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Biochemistry Lecture 1
• Chemistry inside the cell is carried out by
organic and inorganic molecules. One of the most
important molecules to support life is H2O
• Organic molecules in the origin of life:H2O, N2, CO2, CH4, NH3. Reactions among thesesmall molecules are initiated by UV (sun light) or
electricity (lighting in thunderstorm)
• Reaction can also be underwater in the
hydrothermal vent (volcanic) which can have high
temperature and pressure
• Reactions lead to the formation of simple
organic molecules which can be further elaborated toform comple! biological molecules
• Condensation: elimination of water (amide
bond formation glycoside bond formation)
• Hydrolysis is cleavage via water or lysis by
"#O
Organic Functional Grous
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• !mine, car"o#ylic acid, alcohol, thiol, ester, amide are important function in amino
acids and used in modulating protein functions.
o $hese functions groups can all be involved in many noncovalent interactions
including "%bonding.
o &n the biological world noncovalent interactions play 'ey roles in many
processes.
• $hioester is a high energy molecule and are important in metabolism
• !ldehydes and %etones are important for carbohydrates
• !mide is the bond used to form the bac'bone of all proteins ( etide "ond)
• &mine is important for crosslin'ing proteins (eg. elastin in lung tissue and collagen gets
their elastic property from the imine group)
• 'isulfide "onds play an important role in stabiliing protein structures (eg. the disulfide
"onds in insulin hold it together) or as in electron transfer (redo! chemistry)
• (hoshate esters are used to form the bac'bone of *+ and R*+% can be used as
signals
• (hoshoanhydride "onds are high in energy and used as energy carrier in biology
(+$,)
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• $here are 4 ma)or tyes of "iological molecules, 3 of these are "ioolymers
• Bioolymers are lin'ed by co*alent "onds
o *ote that lipids are NO$ polymers since they are not held together by covalent
bonds• ,olymers can fold up into three dimensional shapes or conformations which give them
their function
o ,olymers allow comple!ity to arise from few building bloc's
o -iopolymers are important because of their diversity
(ro"lem+ &t is proposed that ancient organisms only had amino acids. &f so how many
possible different proteins of /00 amino acids in length could e!ist1
o of ossi"le oligomers - . monomers/length
o 2 of possible proteins 3 /00 3 # ! /040 proteins
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• One of the most important features of biological system is that it can replicate itself 3
self0relication % parent leads to daughter cells
• $emplate based synthesis is 'ey for the precise replication of *+ or for the
transmitting of information encoded in *+ to R*+ or proteinso 5or e!ample either *+ replication or R*+ synthesis is mediated by replication
through Comlementarity 3 allows transfer and correction of information.
o Complementarity gives you two things: (/) it allows things to come bac' together
and (#) brings things bac' together in different shapes (this allows for correction
in *+)
• One of the 'ey features of living organism is that they separate their components from the
environments by cell membranes which is called comartmentaliation
(compartmentation)• !d*antages of comartmentation: (/) 6eparate the cellular environment from the
outside (#) 7nrich the molecules of interest for e!ample nutrients (8) 9et rid of to!ic
molecules by efflu!
• (ro%aryotic cells does not ha*e internal comartments. "owever the cytoplasm is
not homogenous. $he cytoplasm is a very viscous environment so there can still be co0
localiation of macromolecules and small molecules.
o (ro%aryotic cells are in general 1 1 m in sie. ("uman hair 3 #0%#00 um)
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• u%aryotic cells are /0 bigger 1 1 m in sie.
• $he 'ey difference between ro%aryotic and eu%aryotic cells are that the eu'aryotic
cells have defined nucleus (separated by nuclear membrane).
• -esides the nucleus eu'aryotic cells can also have the following membrane%separated
comartments:
o ndolasmic reticulum: site for the synthesis of many cellular components
o Golgi aaratus: protein modification and secretion
o 5itochondria: aerobic metabolism (the power plant in eu'aryotic cells)
o
Chlorolast: photosynthesis (plants)o Lysosomes: digestion
o 6acuoles: used for storage (plants some bacteria)
• $he compartments are very organied and are all bounded by lipids which are bounded
together by non0co*alent "onds
• $he Cytolasm is a thic' solution that fills each cell and is enclosed by the cell
membrane. &t is mainly composed of water salts and proteins. &n eu'aryotic cells the
cytoplasm includes all of the material inside the cell and outside of the nucleus.
• $he Cytosol is the part of the cytoplasm that is not held by any of the organelles in the
cell
Cytolasm - cytosol 7 mem"rane0"ound oraganelles8 Organied "y cytos%eleton
• ,ro'aryotic and eu'aryotic cells evolve to suit their living environments.
o ,ro'aryotic cell grow fast and can tolerate significant environmental fluctuations
o 7u'aryotic cells evolved to suit stable environments.
9:no; "asic sies of cells < con*ersion of units .m 0 m/
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$he tree shape is made from ribosomal R*+ and is called a hylogeny tree
o
6hows we are more closely related to plants than bacteriao Compare species by loo'ing at shared polymeric molecules 3 *+ R*+
proteins phylogeny tree
• $he biological systems are roughly divided into three 'ingdoms:
o u%aryotic system: animals plants and fungal. $hey are only a very small
portion of the organisms on earth
o !rachae"acteria .archaea/: are groups of bacteria that are distantly related to
other pro'aryotes; often <e!tremophiles= meaning they live in unusual > e!treme
environments
• "alobacteria: live in high salt concentration
•
?ethanogens: produce C"@
• $hermophiles: live in hot springs
o Bacteria
• (rinciles:
o 7volution is not directed toward a particular goal 3 random changes; those that
are non%destructive continue
o 7volution reAuires certain degree of fle!ibility (bio%diversity 3 less susceptible to
one fungal blight)
o 7volutionary is constrained by its past which means that evolution is a gradual
process
o 7volution is ongoing.
