Chapter 1 Molecular logic of life

General principals that can see and may use

Read these notes on your own. I will probably not cover this material in lecture

1.0 Introduction
A. What is difference between living & nonliving matter? Can I get the class to
bring these up?
I. Complexity
Nonliving - mixtures of relatively simple chemicals
Living thousands of chemicals in various hierarchical organization
and unique 3D structure
ii. Use of energy
Nonliving - does not use - decays toward disordered state
Living - E used & transformed to do work, to keep & maintain
organization
iii. Replication
Nonliving little growth- except maybe crystal
Living - can self replicate
iv. Mechanisms for sensing and responding to environment.
v. Defined function for each component and regulated interactions
between components.
vi. A history of evolutionary change
(Oops - defining life by evolution? Not very creationist)

1.1 Cellular Foundations

A. Cells are Structural and Functional Units of all living organisms
Share certain structural features
I. Plasma membrane (PM)-
Defines periphery of cell
Composed of lipids and proteins
Tough, pliable, hydrophobic
Most polar or charged molecules cannot pass
Need transport proteins
Use hydrophobic interaction to hold together so flexible
ii. Cytoplasm
What’s inside the PM
Cytosol - highly concentrated aqueous solution
Proteins metabolites, RNA & whatnot
Lots of different suspended particles
Ribosomes, mitochondria, etc
iii. Nucleus or nucleoid
Holds genetic material
Eukaryotes permanent membrane bound structure
Prokaryotes not separate from cytoplasm but depending on part of
cell cycle bits and pieces are membrane associated
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B. Cellular dimensions limited by O2 diffusion

On the small side
bacteria 1-2 um long
Smallest bacteria - mycoplasmas
Diameter .1 uM volume 10-14 ml
Ribosome about .02 um diameter
So only a few ribosomes
Probably sets the lower size limit
On the large size
Plant & animal cells 5-100 um
Size probably set by how fast O2 can diffuse from membrane

C. Three Distinct domains of life

Domains or kingdoms Figure 1-4
archaebacteria
Prokaryotes
Recently discovered
Not well characterized
Extreme environments - salt lakes, hot springs, ocean vents, acid
bogs
Probably diverged from eubacteria long ago
eubacteria
Also prokaryotes
All over, soil, surface water, in other organisms, living and dead
Eukarya
Eukaryotes - have a nucleus and other organelles

Archea and Bacteria divided into subgroups based on metabolism

Aerobic - habitats with lots of O2 main energy source oxidation
Anaerobic - habitat devoid of O2 other reaction not using O2
Obligate anaerobes - Die in O2

D. How organisms get Energy and Chemicals Figure 1-5

Phototropes - use sunlight for E
Autotrophes - Get all C needed from CO2
Heterotrophes - require organic nutrients
Chemotrophs - use oxidation chemical reaction for E
(Only heterotrophes here)
Lithotrophs - oxidize inorganic compounds for E
Organotrophs - oxidized organic compounds for E
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E. Escherichia coli is most studied prokaryote

Will see lots of data on this bugger so better talk a bit about him in this
general intro
Figure 1-6
usually harmless, lives in intestinal tract
2 micrometers long <1 micrometer wide
has protective outer membrane outside plasma membrane
Between inner and outer has a peptioglycan layer
Outer layer will not bind Gram’s stain - hence gram negative
Gram positive lack outer membrane and have thicker peptidoglycan
together referred to as cell envelope, relatively rigid, hold cellular shape
plasma membrane has protein for transport of ions
also cytochrome used to make ATP from ADP
Outer membrane may short hairlike have pili to help adhere to other cells
some strains have 1 or more flagella for motion
inside the usual cytoplasm and nucleoid
Cytoplasm
15,000 ribosomes
Thousand of copies of About 1,000 different enzymes
Metabolites, cofactors, inorganic ions
One or more Plasmids small circular pieces of DNA,
independent of nucleoid
Usually genetic code for a small number of useful
proteins
Antibiotic resistance
Toxin resistance
Not necessary so useful for experiments

Nucleoid
Single circular piece of DNA
If single strand 1,000 time length of cell
Packaged in proteins to less than 1 micrometer in longest
dimension

F. Eukaryotic Cells - Membrane bound organelles

Figure 1-7
5-100 um diameter
Volume 1,000 - 1,000,000 x prokaryotes
Nucleus and a variety of membrane bound organelles
Mitochondira
Endoplasmic Reticulum
Golgi complexes
Lysosomes
Plants have chloroplasts
If open up cell gently can separate organelles based on density
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That is how we figure out what proteins are in each organelle

