BCH 5045 Graduate Survey of Biochemistryhort.ifas.ufl.edu/faculty/guy/bch5045/Lecture Files/Lecture 1.pdf · • LEHNINGER • PRINCIPLES OF ... industries are being capitalized in

Images from the Text are protected by Copyright (c) 2008 by W. H. Freeman and Company, and by the licensors of W. H. Freeman and Company. Living Graphs software (c) 2008 Sumanas, Inc. ALL RIGHTS RESERVED.

Commentary by the instructor is protected by Copyright (c) 2010. ALL RIGHTS RESERVED.

BCH 5045

Graduate Survey of Biochemistry

Instructor: Charles GuyProducer: Ron ThomasDirector: Glen Graham

Lecture 1Slide sets available at:

http://hort.ifas.ufl.edu/teach/guyweb/bch5045/index.html

http://hort.ifas.ufl.edu/teach/guyweb/bch5045/index.html�



• LEHNINGER• PRINCIPLES OF BIOCHEMISTRY

• Fifth Edition

David L. Nelson and Michael M. Cox

© 2008 W. H. Freeman and Company

CHAPTER 1

The Foundations of Biochemistry



What is Biochemistry?It is the chemistry of life, and it is the bridge between pure chemistry and biology.

It is the matrix that ties all life forms together, and it collectively sets the ground rules and limits of when, how, and where life can exist.

Literally, all biological processes arise from the actions of molecules. Your ability to read and comprehend this handout is the collective result of a variety of biological chemistries. Therefore, to at least partially describe the mystery of life, one must understand its chemistry.



As you will see, biochemistry is a lot like learning a new language, for it is the language of molecules, large and small, the language of reactions and reaction mechanisms, the language of information storage, decoding and heredity, the language of the physical laws of chemistry, the language of supramolecular structures and integrated systems, the language of recognition and the language of metabolism and much more.



Voet & Voet Biochemistry, 2nd ed. 1995 state that: "Although biochemistry is a highly diverse field, it is largely concerned with a limited number of interrelated issues. These are:

• “What are the chemical and three-dimensional structures of biological molecules and assemblies, how are these structures formed, and how do their properties vary?

• How do proteins work; that is, what are the molecular mechanisms of enzymatic catalysis, how do receptors recognize and bind specific molecules, and what are the intramolecular and intermolecular mechanisms by which receptors transmit information concerning their binding states?

• How is genetic information expressed and how is it transmitted to future generations?



• How are biological molecules and assemblies synthesized?

• What are the control mechanisms that coordinate the myriad biochemical reactions that take place in cells and organisms?

• How do cells and organisms monitor their internal and external conditions?

• How do cells and organisms grow, differentiate, and reproduce?”



Why should you know something about biochemistry?

In biochemistry, you will find at least one pinnacle of human understanding, re-occurring themes and forms observable in the natural world around us, you will find creativity: analytical and artistic, and if you delve far enough, you can find drama in the excitement of discovery and without a doubt, the disappointment of failure.

As a life scientist: agronomist, biologist, ecologist, entomologist, horticulturist, soil scientist, or in animal science, food and nutritional science, or medicine, biochemistry will be an integral part of everything you do and everything you will need to know to do your job. The 21st Century, at least as it ends the first decade, is the century of biochemistry.



The 20th Century laid the foundation for all that is now unfolding on a daily basis in genetics, molecular biology, enzymology, metabolism, host-parasite interactions, and a hundred other areas of research.

On Wall Street where life science-based technologies and industries are being capitalized in numerous large cap and small cap companies and countless nascent start-ups and IPOs.

Total Market Capitalization of biotech companies in 2009 est. at 384 B.

Revenue in 2009 in BillonsAmgen 14.6 Genentech 3.7 Gilead Sciences 7.6 Cellgene 2.7 Genzyme 4.5 Cephalon 2.2 Biogen Idec 4.4 MedImmune 1.3



Potential IPOs in 2010

• Portola Pharmaceuticals boasts two promising Phase II drug candidates and has mega-deals with Merck and Novartis.