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$hermodynamics
9ibbs 5ree 7nergy G
9ibbs 5ree energy 3 energy available for wor' made up of:7nthalpy H
7ntropy S
G = H - TS
9 " and 6 can be e!pressed as a change (B) over the course of a reaction: + - C
Groducts Greactants - =G
> 3 heat 3 random motion of molecules
=H - >
Change in nthaly - change in internal heat of the system
1st La; of $hermodynamics: 7nergy is conserved (heat wor' 3 total)
• -iological systems e!ist under constant pressure B" 3 A (heat)
• Changes in enthalpy B" 3 A
• #othermic 3 release of heat
• ndothermic 3 absorption of heat
"ow to determine direction of flow of heat1 6pontaneity (does reaction move forward1)
ntroy .?/ is disorder in a system; heating a system can also increase disorder
2nd La; of $hermodynamics: 7ntropy of the universe is increasing
B6sys B6surr 3 B6universe D 0
7ntropy change can be calculated from changes in heatEtemperature: B6 D AE$;
-ut since B" 3 BA
B6 D B"E$
$his law defines criteria for spontaneity
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&f the entroy in a system decreases, entroy in surroundings must &NC@!? to satisfy
2nd la;
5or a process to be spontaneous entropy must increase.
Free nergy
B6 D B"E$
$B6 D B" A =H $=? - =G
9ibbs 5ree 7nergy determines spontaneity
B9 F 0 (negative) for sontaneous processes 3 7!ergonic
B9 D 0 (positive) for non0sontaneous 3 7ndergonic
B9 3 0 at e>uili"rium 3 when forward and reverse reactions are eAually balanced
?ontaneity
• " 6 and 9 are state functions.
• Only need initial and final values to calculate
• ,athway%independent
• 5ree energy has two components: the enthaly and entroy
• nthaly change in biological system eAuals to the heat released or absorbed in the
reaction
• ntroy change in any system eAuals to the degree of randomness changes. 5or
e!ample same amount of material in large volume will have more freedom and have
higher randomness
• ntroy increases with volume; therefore depends on concentrations.
• 5ree energy depends on concentration
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• (ro"lem+ 5or the reaction + - at
#4G the change in enthalpy is %H
'IEmol and the change in entropy is%#J IEmol. &s the reaction
spontaneous1
o B" K $B6 3 B9
%H000IEmol K (#4G)(%#J IEmol) 3@J0 IEmol
o *on%spontaneous because
B9 D 0; decrease
temperature to ma'e
spontaneousOne of the ways cells move along is by couling reactions and ma'ing the overall reaction
spontaneous (eg. how glycolysis wor's)
• $he biological system is an oen system. $here is constant e!change of material and
energy between the biosystem and its environment.
• -iological system ta'e up nutrient release waste generate wor' and heat. &t does not
reach eAuilibrium. >uili"rium - 'eath.
• 6ince biological system maintain high order inside the organism (∆6 F 0) thus ∆6 D 0
for the environment. ?ust compensate by ma'ing the environment more disordered.
• 5ood 3 high enthalpy low entropy Laste 3 low enthalpy high entropy (CO# "#O)
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• 7nergy input needed to maintain direction of KB9 (with B6 at constant $). $o have
spontaneous process enough KB".
• Couple energy releasing process to one that reAuire energy input.
• ?teady state Flu# in - flu# out. *o overall net change with time. 6mall perturbations
in molecules restore bac' to steady state.
• 7nergy flow is <downhill= (B9 F 0) and not completely efficient so some energy is lost
to surroundings (B6universe D 0) and increases the overall entropy of the system. (e!: low
entropy inside our bodies to high entropy outside)
• CM"/#OM O# M CO# M "#O; B9 3 %#H0 'IEmol K only /E8 of this energy is
converted into biochemical energy (+$,)
• (hotosynthesis couples favorable redo! reactions to unfavorable reduction of CO#
o (hotosynthesis is coupling the unfavorable reduction (adding hydrogens)
with favorable o!idation (adding o!ygen)
• Cata"olism couples favorable redo! reactions to unfavorable o!idation to CO #
• ?cale+ formaldehyde is more reduced than carbon dio!ide etc.
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@ate of "iological rocess• $hermodynamic control 3 is a reaction spontaneous (possible)1
• :inetic control 3 how fast will a reaction occur1
o &tNs possible for a reaction to be very spontaneous but very very slow. &t depends
on the 'inetics of the reaction
Biological catalyst - enyme, helps the reaction get over the 'inetic barrier
o ,rovide a more favorable pathway from reactants to products
o nymes ro*ide %inetic control "ut NO$ thermodynamic control
• $hermodynamics is pathway independent. Ginetics is not.
• Reaction coordinate to compare change in B9 vs pathway
(ro"lem+ $rue or False
o + reaction is said to be spontaneous when it can proceed in either the forward or
reverse direction. 5alse K spontaneous only in / direction
o + spontaneous process always happens very Auic'ly.
5alse K 'inetics not thermodynamics tells you the rate
o + non%spontaneous reaction will proceed spontaneously in the reverse direction.
$rue
o + spontaneous process can occur with a large decrease in entropy.
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$rue as long as B6 D B"E$ so B9 is negative.
?ummary of Chater 1• ,olymeric structure of 'ey biomolecules
• Comlementarity is important for self%replication
• $hermodynamic control determines spontaneity (%B9) can be adusted by coupling
reactions
• -iological systems are open and at steady state *O$ at eAuilibrium
• Ginetic control determines rate
• 6uggested -oo' ,roblems: Ch /: / /H #8 #J #4 8/ 88 8H 84 @/