G. Cytoplasm is organized by cytoskeleton

Not just a thick liquid, but a 3D meshwork of filaments- the Cytoskeleton
Actin filaments
Microtubles
Intermediate filaments
Not permanent structures
Constantly forming and un-forming
Hold overall cellular structure
Used to move things around in cell
Used for budding, exocytosis and endocytosis

H. Cells build Supramolecular Structures

From Gen Chem you should remember that many interesting biological
chemicals are ‘Biopolymers’ - A polymer built from various biological
monomers Figure 1-10 for instance

But there is a tremendous gap between a biopolymer and the

macromolecular structures you can see in a microscope
Figure 1-11?

These macromolecular structures are complexes of lipids, proteins,

nucleic acids and saccharides hat are held together largely by non-
covalent interactions

You should review

Ionic (Charge/Charge) interactions
Polar interactions
Hydrogen bonding
Van der Waals interactions
And we will add a new one - the hydrophobic interaction
(More on this later)
Bottom line - all of these large complex structures are held together by
100's or 1000's of very weak interactions.

I. In Vitro studies my overlook important interactions

Early Biochemistry - Take it out and isolate it to understand it. Accepted
proof that you understood something was that you had to be able to
synthesize it via organic chemistry and have it function the same way

Very successful, but miss important interactions between things

Central Challenge in Biochemistry is to understand all interaction up and

down the organizational hierarchy to understand how the cell and the
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organism function as a whole.

1.2 Chemical Foundations

99% of all atoms in cell H,C,N,O
Only 30 elements really needed
Most of these are in first 3 rows (Figure 1-12)

A. Biomolecules are C compounds with a variety of functional groups

Keeping in mind H,C,N and O what functional groups can you remember
from O chem?
Amine, Carboxylic acid, alcohol, ketone, aldehyde, ether, ester.
Go through figure 1-15 for others

B. Cells contain a Universal set of small molecules

Codicil of all cells contain the same 100-200 small molecules (MW 100-
500)
Memorize them (that’s a joke)

Small molecules unique to an organism are called the Secondary

Metabolites

Sum total of all small molecules metabolome

(why does everybody have to have a genome knock-off phrase)

C. Macromolecules are the major cell constituents

Proteins - polymers of amino acids
nucleic acids - polymers of nucleotides
polysaccharides - polymers of sugars
lipids - not so much a polymer, but a collection of oily hydrocarbons

Nucleic acids and proteins, exact sequence can be extremely important

polysaccharides and lipids exact sequence less important

D. 3-D structure in described by Configuration & Conformation

As in O Chem, Covalent bond and functional groups are important
But in Biochem will see that arrangement of these atoms in 3-D space is
even more important.

Configuration - Different spatial arrangement that can only be resolved by

breaking bonds
Comes from either double bonds with no freedom of rotation
Or C centers with C compounds with 4 different constituents -
stereoisomers
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Double bonds
Geometric or Cis Trans isomers
Remember these, if not review!

Asymmetric C’s
Chiral centers
C with 4 different substituents
A structure and its mirror image
Called enantiomer
So 2 stereoisomers for each center
What is a diasteromer?
Pairs of steroisomers that are not mirror
images
In O Chem you learned proper nomenclature, and book
reviews at this point. In Biochem we use some older, less
accurate nomenclatures, will review when we get to it.

Have wrong configuration you die!

Will reintroduce concepts of stereo chem as needed

Also configuration around double bonds (cis-trans)

Conformation-
Different spatial arrangements obtained by rotating bonds
Many different conformation will be possible
Certain one will be favored energetically

E. Interactions between biomolecules are stereospecific

When two biomolecules interact they have to have the correct 3-D fit
Hence interactions are stereospecific
-Becomes especially important in making drugs
- wrong stereoisomer can have negligible biological activity
In some cases event has negative effects
- so you organic chemists need to pay attention
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1.3 Physical Foundations

Cells must perform work to stay alive
How cells obtains and use chemical E is another aspect of Biochemistry

