N2, O2 all use covalent bonds
Atoms may also take or donate electrons to
complete their shells
Chemical
reactions
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This creates ions
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Ex. NaCl
When 2 or more atoms bond a chemical reaction takes place
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Reactants- what you start with
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Products- what you end with
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Coefficients- how much you have
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Energy in
reactions
Biochemistry-Bonding
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Making or breaking bonds requires energy
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Energy is defined as the ability to do work
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2 types of energy
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Potential- energy that is stored, not being used
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Ex. a boulder at the top of a hill
Kinetic- energy that is doing work actively
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Exothermic
Rx's
Endothermic
Rx's


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
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As a result energy (heat) is released from the system
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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
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Biochemistry- Polymers
Overview
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The 4 major molecules that make up all organisms are carbon-based
Carbon
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Has 4 valence electrons and therefore can form 4 covalent bonds
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Polymers
Multiple bonds allows for ring, chain, & branched chain shapes
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Single, double, triple bonds able to be formed
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Latin for “Many parts”- long molecules of repeating subunits
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Subunits called Monomers- “single part”
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A.k.a. Biomolecules/Macromolecules
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4 classes of polymers found in living things
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Carbohydrates
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Polymer- polysaccharide; monomer-monosacharride
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Contain C,H, &O only
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Ring structures
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Function in structure and energy storage
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Animals
Structure: Chitin
-Plants
Cellulose
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Storage: Glycogen
Starch
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Biochemistry-Polymers
Lipids
Proteins
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A.k.a Fats
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Polymer- triglycerides; monomers- glycerol and fatty acids
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Contains C,H,O only
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2 types
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Saturated- no double bonds in carbon chain
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Unsaturated- double bonds in carbon chain
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Monounsaturated- only 1 dbl bond
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Poly unsaturated- 2 or more dbl bonds
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Function in energy storage
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Polymer- polypeptides; monomer- amino acid
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Contains C,H,O, & N
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Diverse functions
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Enzymes-speed up chemical reactions
4 levels of structure
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Primary “beads on a string”, secondary a helix or b pleated sheet
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Tertiary “globular”, and quaternary of 2 or more a.a. chains combined
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Biochemistry-Polymers
Nucleic
Acids
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Polymer- DNA/RNA; monomers- nucleotides
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Contains C,H,O,N, & P
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Holds heritable instructions for making proteins
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Nucleotides made up of 3 parts
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5- Carbon Sugar- either deoxyribose or ribose
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Phosphate group (PO4)
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Nitrogenous base
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5 types
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Adenine
Tyrosine
Cystiene
Guanine
Uracil
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Definition
Biochemistry- Enzymes
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Proteins that speed up chemical reactions
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Do this by lower the energy needed to
break bonds- the activation energy (Ea)
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Rx's involve breaking bonds and rearranging
them into products
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Takes energy to begin (Ea ), even if
the reaction is exothermic
How
enzymes
work
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Provide a place for reactants to meet
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This “active site” stresses bonds- lowers Ea
Enzymes are specific for the molecules they
work on (the substrates)- like a lock and key
Inhibition
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Speed of Rx
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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
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Biochemistry- Properties of Water
Overview
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Polar
Covalent
Bonds
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Water is unique because polar covalent bonding
causes the formation of hydrogen bonds
Oxygen is very electronegative
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Electronegativity is the attraction
an element has to electrons
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As a result pulls electrons from hydrogen, which
causes partial charges
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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
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bonds between the oxygen of one H2O
and the hydrogen of another
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Remember opposites attract
Indvidually weak but collectively strong
Hydrogen bonds lead to all of the unique
properties of water
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Biochemistry- Properties of Water
High Specific Specific Heat = the energy to raise 1g of anything by 1oC
Heat
 For water this amount of energy = 1 calorie
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H-bonds are collectively strong so water can absorb much energy (heat) w/o a
big temp change
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Cohesion/
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Adhesion
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Less dense
as a solid
Good
Solvent
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
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Water can H-bond with other water molecules
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Leads to surface tension across bodies of water
Adhesion- the ability of molecules to bond with other molecules
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Water can H-bond with any other slightly charged molecule
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Leads to water “climbing” up the tubes in trees against gravity
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Density- how much mass something has compared to its size
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Ice floats b/c as water freezes H-bonds solidify in a crystalline pattern
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Leads to air pockets between molecules and therefore less density
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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
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Biochemistry- pH
Overview
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How acidic or basic a chemical is is measured by the pH scale
pH Scale
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A logarithmic scale (multiples of 10) that ranges from 0-14
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0 is most acidic
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7 is neutral
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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.
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Definitions &
Logic
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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
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Acids form more H+ ions than Bases
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The more H+ ions formed, the stronger then acid.
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Ex. pH 12 forms 10x more H+ ions than pH 13 and is therefore 10x
more acidic
The pH Scale
Don’t draw
GT
Biochemistry-Review of the Basics
Smallest unit of matter
Atoms

