Essential Cell Biology

Third Edition

Chapter 2 Chemical Components of Cells !

Copyright Garland Science 2010

Vitalism: The Force! Soul! Spirit!

qi!

!"#!
prana!

"living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things."!

Better Living Through Chemistry!

Search for Philosophers Stone!
!

Concentrated human urine!

!

Suddenly, the ask was lled with glowing fumes. Liquid spilled from the ask and burst into ame!
!

Thought he had isolated ! the Vital Essence of Life!

J. Wright (1771)!
!

Hennig Brand ! (circa 1669) !

Hennig Brand Discovered Phosphorus (white allotrope)!

Reds

comprise 99% of all atoms in cells! ! 0.9%! Greens ! trace amounts! Yellows ! in some organisms!

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

H + C + O + N = 99%! ! Account for 99% of all atoms in living cells! ! Life (as we know it) is dominated by carbon chemistry!

Whats so special about Carbon ?!

Outermost Shell is half-full! ! Electronic conguration =! ! !1s2 2s2 2p2! ! 2 stable isotopes = 12C & 13C! ! 1 unstable isotope = 14C! (half life = 5730 years)!

Electronic Conguration of 12Carbon!

1s2 2s2 2p2!

}!
2px! 2s! 1s!
ground state 12C!

energy!

2py!

2pz!

Electronic Conguration of 12Carbon!

1s2 2s2 2p2!

}!
2px! 2s! 1s! 2py! 2pz!

energy!

Whats so special about Carbon ?!

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

sp3 Hybridization (CH4)!

2p!

energy!

sp3! 2s!

sp3!

sp3!

sp3!

1s!

sp3!

sp3!

sp3!

sp3!

sp3!

H3C - CH3!

sp3!

sp2!

H3C - CH3!

H2C = CH2!

Sigma (!) vs Pi (#) Bonding!

!"

!"

sp3!

sp2!

sp!

H3C - CH3!

H2C = CH2!

HC = =! CH!

sp3!

sp2!

sp!

Carbon is the only tetravalent element that readily forms sp3, sp2, and sp hybrid molecular orbitals with itself !

Adenosine!

Figure 2-5 Essential Cell Biology ( Garland Science 2010)

stable cations!

stable cations!
Figure 2-5 Essential Cell Biology ( Garland Science 2010)

excellent electron acceptors!

excellent ! electron ! acceptors!

Figure 2-5 Essential Cell Biology ( Garland Science 2010)

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

Figure 2-5 Essential Cell Biology ( Garland Science 2010)

Figure 2-6 Essential Cell Biology ( Garland Science 2010)

Polar Covalent Bonds!

Covalent Bonds!

Ionic Bonds!

Figure 2-8 Essential Cell Biology ( Garland Science 2010)

Polar Solvents Weaken Ionic Bonds!

Polar ions / molecules dissolve in aqueous media !

waters of hydration! hydration spheres!

Electrostatic Interactions! ! Weak in aqueous medium! (~ 3 kcal/mole)! ! Play an important role in macromolecular recognition! ! Many weak electrostatic interactions can add up to signicant attractive force!

Structure of a water molecule!

-0.66e! $-!

$+! +0.33e!

$+! +0.33e!

Liquid water is a highly dynamic network of hydrogen bonded water molecules.! ! Most water molecules are engaged in 4 H-bonds which can rapidly (10-12 s) re-orient into 3 7 member ring structures! ! Only 15% less hydrogen bonded than ice!

A hydrogen bond between two water molecules!

H-bond acceptor!

$+! +0.33e!

ca. 1.8 !

H-bond donor!

-0.66e! $-!

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

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

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

Keq = 10-14 M!

Polar ions / molecules dissolve in aqueous media !

waters of hydration! hydration spheres!

hydrogen bonds!

The Hydrophobic Effect!

Entropically driven exclusion of non-polar solutes from aqueous media! "!Thermodynamically ! Unfavored!

"!Thermodynamically ! Favored!

biopolymers!

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

biopolymers! = 87% of dry weight !!

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

Figure 2-26 Essential Cell Biology ( Garland Science 2010)

Figure 2-27 Essential Cell Biology ( Garland Science 2010)

Condensation Reaction!

