Biochemistry Overview

Columbian mammoth
(extinct about 12,500 years ago)
African Elephant
American mastodon
(extinct about 11,000 years ago)

The Chemical Nature of Life

everything that living things do can be understood in terms of the
jiggling and wiggling of atoms.
-Richard Feynman
Almost all aspects of life are engineered at the molecular level, and without
understanding molecules we can only have a very sketchy understanding of life itself.
-Francis Crick
Living things obey the standard laws of physics and chemistry. No vitalistic force
is required to explain life at the molecular level.
-Principles of Biochemistry (Moran)

What is Biochemistry?
Biochemistry uses the principles and language of chemistry to understand
and explain biology.

Why is it important?
Many aspects of life are still a mystery.
Yet, particularly in the last 40-50 years, we have come to learn a great deal about
how biological systems work at the molecular level.

It is now clear that in organisms as diverse and distantly related as bacteria, plants,
and humans the same chemicals compounds and central metabolic
processes are used.
The same basic principles of biochemistry are common to all biological entities.
All phenotypes are emergent from biochemical and molecular genetic processes.
Life is the most interesting phenomenon in the universe (so I say)!

Anything found to be true of E. coli must

also be true of elephants.
-Jacques Monod

Differences in scale and variations of common themes

What are the distinct properties of living things?

complicated and highly organized. Composed of simple molecules mostly, but these
are organized and interact in complex ways

all biological structures, from wings and hearts to amino acids and enzymes,
carry out functions critical for the existence and replication of the organism
carry out energy transformations. Almost all life on earth is dependent on the sun.
How living things capture this energy and use it to power the structures
and functions of life is one of the most important topics in biology.
the essence of living things is the propensity for self-replication. Inanimate entities
lack this property.

The Chemical Elements of Life

Six non-metallic elements:
Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
account for about 97% of your mass
In addition to these 6 main elements (CHNOPS), 23 other elements are common.
Five elements in their ionized forms are essential to all life forms.
Ca2+, K+, Na+, Mg2+, Cl-

The Periodic Table

-relatively few elements are involved in this phenomenon called Life (CHNOPS).
most abundant
essential ions

trace elements

Why so few elements contributing so much?

Four of the CHNOPS series, H, O, C, N are the most abundant elements
in living things.
-these 4 elements make up about 99% of the atoms in your body and in
everything from viruses to bacteria to earthworms to elephants.

Why these elements?

their ability to form covalent bonds by electron pair sharing.

they are among the lightest elements capable of forming covalent bonds with
other atoms.
inverse relationship: the lighter the element, the stronger the covalent bonds
they can form.
forming larger molecules through covalent interactions is necessary for life. An
astonishing array of complex biochemicals can be formed.

Life is Carbon-Based
Though most of your body is water, the rest is formed primarily from
Carbon-based compounds
Carbon is one of the lightest elements that routinely forms covalent interactions
with other atoms
Carbon is very versatile in its ability to form large, complex, and diverse molecules.
Carbon accounts for the great diversity of biological molecules and in turn has made
possible a great diversity of living things.
Proteins, DNA, carbohydrates, and other molecules that distinguish living matter
from inorganic material are all composed of carbon atoms bonded to
each other and to atoms of other elements.

Tetravalence: the ability to form four bonds with other elements including itself
makes large, complex molecules possible.

light element with propensity to form covalent bonds instead of ionic bonds
forms covalent bonds of significant strength (energy)
tetravalency: multiple bonds, complex molecules

Hydrocarbons are the

building blocks of most
biomolecules

methane
CH4

ethane C2H6

Alkane

Alkene

Alkyne

methane
ethane
propane
butane
pentane
hexane
heptane
octane
nonane
decane

-ethene
propene

-ethyne
propyne

ethene C2H4

ethyne C2H2

Functional Groups on molecules are of great importance

Consider the alkane ethane

a gas at RT

the addition of an OH group (hydroxyl group) forms an organic alcohol with

substantially different properties than ethane.

OH

ethanol, a liquid at RT

the addition of a carboxyl group forms the organic acid

ethanoic acid (acetic acid)

Consider the amino acid Alanine

Consider the sugar glucose

Why are amino acids called amino acids?

What kind of molecule is glucose?

