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.

• light element with propensity to form covalent bonds instead of ionic bonds

• forms covalent bonds of significant strength (energy)

• tetravalency: multiple bonds, complex molecules

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

Alkane Alkene Alkyne

methane -- -- ethane ethene ethyne propane propene propyne butane pentane hexane heptane octane nonane decane

ethane C2H6 ethene C2H4 ethyne C2H2

Hydrocarbons are the building blocks of most biomolecules

methane CH4

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 don’t drink methanal formaldehyde embalming fluid methanoic acid formic acid ant bites

Ant – family Formicidae

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

#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.

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.

The Satere-Mawe people of Brazil use intentional bullet ant stings as part of their initiation rites to become a warrior. The ants…are 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.

Didier Descouens

Bullet Ant (Paraponera clavata)

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

polyethene or polyethylene

ethene is a gas

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

Learn to recognize the nitrogenous bases

pyrimidine ring

imidazole ring

CUT the Pie

http://www.google.ca/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=Ed3qTmhJk9MBCM&tbnid=yASDqAsUAMVBfM:&ved=0CAUQjRw&url=http://www.salon.com/2012/10/11/cheaper_dna_sequencing_brings_privacy_risks/&ei=_s0nUpumKs__4AO0y4GYAg&bvm=bv.51773540,d.dmg&psig=AFQjCNH1E0_AKJWjcZ3bJSadJEbGbu9_EQ&ust=1378426701092110

Amino Acids and Proteins

Learn the structures and chemical characteristics of all 20 common amino acids

H2N – C – C O

OH H

R

– –

All possess: -an α Carbon to which is attached -an amino group -a carboxylic acid group -a hydrogen atom -a unique sidechain (R)

Hints to get started on becoming familiar with Amino acids

H3N – C – C O

O- H

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:

The zwitterionic form of an amino acid

Furthermore…

H3N – C – C O

O- H

R

– – +

H3N – C – COO-

H

R

– – +

Abbreviation

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/

D2L is up an running Advise of any problems Note that lecture slides can only be provided as PDF files Next Class - The nature of molecular interactions