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Amino Acids
Amino acids are molecules containing an amine group, a carboxyl group and a side chain (R group). -optical isomers that are MIRROR images 2 forms= L and D (only L is biologically active) -20 diff amino acids build thousands of proteins -linked covalently by peptide bonds TERM 2
Elements Essential to Life
DEFINITION 2 C, H, O, N -> 96% of every organism P, Ca -> 1-2% TERM 3
Atomic Mass
DEFINITION 3 proton- 1 AMU neutron- 1 AMU Electron- 0 atomic mass (mass number)= the sum of protons and neutrons Reflects the natural occurrence of isotopes TERM 4
Isotopes
DEFINITION 4 Atoms of the same element with a different number of NEUTRONS They weigh differently and the sum of the isotope masses( weighed in accordance to the percentage) is the Atomic Mass of an element. TERM 5
Covalent bonds
DEFINITION 5 the sharing of electrons between the valence sheels of two atoms where each electron is attracted to the protons of each nucleus single, double, or triple bonds Covalent polar- electrons are NOT shared equally (electrons are drawn to the element with the most protons) Covalent nonpolar- atoms equally electronegative share the e- equally!
Ionic bonds
the transfering of electrons between two atoms normally a metal and a nonmetal ion create polyatomic ions anion- negatively charged cation- positively charged TERM 7
Electronegativity
DEFINITION 7 a measure of an atom's attraction for electrons TERM 8
Bonding Continuum
DEFINITION 8 nonpolar covalent polar cov ionic TERM 9
Molarity
DEFINITION 9 a measure of the concentration of a solute in a solution concentration [ ] -the number of moles in a solution (Avagadro's number) 1 mole = 6.022 X 10^23 molecules a mole of any compound contains the SAME NUMBER OF MOLECULES -> the molecular weight=1 mole of the compound TERM 10
H2O
DEFINITION 10 -polar, due to extreme electronegativity of oxygen (create + and - poles of attraction) - partial charges allow hydrogen bonds (the strongest of the WEAK bonds) -tendency to ionize
- most versatile=> cohesive and adhesive (result of hydrogen bonds) cohesion-> water molecules stick to eachother adhesion-> water molecules stick to other molecules
Entropy
a measure of disorder AS TERM 17
Reversing Reactions
DEFINITION 17 2 ways... 1. imput of energy (one one side drives the equation the opposite way) (change in AG) 2. adding more product/reactant ( change in [ ] affects direction) chemical equilibrium-> when rate of forward reaction= the rate of reverse reaction (equilibrium is dynamic but stable) AG= TERM 18
Endergonic
DEFINITION 18 a reaction that requires energy to occur +AG (positive change in free energy) products have more free energy than reactants TERM 19
Exergonic
DEFINITION 19 reaction that releases energy -AG (negative change in free energy) spontaneous usually involves breakdown of ATP TERM 20
ATP (Adenosine Triphosphate)
DEFINITION 20 nucleotide-> adenine (nitrogenous base) ribose (5 carbond sugar) three phosphate groups (where the energy is held) --hydrolysis of ATP: ATP + H20 -> ADP + Pi (exergonic, releases energy from breaking the phosphate bonds) ,high AG (-7.3 Kcal/mol) -- regeneration of ATP: ADP + Pi + free energy = ATP OR AMP + Pi = ADP (endergonic, energy supplied form cellular respiration reactions) cells store high ration of ATP to ADP, not high [ ] of ATP
Coupling Reactions
coupled via a phosphorylation reaction: transfer of Pi TERM 22
Redox reactions
DEFINITION 22
- oxidation- reduction reactions - how electrons and energy are transferred energy is potential energy in chemical bonds partial or complete transfer of e- if partial= energy is lost as heat electrons are always moved with a hydrogen (not by themselves) reduction= gain of H OR loss of O oxidation= loss of H OR gain of O TERM 23
Functional Groups
DEFINITION 23 -groups of atoms (particular arrangements) seen repeatedly in organic compounds -have specific chemical and physical properties -are the chemically reactive regions of organic molecules -determine unique chemical properties of the molecules - the double/triple bonds cause the kinks in the "lines" TERM 24
macromolecule
DEFINITION 24 -a very large molecule (giant polymers) -formed from chemically bonding (linking) small monomers into repeated units TERM 25
polymers
