Molecules of Living Systems

    The Chemistry of Life involves... the reactivity of the Molecules in Living Systems

              The STRUCTURE of biological molecules and their SHAPE determines the roles
   they play in the complex chemical processes of LIFE; yet even the most complicated
               biological molecules can be divided into smaller and smaller FUNCTIONAL GROUPS*

	*
This Lecture Topic - Chemistry of Life - is a review of your freshman biology course material & describes the structure of the fundamental biomolecules (sugars, fatty acids & lipids, nucleotides, and amino acids) which make up the major macromolecules of cells: starches/glycogen, triglycerides, phospholipids, nucleic acids and proteins.
You are responsible for reviewing topic # 5 (below)* on your own and at the end of the review below is a Practice Questions Module. refer to chapter 2 - panel 2 - pg 66-79*
after your review our next lecture will be Molecular Shape *

All the presentation material below is for review of freshman biological chemistry

Elementary Chemistry is based upon...   Periodic Table
   - The Periodic Elements are matter composed of ATOMS with an identical number of Protons
   which cannot be reduced to simpler substances by normal chemical means, and
     only 30 of the 92 natural elements commonly occur in Living Systems.

     99% of Living Matter is made of   C H O P S N
              All have low atomic numbers      ecb fig 2.7*    Table ecb 2.5 (valance electrons)*
              and are very reactive forming covalent* bonds with precise 3D geometries*.

Molecular composition of cells...
	Water (H₂O)	70 %
	Inorganic ions (as...Na, K, Cl, PO₄)	1 %
	Small monomers (amino acids, sugars, nucleotides)	5 %
	Macromolecules (protein, nucleic acids, etc)	24 %
chemical composition of bacteria ecb 2.27*

let's look at small biomolecules [MONOMERS]  made via Chemical Bonds & Functional Groups
          [Review Panels 1 to 7 in chapter 2]

Small biomolecules, the monomers, [ecb 2.28*] that make the cellular biopolymers.

    a. Hexose sugars - compounds with repeat formula of...     [CH₂O]_n
                  aldoses vs. ketoses*, rings*, alpha & beta-links*,  isomers: glucose vs. galactose*
*                glucose + glucose = mono-,   disaccharides*,  tri-, polysaccharides*
                  & long chain polymers of monosaccharides

     b.   Fatty Acids - fatty acids: saturated FA vs unsaturated*       [Table 2.4]
                     form triacylglycerols* = lipid - 3 chain hydrocarbons* animal fats* & trans fat
*            and phospholipids* easily assemble into membranes*)
                    easily self-assembly into aggregates*: soap micelles   & bilayers* with fluidity*

              fats also include steroid & cholesterols* (4-ring skeleton) as lipids because
                             they're insoluble & occur in membranes (mcb fig 1.13)*


c. NUCLEOTIDES parts* & nomenclature* are nitrogen containing "ring" compounds made of... a nitrogenous-base (ecb p2.6a) linked to a 5-carbon sugar (fig 2.16) & an inorgainic phosphate [PO₄] pyrimidines = C, T, & U purine = A & G single rings double rings ribose vs. deoxyribose sugars nucleotides are also the energy rich compounds of cells... (as ATP* & GMP), as well as the nucleic acids. all are acidic for PO₄ group releases H⁺ leaving an anion
*
d. Amino Acids ecb p2-5c* & Panel 2-5 & peptide bond* (pics)
100s known, but only 20 are common to cell proteins. once established in the "primordial cell", certain small biomolecules, as covalent themes, seem to have been preserved throughout evolution (i.e., they were favored energetically)

1st amino acid discovered was asparagine (1806 in asparagus) last amino acid described was threonine (1938)
STRUCTURE* - amino acids have a carboxyl group (- COOH) & amino group (-NH₂) ...bound to an asymmetric carbon 20 ubiquitous aa's have 4 groups on α -C in a tetrahedral shape
charge of Amino Acids - an ACID molecule that tends to release a H⁺ (-COO^-) & a BASE with a group that readily combines with a H⁺ (NH₃⁺)
Zwitterion - an ampholyte* molecule carries charges on different groups, as an amino acid, but is neutral; [amphoteric - can react as either an acid or base]
Isoelectric Point - pH where no net charge in molecule
pK (table of aa pK's) - pH where groups are 50% ionized & 50% non-ionized

classes of amino acids... [classified by chemistry of R-Groups]

polar charged	ACIDIC*... negatively charged ASP & GLU R group with 2nd COOH that ionizes above pH 7.0
polar charged	BASIC... positively charged LYS, ARG, HIS* R group with 2nd amide that protonates below pH 7.0
polar uncharged	POLAR UNCHARGED*... SER, THR, ASN, GLN, TYR, are soluble in water, i.e., hydrophilic
nonpolar aromatic	NON-POLAR*... (aliphatic) ALA, VAL, ILE, LEU, PHE, TRP contain only hydrocarbons R groups = hydrophobicity
	AROMATIC & SPECIAL* TRP, PHE, TYR, GLY, PRO, CYS contain R groups with ring structures & others
	Table of polar vs. nonpolar amino acids*

next - Molecular Shape practice questions (ans)