A. Living Organisms never at equilibrium, but rather a dynamic steady state

I. From Gen Chem - How do you tell if at equilibrium?
Concentrations do not change
But that wasn’t the whole story talked about kinetics
Some reaction are slow, so take very long to reach
equilibrium
Given the above, how do you tell if at equilibrium?
Calculate Q Q/= K not at equilibrium
Calculate ÄG, if ÄG /=0 not at equilibrium

ii. Chemical composition of a mature individual may not appear to change

But population of molecules is under constant revision
All molecules from small to macro are constantly being torn down
and rebuilt.
Even though conc of Hemoglobin and glucose in blood is
relatively constant
Glucose from breakfast will not last the day. Either
oxidized to CO2 or transformed to fat or glycogen

Hemoglobin carrying O2 in blood will not last the

month, will be degraded and replaced
iii. Referred to as dynamic steady state
Rate of breakdown is balanced by rate of creation

Still sounds like could be equilibrium, because equilibrium is

achieved when rate of forward reaction = rate of backward reaction

So lets check ÄG of reaction:

Chemicals in organism 6Chemical in environment
ÄG of almost every compound will be big and positive
That means unfavorable
That means want to break down
IF Energy says we should be breaking down, why don’t we?

Maintenance of dynamic steady state requires E

Run out of E you die, then start to achieve true equilibrium with
surroundings

So life is a scramble to intake enough E that you maintain your

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overall E above that of the environment

B. Organisms transform E and matter from surroundings

Back to Thermodynamic terms
I. The System - reactants, products, and any needed solvent
ii. The Surroundings - everything else in universe
iii. New terms
Isolated system - system exchanges neither E nor matter with
surroundings
Closed system - system exchanges E but not matter with
surroundings
Open system - system exchanges E and matter with surroundings

iv. Organisms are open systems - exchange E and matter with

surroundings
Derive E either by chemical transformations of matter
Or direct absorption of sunlight

C. Flow of electrons provides E for organisms

Nearly all organisms get their E directly or indirectly from the sun
Plants:
6CO2 + 6 H2O + light 6 C6H12O6 + 6O2
Non plants
C6H12O6 + 6O2 66CO2 + 6 H2O + Energy
Both oxidation reduction reaction
most reaction in between are oxidation reduction reaction
Can understand much of E flow by looking at potentials of redox reactions
Will review when we get there

D. Creating and maintaining order requires Work and E

Remember the second law of thermodynamics?
Entropy (disorder) of universe is constantly increasing?
What is wrong with living organisms form this point of view?
Big theme so far is that organisms are highly organized
So the Universe is greatly displeased with us.
I. A reminder of terminology
Entropy (S) a measure of randomness
Is defined at + when randomness increases
Enthaply (H) a measure of E stored chemical bonds
Free Energy (G) - for a closed system
Energy available to do work
ÄG = ÄH-TÄS
Spontaneous only if negative
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Endergonic energy requiring reaction

Exergonic energy releasing reaction

To make a E rich compound like ATP you will have to mix a

strongly exergonic reaction with an second endergonic reaction so
the net reaction is favorable. This leads us to:

E. Energy Coupling links reaction in Biology

Bioenergetics - Study of energy transformations in living systems
In general link an unfavorable reaction with a + ÄG
with a second favorable reaction with a more - ÄG
So the NET of adding the two reaction together has a net -ÄG and is
favorable

F. Keq and ÄG are measures of a reaction’s tendency toward spontaneity

aA + bB 6cC + dD
Keq = [C]c[D]d/[A]a[B]b
K>1 spontaneous (reaction go to right)
K <1 non spontanteous (reaction goes toward left)

ÄG <0 Spontaneous
ÄG > 0 non-spontaneous
ÄG =0 at equilibrium

Can transform one into the other

ÄGo = -RT ln Keq

But don’t forget kinetics: Just because favorable, still may not occur if
kinetics is slow

G. Enzymes promote sequences of chemical reactions

Just mentioned that a reaction may be kinetically slow
can speed it up with a catalyst
Enzymes are biological catalysts

How do catalysts work?

Figure 1-28
Most reaction have a activation energy
Energy required to get to a transition state
Enzyme lower activation E
(Will discuss how in a later chapter)

Most enzymes highly specific

1 reaction 1 or more enzymes
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So 100's of enzymes
Most enzymes are proteins
But there are a few that use RNA!