Figure 2-28 Essential Cell Biology ( Garland Science 2010)

Biopolymers!

Figure 2-15 Essential Cell Biology ( Garland Science 2010)

Biopolymers!

*!

Figure 2-15 Essential Cell Biology ( Garland Science 2010)

Saccharides ! (sugars)! ! (C H2O)n! where n " 3! ! Monosaccharides (1 residue) ! ! Oligosaccharides (2 ~ 10 residues)! ! Polysaccharides (> 10 residues)!

*!

Carbohydrates ! (saccharides)! ! (C H2O)n! where n " 3!

Monosaccharides are aldehyde or ketone derivatives of straight-chain polyhydroxy alcohols containing at least three carbon atoms. !

*!

Aldohexose!

Ketohexose!

Aldohexose!

Ketohexose!

*!

Fisher Projections!

Aldohexose!

Ketohexose!

*!

Fisher Projections!

*!

epimers!

C4 epimers!

*!

C2 epimers!

Know the structures ! of the FIVE compounds! in the boxes !!!

Intra-molecular condensation resulting in cyclic hemiacetal / hemiketal !

%-D-Glucopyranose (Glucose)!

*!

Chair conformer! Fisher! Projection!

Figure 2-16 Essential Cell Biology ( Garland Science 2010)

Haworth! Projections!

% & & anomers of D-glucose!

*!

OH H

%-D-glucose!

&-D-glucose!

Figure 2-17 Essential Cell Biology ( Garland Science 2010)

%-Amylose!

%(1 ! 4) linkage! ! ! Starch! ! Glycogen! !

*!

&(1 ! 4) linkage! ! ! Cellulose! ! Cellobiose!

*!

Peptidoglycan

Lipids!

Figure 2-15 Essential Cell Biology ( Garland Science 2010)

Palmitate! ! a saturated ! fatty acid! ! amphipathic! ! amphiphilic!

Figure 2-18 Essential Cell Biology ( Garland Science 2010)

Triglycerides!

*!

Figure 2-19 Essential Cell Biology ( Garland Science 2010)

Triglycerides ! ester linkage!

Figure 2-19 Essential Cell Biology ( Garland Science 2010)

cis double bonds introduce a kink in the hydrocarbon chain!

Cells can metabolize only cis unsaturated fatty acids!

Phospholipids: Foundation of Biomembranes!

Figure 2-20 Essential Cell Biology ( Garland Science 2010)

Phosphatidylcholine is the most common phosphoglyceride in biomembranes

These 5 Lipids Comprise 65 - 85 % of Biomembranes

These 5 Comprise 65 - 85 % of Biomembrane Lipids

*!

phosphoglycerides!

Biopolymers!

Figure 2-15 Essential Cell Biology ( Garland Science 2010)

% Amino Acids!

zwitterion!

Figure 2-21 Essential Cell Biology ( Garland Science 2010)

Only %-L-Amino Acids are incorporated into proteins!

zwitterion!

Figure 2-21 Essential Cell Biology ( Garland Science 2010)

Proteins are polypeptides!

04_02_polypeptide back.jpg!

Proteins! ! (Coming soon in Chapter 4)!

Figure 2-22 Essential Cell Biology ( Garland Science 2010)

Figure 2-31 Essential Cell Biology ( Garland Science 2010)

Biopolymers!

Figure 2-15 Essential Cell Biology ( Garland Science 2010)

Nucleotides are modied sugar phosphates!

*!

Adenosine-5-triphosphate (ATP)!

Hydrolysis of phosphoanhydride bonds provides the energy that drives most cellular processes. !
Figure 2-23 Essential Cell Biology ( Garland Science 2010)

Adenosine-5-triphosphate (ATP)!

*!

Hydrolysis of phosphoanhydride bonds provides the energy that drives most cellular processes. !
Figure 2-23 Essential Cell Biology ( Garland Science 2010)

Adenosine-5-triphosphate (ATP)!

Hydrolysis of phosphoanhydride bonds provides the energy that drives most cellular processes. ! ! Perhaps Hennig Brand wasnt entirely wrong !

Nucleic Acids! ! (Coming soon in Chapter 5)!

*!

Figure 2-33 Essential Cell Biology ( Garland Science 2010)