atom
-smallest unit of matter that retains properties of an element
-element properties depends on this structure
valence electrons
-number of electons in the outermost shell
-chemical properties of an atom is most related to this
covalent bonds
-electrons are shared
-stable and strong (50-200 kcal/mol)
-atoms very close (0.1-0.2 nm apart)
-usually represented by a line (--)
-non-polar
-polar
-define the spatial arrangements of atoms in biological molecules
non-polar covalent bonds
-electrons are shared equally
~hydrogen (H2)
~oxygen (O2)
~methane (CH4)
polar covalent bonds
-electrons are not shared equally
~water (H20)
electronegativity
-dictates equal or unequal sharing of electron pairs
~N and O in polar covalent bonds because they have unshared electron pairs
non-covalent bonds
-binding interactions that do not involve shared electrons
-weak bonds (1-7 kcal/mole)
-distance between atoms (0.3 nm)
-reversible
>hydrogen bonds
>van der waals attraction
>hydrophobic effect
>ionic bonds
-define interactions between molecules or parts
hydrogen bonds
-when a H atom is covalently bonded to an electronegative atom (N and O), the H atom becomes slightly polarized and slightly positive in charge
-there the H atom that is slightly positive can form a weak non-covalent interaction with electron rich (electr
van der waals attraction
-weak non-covalent interaction between non-polar hydrophobic molecules
-1kcal/mole
hydrophobic effect
-molecules that cannot form H-bonds with water will form a separate phase
~oil and water
ionic bonds
-non-covalent (no electrons shared)
-one atom donates electron to another
-fills outer shell of both atoms (produces positive and negative ion)
3-7 kcal/mole
functional groups
-parts of organic molecules that are involved in chemical reactions
-found in many types of organic molecules (especially macromolecules)
-have properties that involve acid base chemistry
~amine
~carboxyl
-always negatively charged at physiological pH
~ph
amphipathic molecules
-consists of polar and nonpolar bonds
-hydrophobic (water hating)
~sulfate
~dodecane
-hydrophilic (water loving)
micelles
-create a space where water cannot enter
-amphipathic molecules of the same size will form a ball
>but cells need a wall to contain an aqueous environment
phospholipids
-solution to the containment problem
-sheet of amphipathic molecules
-closed structure so there are no hydrophobic edges
-inner aqueous environment separated from outer aqueous environment
>bilayer is poorly permeable to ions and to big molecules
>stable
isomers
-same number of atoms, but different structures
-structural
~pentane
-geometric
~cis and trans
-enantiomers
>mirror images
macromolecules
-polymers (built from monomers)
-carbohydrates (polysaccharides)
-proteins
-lipids (fats, phospholipids)
-nucleic acids (DNA, RNA)
lipids
-fatty acids
>not a polymer
>large molecules that are assembled by dehydration reaction
>carboxylic acid with a long unbranched aliphatic tail (hydrocarbon chain), which is either saturated or unsaturated
~stearic acid
~oleic acid
polysaccharides
-carbohydrates
>sugars and polymers of sugars
-store energy
~animals: glycogen
~plants: starch
-structural support
~plants: cellulose (wood)
~insects: exoskeleton (chitin)
-when placed in water, ring form is much more favored
-sugars in nucleic acids
>DNA
proteins
-polypeptides
>polymers of amino acids
>20 different R groups (side chains)
>in cell: pH7 - ionize
-responsible for over 50% cellular mass
>enzymes, which speed up chemical reactions
>structural support
>storage
>transport
>communication
>movement
>defens
primary structure
-list of amino acids
-from N term to C term
-cannot be denatured
>covalent bonds
secondary structure
-interactions between peptide backbone
-type of non-covalent interaction
>H-bonds
~alpha-helix
~beta pleated sheet
-can be denatured
>non-covalent bonds
tertiary structure
-interactions between R groups (20 of them)
-3D structure
-hydrophobic interactions and van der waals interactions
-can be denatured
>non-covalent bonds
quaternary structure
-interactions between proteins
-can be denatured
>non-covalent bonds
small molecule recognition
-sugar
-antibodies are large groups of proteins that recognize small molecular signals on invading organisms, etc.