Can organize a series of sequential reactions into a pathway

Catabolic pathways - Catabolism - degrade compounds to release E
Anabolic pathways - Anabolism - use E to make compounds

ATP is link between the two

Overall sum referred to a metabolism

H. Metabolism is regulated to achieve balance and economy

Can break down metabolism into lot’s of individual pathways
Can study regulation of each pathway
Cell strives to make just enough for its need and no more
Will see lots of way to achieve this regulation
But again cell is complex and can’t look at one piece without seeing how it
fits into the whole

1.4 Genetic Foundations

Major biological discovery of 20th century - first discovery that DNA is genetic
material - then second, figuring out how it worked on the atomic scale

A. Genetic Continuity is Vested in a Single DNA molecule

E coli - thousand of genes incorporated into a single DNA
Humans 23 single DNAs (chromosomes)
Each had to be replicated EXACTLY for next generation

B. Structure of DNA responsible for exact replication and repair

2 complimentary strands
use one as template to make other or for fix damage

C. Linear sequence of DNA encodes protein 3D structure

information in DNA is 1d (linear sequence)
Have seen that protein have and need precise 3-D structure to operate
DNA sequence make Protein sequence
Protein sequence then fold into precise 3-D structure via mostly non-
covalent interactions
How this is encoded into sequence sometimes called the
‘second genetic code’
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1.5 Evolutionary Foundations

Note: Interesting theories, but nothing I would test on
A. Changes in DNA allow evolution
Replication of DNA is not perfect
Occasional mistakes called mutations
Some mutation harmful even lethal
Some silent
Some helpful
(Some both helpful and harmful)
If a mix of wild type and mutants find themselves in an environment when
the mutant has an advantage,
Strong (mutant)survive
Weak (wild type) die off
Evolution

B. Biomolecules arose by chemical evolution

Oparin theory (1922)
Early earth rich in CH4 NH3 H2O lacking O2
E from various sources combined to give organic substances
Washed into sea and concentrated there
-Primordial soup-
Chemistry evolved into first cells

C. Chemical evolution can be simulated in the lab

1953 Miller in Urey’s lab
Figure 1-34
Could make some needed organic compounds
more refined experiment have made polypetde and RNA-like compounds

D. RNA or it precursors may have been first genes

Which came first DNA or protein?
Probably RNA
Has properties of both
Can replicate
Can catalyze reactions

E. Biological evolution began >3.5 billion years ago

earth formed 4.5 billion years ago
3.85 billion, Rock in Greenland with C in rock appears to have biological
origin

F. First cell was probably a Chemotroph

primordial cell sitting in soup rich in organic chemicals, all it needed was to
figure out how to use the E available
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Next step probably use light to change H2S to S or SO4

(The organisms still around as cyanobacteria)
Then on to H2O and release O2 as a waste product

Atmosphere then slowly changed from O2 deficient to O2 rich

A lot of obligate anaerobes probably died in a mass extinction

G. Eukaryotes evolved from prokaryotes in several stages

1.5 billion year ago probably first eukaryotic cells
Can’t do with fossil records
Use morphology and DNA of cells to trace

Several things needed to be done

1. Evolve DNA higher level chromosome structure
2. Evolve membrane covered organelles including a membrane around
the nucleus
3. Evolve endosymbiotic relationship
With light harvesting bacteria for photosynthesis
With good aerobic bacteria for mitochondira

H. Molecular anatomy reveals the above evolution

Genome - Complete genetic endowment of a organism
Have genome of several organisms from e coli to humans

By comparing sequences can begin to trace evolution

Consistent with but more precise than looking at physical shape
(phenotypes)

Homologs - two proteins that have a readily apparent genetic sequence

Paralogs - two homologous protein gene in the same species

Presumably arise from gene duplication
Similar in sequence and 3-D shape
But may have acquired different function

Orthologs - homologous gene found in different species

Usually have same function in both species
Comparison of sequence changes helps trace evolution
Sequence close, closely related
Sequences different, not so closely related

Annotated Genome
Not only gene sequences but a guess of what each gene sequence
actually does. Often based on Orthologs (above)
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I. Functional genomics shows allocation of gene to specific processes

Look at annotated genome and figure out how many protein are allocated
to different specific functions

Right now ~40% in ecoli to human - function unknown

Cell transporters 10% e coli 8 % Arabidosis thaliana (plant) 4% Human
Gene for protein and RNA for protein synthesis ~ 4% Ecoli
H thaliana 2% synthesis 6% target to proper place in cell
More complex, more genome devoted to regulation

J. Genomic comparisons important to Medicine

what can I say