• Pacific Biosciences says in two years time it will have new instruments on the market that will sequence DNA dramatically faster and at a far lower cost than today's products.

• Regulus Therapeutics is developing new drugs based on micro-RNA.

• Concert Pharmaceuticals is developing technology that positively influences efficacy and side effect profiles of drugs.



• GlaxoSmithKline inked a potential $1 billion deal with Concert for new products including CTP-518, a protease inhibitor for the treatment of HIV expected to soon enter Phase I clinical trials.

• MacroGenics has a pipeline of autoimmune, cancer and anti-infectious disease products. The company raised $25 million in VC to advance cancer stem cell technology the company acquired in a buyout of Raven Biotechnologies.



We use biochemistry in our everyday lives already.

It’s what we eat and drink. It’s the vitamins we take. It is the medicines we need. It is the pesticides we spray on our lawns and in our homes, and many more daily use items we take for granted.

Unfortunately, it’s misuse and misinformation is rampant in the ubiquitous infomercials and self-improvement popular press. So even if you were not in graduate school and pursuing a degree in the life sciences, it is most beneficial (almost essential in the 21st

century) to have some knowledge of biochemistry.





Note: All information in this slide set following this slide is information that can be included on quizzes and exams even though it was not included in the lecture.



CellsConsidering prokaryotes and eukaryotes, why does compartmentation at the level of the cell exist?

Why do eukayotes possess a greater level of compartmentationthan prokaryotes?

Are there likely to be additional layers of compartmentation at the suborganellar level of cells?

What biochemical benefits accrue from compartmentation?

How are functions of the various compartments integrated into the overall operation of the cell?

How is biochemical information transmitted from one compartment to another?



What additional questions arise in your mind? Welcome to BCH 5045, let’s make it interesting, productive and most of all fun!

Celeb Biochemistry

http://hort.ifas.ufl.edu/teach/guyweb/bch5045/WMVFiles/Celebrity Biochemistry.WMV�

http://hort.ifas.ufl.edu/teach/guyweb/bch5045/WMVFiles/Celebrity Biochemistry.WMV�



“Biochemistry with the Celebrity Stars”

From the Conan O’Brien Show



Boron has been recognized since 1923 as an essential micronutrient element for higher plants and is required for optimal growth. Silicon is also abundant in plants and in some plants is required for optimum disease resistance.

The Elements of Life



CN

O

H

CaP

K S Cl Na MgTrace

C

O

H

N K Ca Mg P S Si Trace

Human Body Elemental Composition1

1Based on percent dry weight excluding H and O in water. Calculated from Frieden, E. (1972) Sci. Am. 227, 54-55.

Trace elements include: B, Co, Cr, Cu, F, Fe, I, Mo, Mn, Na, Se, Si, Sn, V, Zn

Color coding follows color scheme used by the molecular visualizer Jmol.

Trace elements include: Al, Ba, B, Cl, Co, Cu, Fe, Mo, Mn, Na, Ni, Rb, Se, Sr, Zn

Plant Elemental Composition2

2Based on percent dry weight excluding H and O in water. Calculated from Taiz, L. & E. Zeiger (1998) .



What limits the size of cells?

E. coli, the most studied prokaryotic cell!







Everyone should know the labeled parts of cells





Cytoskeletal filaments: a) actin filaments (red), microtubules (green), and b) intermediate filaments (shown in red); Chromosomes (blue)





All forms of life are connected, and that is now undeniable and the evidence is DNA sequence information. This tree is based on the similarity in nucleotide (DNA) sequences of the ribosomal RNAs of each group.



We will see later that this list is just a small sampling of the genome sequences that are now available, and yet to come as we have recently entered the era of the $1,000 cost per genome sequence.

Documents

BCH 5045 Graduate Survey of Biochemistryhort.ifas.ufl.edu/faculty/guy/bch5045/Lecture Files/Lecture 1.pdf · • LEHNINGER • PRINCIPLES OF ... industries are being capitalized in