(T/F) ALL of the organic molecules listed before are polymers
FALSE - lipids are NOT polymers
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Why care about biochemistry?
provides underlying principles that govern life in all its diverse forms, helps understand mechanisms of disease, drug + vaccine development
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Definition of life
1. ability to acquire, store and transport energy 2. organization in membrane-bound compartments (cells) 3. self-contained genetic information (nucleic acids) 4. ability to replice
1. evolves/changes over time - growth and response to stimuli
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3 domains of life
bacteria, eukaryotes, archaea
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LUCA
last universal common ancestor - most recent form from which all surviving life on Earth is descended
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(T/F) LUCA is the first life on Earth
FALSE
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which rRNA genes are most used for making phylogenetic trees?
16S or 18S
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Why is 16S or 18S rRNA genes most used for making phylogenetic genes?
because they are the most conserved between species
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Prokaryotes are unicellular
Eukaryotes can be unicellular OR multicellular
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prokaryotic cell vs eukaryotic cell
prokaryotic
1. nucleoid 2. no membrane-bound organelles
eukaryotic
1. nucleus 2. membrane-bound organelles
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what determines a cellular size LOWER limit?
size of genetic information, cell structure, biomolecules
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what determines a cell UPPER limit?
efficiency of nutrient uptake, transport, and metabolism
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source of chemical elements of life
big bang → star formation → star lifecycles
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What are the most common elements making up life?
CHNOPS (over 97% of the mass of cells)
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Why is carbon so well suited for life?
1. widespread abundance 2. ability to form stable bonds with numerous elements 3. ability to form polymers at common Earth temperatures
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methyl
RCH3
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phenyl
aromatic carbon group
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carbonyl (aldehyde)
RHC=O
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carbonyl (ketone)
RRC=O
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carboxyl
ROC=O
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hydroxyl
ROH
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amino
CNH3
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amide
O=CNH2
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sulfhydryl
RSH
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disulfide
RSSR
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thioester
RC=OSR
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purposes of functional groups
1. structure + stability 2. molecular interactions with water or other biomolecules 3. activity (enzymes)
1. energy storage/transfer
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different ways to visualize biomolecules
fischer projection, Lewis strucures, bond-line formation, ball-and-stick, wireframe, backbone
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stereoisomers (spatial isomers)
same molecular formula, unique 3D orientations of atoms in space
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structural/constitutional isomers
same molecular formula, differ in the way that the atoms are connnected
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enantiomers
mirror images, identical physical configuration (type of stereoisomer)
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diastereomers
non-mirror images, can have unique chemical properties (type of stereoisomer)
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most biomolecules are ___ and __
chiral, have a few chiral centers, and are a single type enantiomer
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Cells primarily synthesize _ amino acids and _ sugars
L-amino acids, D-sugars
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(T/F) biomolecules are static
FALSE - undergo conformational changes where stereochemistry is importanta
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thermodynamics
energetics of chemical reactions and molecular interactions in cells
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first law of thermodynamics
cells absorb/release energy and convert it into different forms
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second law of thermodynamics
overall randomness (entropy) in the universive tends to increase over time
* cells release energy as heat which increases S(surr)
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Gibbs free energy equation
delta G = delta H - T(delta S)
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delta G in the Gibbs equation
Gibbs free energy, change in energy available for work (units: kJ/mol)
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delta H in Gibbs equation
enthalpy, change in heat content (units: kJ/mol)
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delta S in the Gibbs equation
entropy, change in degree of disorder (units: kJ/Kelvin\*mol)
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T in Gibbs equation
temperature (units: Kelvin)
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delta G degree in Gibbs equation
standard free-energy change - G at “standard conditions”
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reactions where delta G are < 0 are ___
spontaneous
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reactions where delta H < 0
reaction releases heat
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when delta S < 0
reaction is more ordered
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Reactions in cells need to be __ or become coupled with other favorable ones
spontaneous
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what signs should delta H and delta S be for a spontaneous reaction
negative delta H and a positive delta S
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endergonic reaction
energy is absorbed, delta G > 0, not spontaneouse
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exergonic
energy is released, G < 0, spontaneous
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kinetics
speed/rate that chemical reactions and molecular interactions occur in cells
