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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



• !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

(+$,)



• $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



• 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)



• 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/



$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.



$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



&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



• (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)



• 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.



@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.



$rue as long as B6 D B"E$ 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 @/