DEFINITION 25 -long chains of repeated monomers linked covalently -process of polymerization (lengthening)= condensation/dehydration -the removal of a water molecule (endergonic) -shortened/broken into monomers by hydrolysis- addition of water molecule (exergonic) - polymers differ in their monomer components and those arrangements -3 most important: 1. proteins 2. nucleic acids 3. carbohydrates
N-Terminus
determine polarity of polypeptide terminal amino group ( + or basic) TERM 32
C-terminus
DEFINITION 32 determine polarity of polypeptide terminal carboxyl group ( - or acidic) TERM 33
protein conformation
DEFINITION 33 three dimensional shape of a protein TERM 34
native conformation
DEFINITION 34 functional conformation of a protein under normal biological conditions TERM 35
Primary Structure
DEFINITION 35 -the amino acid sequence (determined by genes) (insulin was the first one to be automated in a lab) -changes in the primary structure can affect the protein conformation and function -influences all the other structure levels
Secondary Structure
- the coils and folds of the primary chain -a result from the hydrogen bonding between the amino and carboxyl groups of the peptide bonds (have polarity) even though H bonds are weak, there are so many of them, the structure holds well - types: Alpha-helix B-pleated sheets (can be a combination of the 2) TERM 37
Alpha-Helix Structure
DEFINITION 37 -one type of secondary structure of a protein - designates the direction of the coil - H bonds on every 4th peptide bond - can be in part of polypeptide chain or across the length - i.e. a-keratin of hair; collagen TERM 38
B-pleated Sheets Structure
DEFINITION 38 -folds back and forth -H bonds hold the neighboring strands together -does not have the elasticity that Alpha-helix coil has i.e. silk structure TERM 39
Tertiary Structure
DEFINITION 39 native conformation - irregular contortions of protein due to interactions between side chains -2 kinds: Weak interactions Strong interactions TERM 40
Strong Interactions
DEFINITION 40
- type of tertiary structure -Disulfide bonds= Covalent bonds between sulfur atoms of Cysteine (amino acid)
functions of proteins
-transportation within and outside cells -storage(can be broken down for energy) -signaling (hormones) -movement - cell recognition -defense against foreign substances !!!!!!!!!!!act as ENZYMES TERM 47
Regulating enzymatic activity
DEFINITION 47
- cellular structures compartmentalize/order metabolic pathways 2. concentration of enzyme and/or substrate - increased [] = increased reaction rate to a limit (until enzyme is saturated) - when enzyme is saturated, rate depends of how fast active sites can work if it is saturated- the [enzyme] increases reaction rate TERM 48
Feedback inhibition
DEFINITION 48 way to regular enzymatic activity by its final product -final product inhibits an enzyme in the pathway TERM 49
deactivation
DEFINITION 49 way to regulate enzymatic activity -change of pH and [ion] - co factors (can control enzymes) TERM 50
Enzyme inhibitors
DEFINITION 50 -chemicals that selectively inhibit enzyme activity -reversible or permanent 1. competitive inhibition- chemicals resemble normal substrate and compete for the active site (the bad one wins, then blocks active site) if reversible, it can be overcome be increase in [substrate] 2. non competitive inhibition- inhibitor is bound to another site (NOT active site on substrate)-> the allosteric site it causes a conformational change so that active site no longer works
Allosteric Regulation
-where other substance binds to other site-- allosteric enzymes can either be active or inactive (depending on conformation) -2 kinds of regulators- 1. activator- stabilizes active form 2. inhibitor- stabilizes inactive form TERM 52
Nucleic Acids
DEFINITION 52 deoxyribonucleic acid/ ribonucleic acid - consist of: 5 carbon sugar (pentose) (ribose RNA/Deoxyribose DNA) 1+ phosphate groups nitrogenous base (purines AG/pyrimadines CUT) -polymers of nucleotide -phosphodiester bonds (condensation forms bond & creates water) leaves a 3' and a 5' end-> creates the backbone - covalent bond btwn phosphate group & pentose sugar TERM 53
Differences between DNA and RNA
DEFINITION 53 -absence of -OH group on DNA -substitution of Uracil for Thymine in RNA -DNA-anti parallel strands (more stable) base pairing protects code -RNA- single stranded; degrades easily (changes in pH, temp; attack by degradation enzymes; due to highly reactive hydroxyl groups) TERM 54
Condensation Synthesis
DEFINITION 54 endergonic nucleotides get their energy from the addition of the extra phosphate groups -dephosphorylation is exergonic- provides energy for polymerization