Elements

ONLY 1 type of atom

Molecule
C. HOPKINS CaFe
2+ atoms of SAME element

Compound

2+ atoms of DIFF elements
Atomic
Structure
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3 subatomic particles
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Protons- + - nucleus- 1amu
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Neutrons- 0 – nucleus- 1amu
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Electrons- - - orbits- Ø mass
Electron
Orbits
1st - 2
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2Nd - 8
3rd - 8
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When #'s 
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Atoms want orbits full
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Electrons → ions; + lost, - gained ( Ca2+ )
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Neutrons → isotopes (14C)
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V. useful
GT
Chemical
Bonds
Covalent
Bonds
Biochemistry-Bonding
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All want complete electron shells-bond to get them
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
Share electrons

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Ionic bonds
Chemical
Rx's
Energy in
reactions
Exothermic
Rx's
Endothermic
Rx's
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Complete shells=low energy state
1 pair = single bond, 2=double, 3=triple
Take or donate electrons
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Creates ions
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Bonds require a chemical reaction
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= heat (ability to work)
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Potential (in bonds) vs. Kinetic (released)
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Energy of products < reactants
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Spontaneous- releases heat
Energy of products > reactants
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Non-spontaneous- consumes heat
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Biochemistry- Polymers
Overview
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All org's C-based (organic)
Carbon
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4 poss. bonds
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Polymers
Rings, chains, branched chains
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Single, double, triple bonds
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“Many parts”
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Monomer subunits
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A.k.a. Biomolecules/Macromolecules
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4 classes
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Carbohydrates (polysaccharides)- monomer (monosachharides)
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C.H.O only- fnx in structure/energy
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
Plants- cellulose/starch
 Animals- chitin/glycogen
Fats/Lipids (triglycerides)- monomer (fatty acids/glycerol)
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CHO only- fnx in energy
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Saturated- Ø dbl bonds

Unsaturated- >/= 1 dbl bond
GT
Polymers
Biochemistry- Polymers

Proteins: polymer (polypeptides)- monomer (amino acids)
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C,H,O, N, P, S
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20 a.a's
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Most diverse fnx's-made via DNA
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Enzymes-speed Rx's
4 levels of structure
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1o- “Beads on a string”- Peptide bonds
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2o-  helix or  pleated sheet
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3o- “globular”
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4o- >/+ 1 polypeptide (Not all)
Nucleic Acids: polymer (DNA/RNA)- monomer (nucleotides)
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C,N,O, N, P
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Genetic info- makes proteins
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Nucleotide parts
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Sugar
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Phosphate
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N-Base (A,T,G,C,U)
Biochemistry- Enzymes
GT
Definition

Proteins-facilitate Rx's
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Metabolism
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Sum of Rx's in org
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Rx's break bonds and rearrange
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How
enzymes
work

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 
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Negative- product blocks active site
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Positive- product is coenzyme/cofactor

Depends on:
Inhibition
Regulation
Speed of Rx
Lower Ea

Temp
-Amnt substrate

pH
-Amnt enzyme
GT
Biochemistry- Properties of Water
Overview
Polar
Covalent
Bonds
Properties

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


High heat of vaporization → evap cooling


S.H. = E to raise 1g by 1oC = 1 Calorie
HoV = E to vaporize 1g
Cohesion/Adhesion → Surface tension &
Rise against gravity

Less dense as a solid → Insulation of lakes/streams

Good solvent → medicine
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Biochemistry- pH
Overview

Acidity/Alkalinity- pH scale measures
pH Scale

Logarithmic scale -0-14
Definitions &
Logic


0 most acidic

7 neutral
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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.
The pH Scale
Don’t draw