-many toxins are proteins that can find target cells through binding to small molecular signals on target cells
-a way for signals and infor
big molecule recognition
-protein - protein interaction
-cell recognition
-structural proteins
-protein receptors
~insulin
~endorphins
-specificity in membrane dynamics
~endosomes
~Golgi
nucleic acids
-polymer of nucleotides linked by phosphodiester bonds
-function
>information storage molecule
>store energy (ATP)
-2 types (both involved in protein synthesis)
>DNA (deoxyribonucleic acid)
>>permanent blueprint for specifying proteins
>>make up genes
>RN
spontaneous
-does not require energy to proceed
-deltaG<0
non-spontaneous
-require energy to proceed
-deltaG>0
Gibbs free energy
-deltaG = [G(products) - G (reactants)]
-free energy of a reaction from the final state and the initial state
-free energy (amount of energy that can do work)
-deltaG = deltaH - TdeltaS
-deltaG<0
>spontaneous (exergonic) because deltaH<0 (released heat) a
bioenergetics
-chemical reactions in the cell
-all controlled, stepwise fashion
-compartmentalized
deltaH
-enthalpy (heat)
-deltaH<0
>heat released
>break a bond
-deltaH>0
>heat infused (absorbed)
>create a bond
deltaS
-entropy
-deltaS<0
>create order
-deltaS>0
>create disorder
enzymes
-increase rate of the reaction
-serve as a catalyst - can be reused
-allows for the influx of energy
-lowers energy of activation
-deltaG is unchanged
-works for forward and reverse reactions
-substrate specific (specificity)
>substrate is acted on by thi
active site
-pocket on enzyme where substrate can bind
specificity
-compatible fit between enzyme and substrate
induced fit
-substrate binding induces 3D structural change of enzyme
enzyme kinetics
-reaction rates with and without an enzyme
saturation curve
-substrate is in vast abundance to study enzyme kinetics
-helps determine type of regulation
Michaelis-Menten constant
-Km
-since the substrate concentrate of Vmax cannot be measured exactly, enzymes must be characterized by the substrate concentration at which the rate of reaction is half its maximum
-1/2(Vmax)
competitive inhibitors
-reversible
>bind
>release
>substrate can now bind
-inhibition can be overcome by increasing the concentration of S
reversible inhibitors
-have affinity for an enzyme via non-covalent interactions
non-competitive inhibitors
-inhibition cannot be overcome by increasing the concentration of S
irreversible inhibitors
-may bind at the active site, or at a different site
-small amount will look a lot like the reversible non-competitive
>reduction in Vmax and Km is unaffected
allosteric regulation
-noncompetitive binding
-binding causes change in 3D conformation of the enzyme
-could have a positive or negative affect on reaction rate
-small molecules downstream in a metabolic pathway can act as this
~conversion of threonine to isoleucine
cooperativity
-only seen in multisubunit protein where all the subunits do the same thing
~hemoglobin
-sigmoid curve
kinase
-enzyme which transfers phosphate from ATP to another molecule
cellular respiration
-pathway that produces energy in the form of ATP during the oxidation of organic fuels (exergonic, catabolic pathway)
-oxidation-reduction reaction (redox reaction)
-occurs in discrete stages
>glycolysis
>citric acid cycle (krebs cycle)
>oxidative-phospho
oxidation
-loss of electrons
reduction
-gain of electrons
mitochondria
-outer membrane
-intermembrane space
-inner membrane
-matrix
glycolysis
-cytoplasm
-split sugars
-6C sugar (glucose) --> 2*3C sugars (pyruvate - goes to Kreb's cycle)
-two phases
>energy investment phase
>>2 ATP
>energy payoff phase
>>4 ATP, 2NADH + 2H+
>net
>>2 ATP, 2NADH + 2H+, 2 pyruvate + 2H2O
-key step
>G3P (intermediate
kreb's cycle
-matrix
-citric acid cycle
-3C sugar (pyruvate in cytosol) --redox to mitochondria--> CO2 + NADH + FADH2 (acetyl coA)
-72 protein transport complex
>oxidation to release CO2
>reduction of NAD+ to NADH + H+
> coenzyme A linked to remaining 2 carbon sugar
-
oxidative phosphorylation
-matrix
-NADH + FADH2 --oxidized--> NAD+ and FAD
-ADP + Pi --> ATP made
-O2 is used (aerobic)
-electron transport
>oxidation of NADH and FADH2 to NAD+ and FAD
-chemiosmosis will generate ATP
-net
>30 ATP
electron transport chain
-NADH + H+ + 1/2 O2 --> NAD + + H2O
-deltaG<<0
-separate electron
-transport them through several proteins
-multiple small reactions
-O2 is ultimate acceptor of electron
-main goal
>accept electrons
>pump protons across (against concentration gradient)
chemiosmosis
-proton (H+) motive force
>linking electron transport and H+ shuttling to ATP synthesis
-as electron enters the ETC, H+ are pumped across membrane (from matrix to intermembrane space
-now high [H+] in intermembrane space
ATP synthase
-linking ETC and H+ shuttling
-H+ gradient + ADP + Pi --> ATP
-energy is generated from ion gradient
>H+ ions: higher in intermembrane space than in matrix
>key is diffusion
>>spontaneous movement of a molecule from high to low concentration
>>H+ repel ba