SKIP ALL THE MATERIAL BELOW THIS POINT...

There are only 3 known ways to make a peptide bond...

1. chemical abiotic synthesis in the laboratory... PPTI

2. genetic engineering cloning mechanisms... humulin

3. biologically, in cells... (@ rate of 25aa/sec in prokaryotic cells)

Some common peptide terminology:

dipeptide, tripeptide, pentapeptide, oligopeptide, polypeptide...

protein - polymer of a-L-amino acids joined by peptide bonds

ways of depicting polypeptides: Ras* whale myoglobin - ecb2.e panel 4.2 pg 132-133

next lecture*

SKIP THIS TABLE and all material below this point

examples of naturally occurring small oligopeptides - [many are vertebrate hormones]

Nutra Sweet - a dipeptide* (2aa) of L-aspartyl-phenylalanyl-methyl ester... aspartame

insulin - two polypeptides... controls carbohydrate metabolism
1. alpha chain of 30 aa’s & 2. beta chain of 21 aa

glucagon - pancreatic hormone 29 aa... opposes insulin action

corticotropin - 39aa - anterior pituitary hormone... stimulates adrenal cortex

oxytocin - 9aa - hormone of posterior pituitary... stimulates uterine contractions

bradykinin - 9aa – hormone acts on smooth muscle... vasodilatation/inflammation

angiotensin - octapeptide (derived from angiotensinogen by kidney enzyme renin)
- increases blood pressure ACE Inhibitors block AT & lower bp. [sport]

thyrotropin relasing factor (TSH) - 3 aa’s [Glu-His-Pro] of hypothalmus...
- stimulates thyroid to release thyroid hormone

enkephalins     - either of two penta-peptides with opiate & analgesic activity.
endorphins     - pituitary made opioid polypeptides; produce analgesia.

next lecture* e5-s15

Proteins - the penultimate molecules ?
            structurally complex
             functionally sophisticated
             most abundant molecule in cells
                                                  15% of cell’s dry mass
             long repeats of individual monomers...
                         Amino Acids

                 R
                      H₂N - C - COOH
                           H

20 common amino acids - ecb4e-panel 2-5*

              lys-arg-his-asp-glu-ala-val-leu-ile-pro-phe-met-trp-gly-cys-ser-thr-tyr
               k - r -  h - d -   e - a - v -   l - i -   p - f - m - w - g - c - s - t - y

SKIP this slide why these 20 ?
all are α-amino acids:
α = N-C-COOH β = N-C-C-COOH γ = N-C-C-C-COOH

an alpha carbon is asymmetric allowing formatiom of
2 optical isomers (ecb p2-5d*) mirror images of the aa's
    exist Levorotatory & Dextrorotatory, but only the
    the L-stereoisomer of amino acids occur in biological proteins...

    How: possibly by molecular selection*?

also, there are some unusual aa’s… that play structurally important roles...

4-hydroxy proline         occurs in plant cell wall proteins
5-hydroxy lysine           occurs in fibrous proteins as collagen
N-methyl lysine             occurs in myosin contractile proteins
γ-carboxy glutamate      occurs in prothrombin

Biomolecules & Chemical Structure of Cells... [Review Panels 1 to 7 in chapter 2]

The properties of chemicals are essential for all Cellular processes and
         may have lead to the EMERGENT PROPERTIES characteristic of life.

BIOMOLECULES... are mostly CARBON compounds & are found in all living systems…

     WHY Carbon ?              (carbon skeletons - ecb Panel 2-1)*

- an atomic # of 6 allows easy formation 4 strong covalent bonds…
   thus making many small biomolecules...
       i.e., carbons's electronegativity is able to attract electrons from other atoms
      forms nonpolar covalent bond: equal electronegativity/equal sharing of e-'s [C-C, C-H]
         forms polar covalent bonds: unequal electronegativity --> unequal charge distribution
                                          within an electrically neutral molecule [as water - ecb Panel 2.2*]