rea lec 3 chemical composition fp

8/13/2019 Rea Lec 3 Chemical Composition FP

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Chapter 2Chemical Components of Cells

EssentialCell Biology

Third Edition

Copyright Garland Science 2010


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Vitalism: The Force

!"#

"living organisms are fundamentally different fromnon-living entities because they contain some non-physicalelement or are governed by different principles than areinanimate things."

SoulSpirit

qi prana


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Hennig Brand

(circa 1669)

Better Living Through Chemistry

Search for Philosophers Stone

Concentrated human urine

Suddenly, the flask was filled

with glowing fumes. Liquidspilled from the flask and burstinto flame

Thought he had isolatedthe Vital Essenceof Life

J. Wright (1771)


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Hennig Brand Discovered Phosphorus (white allotrope)


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Figure 2-7 Essential Cell Biology ( Garland Science 2010)

Reds comprise 99% of all atoms in cells!0.9%

Greens !trace amountsYellows!in some organisms


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H + C + O + N = 99%

Account for 99% of allatoms in living cells

Life (as we know it) isdominated by carbonchemistry


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Outermost Shellis half-full

Electronic configuration =

1s22s22p2

2 stable isotopes = 12C & 13C

1 unstable isotope = 14C(half life = 5730 years)

Whats so special about Carbon ?


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Electronic Configuration of 12Carbon

1s22s22p2}

1s

2s

2px 2py 2pz

energy

ground state 12

C


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1s22s22p2}

1s

2s2px 2py 2pz

energy

Electronic Configuration of 12Carbon


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Whats so special about Carbon ?

In methane, all C-H bonds are equivalent, and directedtoward the 4 corners of a right tetrahedron


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sp3 Hybridization (CH4)

1s

2ssp3

2p

sp3 sp3 sp3

energ

y


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sp3

H3C - CH

3

sp3 sp3 sp3 sp3


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sp3 sp2

H3C - CH

3H

2C = CH

2


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Sigma ( vs Pi (#) Bonding


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sp3 sp2 sp

H3C - CH

3H

2C = CH

2HC = CH

=


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sp3 sp2 sp

Carbon is the only tetravalent element that readily formssp3, sp2, andsp hybrid molecular orbitals with itself


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Adenosine


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stable cations

stable cations


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excellent

electronacceptors

excellent electron acceptors


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can go either way (covalent or ionic) in water, exists as H3O+


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Polar Covalent Bonds Covalent Bonds


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Ionic Bonds


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Polar Solvents Weaken Ionic Bonds


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Polar ions / molecules dissolvein aqueous media

waters of hydrationhydration spheres


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Electrostatic Interactions

Weak in aqueous medium(~ 3 kcal/mole)

Play an important role inmacromolecular recognition

Many weak electrostatic

interactions can add up tosignificant attractive force


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Structure of a water molecule

+0.33e+0.33e

-0.66e

$+$+

$-


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Liquid water is a highly

dynamic network of hydrogenbonded water molecules.

Most water molecules are

engaged in 4 H-bonds whichcan rapidly (10-12 s) re-orientinto 3 7 member ringstructures

Only 15% less hydrogenbonded than ice


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A hydrogen bond between two water molecules

ca. 1.8

H-bonds are 0.8 shorter than the sum of the H (1.2 ) andO (1.4 ) VDW radii (which would be 2.6 )

H-bond donor

H-bond acceptor

+0.33e

$+

-0.66e

$-


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Table 2-1 Essential Cell Biology ( Garland Science 2010)


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In aqueous media, hydrogen atoms engaged in polar covalentbonds within solute molecules, readily give up electrons

Keq = 10-14M


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Polar ions / molecules dissolvein aqueous media

waters of hydrationhydration spheres

hydrogen bonds


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The Hydrophobic Effect Entropically drivenexclusion of non-polarsolutes from aqueousmedia

"ThermodynamicallyUnfavored

"ThermodynamicallyFavored


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biopolymers


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biopolymers = 87% of dry weight !


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Condensation Reaction


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Biopolymers


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Biopolymers *


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Saccharides

(sugars)

(C H2O)n

where n"

3

Monosaccharides (1 residue)

Oligosaccharides (2 ~ 10 residues)

Polysaccharides (> 10 residues)

*


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Carbohydrates

(saccharides)

(C H2O)nwhere n "3

Monosaccharides are aldehydeor ketonederivatives

of straight-chain polyhydroxy alcohols containing atleast three carbon atoms.

*


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Aldohexose Ketohexose


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Fisher Projections

*


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Fisher Projections

*


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*


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epimers


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C2 epimers

C4 epimers *


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Know the structuresof the FIVE compoundsin the boxes !!


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Intra-molecular condensation resultingin cyclic hemiacetal / hemiketal


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%-D-Glucopyranose (Glucose)

FisherProjection

HaworthProjections

Chairconformer

*


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%(1!4) linkage

! Starch! Glycogen

&(1!4) linkage

! Cellulose

%-Amylose

Cellobiose

*


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Peptidoglycan

*


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Triglycerides *


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Triglyceridesester linkage


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Phospholipids: Foundation of Biomembranes


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Phosphatidylcholine is the most common

phosphoglyceridein biomembranes


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These 5 Comprise 65 - 85 % of Biomembrane Lipids

phosphoglycerides

*


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Biopolymers


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%Amino Acids

zwitterion


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Only %-L-Amino Acids are incorporated into proteins

zwitterion


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04_02_polypeptide back.jpg

Proteins are polypeptides


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Proteins

(Coming soon in Chapter 4)


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Biopolymers


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Nucleotides are modified sugar phosphates *


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Adenosine-5-triphosphate (ATP)

Hydrolysis of phosphoanhydridebonds provides theenergy that drives most cellular processes.


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Adenosine-5-triphosphate (ATP) *


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Perhaps Hennig Brand wasnt entirely wrong

Adenosine-5-triphosphate (ATP)


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Nucleic Acids

(Coming soon in Chapter 5)


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*

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