Functional groups on molecules are involved in chemical

reactions.
The components of organic molecules that are most commonly involved in chemical
reactions are known as functional groups.
Hydrocarbons are the simplest organic molecules, functional groups are
attachments that replace one or more of the H atoms bonded to the
carbon skeleton of the hydrocarbon.
Each functional group behaves consistently from one organic molecule to another.
The number and arrangement of functional groups help give each molecule
its unique properties.

Organic molecules can be linked together

You should be able to recognize functional groups and linkages when

you see them

Oxidation state

Common name Common occurrence

methane

natural gas

heat source

methanol

wood alcohol

dont drink

methanal

formaldehyde

embalming fluid

methanoic acid

formic acid

ant bites

Ant family Formicidae

The Schmidt Sting Pain Index

The Schmidt sting pain index is a pain scale rating the relative pain caused by different
ant, wasp, and bee stings. Justin O. Schmidt (entomologist)
Carl Hayden Bee Research Center in Arizona.
#5 Honey Bee
The sensation is like a matchhead that
flips off and burns on your skin.
#4 Red Harvester Ant
Bold and unrelenting. Somebody is
using a drill to excavate your
ingrown toenail.

#1 Bullet Ant
Like fire-walking over flaming charcoal with a 3-inch rusty nail
grinding into your heel.

http://www.dailymail.co.uk/sciencetech/article-2148089/The-10-painful-stings-planet-self-sacrificing-man-tried-150-different-varieties-science.html

Bullet Ant
(Paraponera clavata)

Didier Descouens

The Satere-Mawe people of Brazil use intentional bullet ant stings as part
of their initiation rites to become a warrior. The antsare woven into a
glove made of leaves (which resembles a large oven mitt), stingers facing
inward. A boy slips the glove onto his hand. The goal of this initiation rite is
to keep the glove on for a full 10 minutes.

Oxidation state Class

Common name Common occurrence

ethane

alkane

--

industry

ethanol

alcohol

booze

drinkable

ethanal

aldehyde

acetaldehyde

fixative

ethanoic acid

organic acid

acetic acid

vinegar

Many small molecules can be linked together in larger molecules called polymers.
Polymers are very important in living things.
Polymerization changes the properties of chemicals.

ethene is a gas
ethene

polyethene or polyethylene

A Survey of the 4 major Classes of Biomolecules

Monomers

Polymers

Nucleotides

Nucleic acids

Amino acids

Proteins/Enzymes

Sugars (monsaccharides)

Polysaccharides

Fatty acids

components of lipids

Nucleotides and Nucleic Acids

the DNA nucleotide adenosine monophosphate

pyrimidine
ring

Learn to recognize
the nitrogenous bases
CUT the Pie

imidazole
ring

Amino Acids and Proteins

Learn the structures and chemical

characteristics of all 20 common amino acids

Hints to get started on becoming familiar with Amino acids

All possess:

H2N C C
OH
H

-an Carbon to which is attached

-an amino group
-a carboxylic acid group
-a hydrogen atom

-a unique sidechain (R)

The amino and carboxyl group can be ionized depending on the surrounding pH.
At the pH typical of cytoplasm (pH 6.8 7.4, physiological pH) the amino group will be
protonated and the carboxyl group will be deprotonated.
Thus we typically draw amino acids in this form:

H3N C C
O
H

The
zwitterionic form of
an amino acid

Furthermore

H3N C C
O
H

Abbreviation

R
H3N C COOH

Memorizing the amino acid structures is mainly an exercise in memorizing unique side chains

Amino acids polymerize to form proteins

Carbohydrates
Monosaccharides to Polysaccharides

Cellulose

Fatty acids

Most of this course will be concerned with learning about:

-the structures

-the synthesis
-the functions

of the preceding 4 classes of biological molecules

Molecular representations

Ball and stick

Space-filling models

Structural Formula
C-black
H-white
O-red
N-blue
S-yellow

Become familiar with dimension prefixes

Angstrom = 10-10 m or 0.1 nm

As humans, we evolved in a middling world of space and time and

our brains evolved accordingly.

It is virtually impossible for us to appreciate very large or small scales

of size, distance, and time.

It is easy to say the dinosaurs went extinct 65 million years ago

But if you think you can evenly slightly comprehend how long ago
that was, you are deluding yourself.

Check out this website for a perspective on the sizes of the sorts of molecules we will talk
about in this course
http://learn.genetics.utah.edu/content/begin/cells/scale/

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