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equilibilrium
occurs when the rate of product formation is equal to the rate of reactant formation
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Q
reaction quotient
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Keq - equilibrium constant
relative amounts of products vs reactants at equilibrium
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when Keq>1
more products at equilibrium, delta G < 0
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when Keq
more reactants at equilibrium, delta G > 0
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when Keq = 1
equal amounts of products and reactants at equilibrium, delta G = 0
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equation relating delta G to Keq
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Le’Chateliers principle
passive process - when equilibrium is disturbed the equilibrium shifts to counteract and reestablish equilibrium
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homeostasis
dynamic steady state at cellular level, active process requiring biomolecules
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Le-Chatelier vs homeostasis
both resist changes to a system, Le’Chatlier is passive while homeostasis is active
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steady state vs equilibrium
equilibrium is a reversible process A→B AND B→A
steady state requires more steps A→B→C
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metabolism
set of life-sustaining chemical reactions in a cell
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metabolite
an intermediate or end product of metabolism
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metabolic pathway
coordinated series of chemical reactions (product of one reaction becomes the substrate for the next reaction)
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anabolic
the building up (synthesis) of metabolites and biomolecules
* usually consumes/requires energy
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catabolic
breaking down of compounds
* energy is either stored or released as heat
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chemical oxidation is to _ as sunlight is to _
cellular respiration, photosynthesis
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cellular respiration
glucose is oxidized with oxygen to release ATP (spontaneous)
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photosynthesis
light drives synthesis of glucose and oxygen from CO2 and H20
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are humans aerobic or anaerobic?
aerobic
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ATP
energy currency of the cell, hydrolyzed to release ADP and energy
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reaction coupling
pairing a energetically favorable reaction with an energetically unfavorable reaction (add the delta Gs of both reactions)
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activation energy (Ea)
minimum energy required to cause a process to occur
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what is the source for activation energy needed to push reactions forward
catalysts or heat energy from the surroundings
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catalysts
enzyme or RNA that increases the rate of a chemical reaction
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G++
activation free energy - catalysts lower this
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(T/F) Catalysts alter delta G\*
FALSE - enzymes lower the activation free energy G++
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gene
region of DNA that encodes cellular function
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genome
entire set of DNA found in a cell
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allele
different versions of a gene
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central dogma
DNA→RNA→proteins (in reality it goes in many directions)
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modern view of central dogma
central dogma + works in the reverse direction/proteins can create more proteins
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evolution
change in heritable characteristics of bio populations over successive generations
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5 forces of evolution
1. mutation - mistake/change in DNA 2. genetic drift - random small population 3. gene flow - movement of people/migration 4. non-random mating 5. natural selection
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homolog
proteins diverged from a common origin
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ortholog
genes which evolved from a common ancestral gene by speciation that usually have retained a similar function in different species
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paralog
genes related by duplication within the genome and often they acquire a new function
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germline mutation
occur in sperm and egg, more important to evolution, can be passed on to offspring
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somatic mutations
occur in body cells, NOT passed on to offspring
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gene duplications
* source of genetic novelty that can lead to evolutionary innovation w/o deactivating original gene function * common cause of disease (cancer) * can occur as the result of an error in recombination or replication * often immune to selective pressure under which genes normally exist
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water is some form (liquid, ice, vapor) is necessary for every llife form, which is why
we are looking for water on other planets
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role of water in biochemistry
1. water as a solvent - chemical reactions in a cell or btwn a cell and the environment occurs in aqueous solutions 2. water actively participates in many biochemical reactions (30-50% of known biochem reaction involve water consumption or production) 3. biomolecules assume their shapes and function in response to the properties of water 4. the reactivity of the functional groups in many biomolecules depends on the relative concentration of H+ and OH- in solution 5. properties of water shape homeostasis and the evolution of life
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(T/F): Water is just a medium/solvent
FALSE - is also an active chemical participant
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water dictates almost all of what process?
cellular metabolism
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condensation
dehydration synthesis - molecules combined with the loss of a water