Table of Contents

Fundamentals of Biochemistry

Biochem 380 - Fall 2006

Lecture 003


Outline

Announcements


Questions


Section 5: Biochemistry and Evolution


The Origins of Life


OOL Theories


Mechanisms of Evolution


Evolution Demo


Evolution Demo Implementation

Evolution Demo


  • The demo is available for download from the course web pages
  • Currently, there is only a Windows version
  • However, the source code is available (any volunteers to port the code to other platforms?)
  • Survey: who has a computer at home?
  • What OS do you run? Windows/Mac/Gnu-Linux/Other?
  • (Run demo)

    The Cell is the Unit of Life


    • The cell is the smallest system of biomolecules that is considered to be 'alive'

    • A cell can be thought of as a droplet of water surrounded by a plasma membrane. As we will see later, it is actually a droplet of water jam-packed with 'stuff'

    • Everything inside the outer membrane, except for the nucleus, is referred to as the cytoplasm

    • The part of the cytoplasm that does not include internal membrane-bound organelles is called the cytosol

    Viruses

    • What about viruses? Are they alive? Why or why not?

    • Virus are subcellular infectious particles consisting of nucleic acid molecules surrounded by a protein coat. Although they can reproduce, they require the machinery of a living cell to do so, and therefore are not considered to be independent living organisms

    • The simplicity of viruses makes them useful for understanding biochemistry, however. Viruses that infect bacteria, called phages (bacteriophages), were important tools for understanding the genetic machinery of the cell

    • Recently, there has been renewed interest in bacteriophages as a possible solution to the growing problem of antibiotic resistance

    Prokaryotic Cells


    • Prokaryotes are the simplest kinds of single-celled organisms. Some species have as few as 1000 genes

    • Although much simpler than eukaryotes, prokaryotic species are incredibly diverse. They can be thought of as 'biochemical specialists' that are able to inhabit almost every kind of environment on Earth

    • The most well studied bacterial species is Escherichia coli (E. coli). The biochemistry of this model organism is used as an example in many parts of the text

    Structure of Prokaryotic Cells


    • Most bacteria have a rigid cell wall and lack interior membrane compartments

    • Many bacteria, including E. coli, also have a second, 'outer' membrane surrounding the cell wall. This second layer acts as a 'filter', protecting the bacteria from the external environment, while still allowing nutrients to enter

    Eukaryotic Cells


    • Eukaryotic organisms can be classified into 4 main groups: plants, animals, fungi and protists

    • Eukaryotic cells are more complex than prokaryotic cells. The interior of a eukaryotic cell has many different kinds of organelles, surrounded and organized by a cytoskeleton architecture

    • The most distinctive organelle is the nucleus, which is tightly packed with the cell's DNA. The nucleus is also where RNA synthesis and ribosome assembly take place

    • Other organelles include the endoplasmic reticulum, the golgi apparatus, mitochondria, lysosomes and peroxisomes

    An Animal Eukaryotic Cell

    The Endoplasmic Reticulum

    • The endoplasmic reticulum (ER) is a network of membrane sheets and tubes that extend out from the periphery of the nucleus. The interior of the ER is called the lumen

    • The ER serves as a sorting and packaging system for newly-synthesized proteins. Ribosomes attached to the outside of the ER translate RNA transcripts into new proteins by extruding the proteins across the ER membrane into the lumen

    The Golgi Apparatus


    • The Golgi apparatus extend the processing and transport capabilities of the ER through a collection of sacs and vesicles

    • These are lipid membrane compartments that contain collections of biomolecules for sequential processing, transport, and in some cases, secretion outside of the cell

    The Mitochondrion


    • The mitochondrion is another important organelle found in most eukaryotic cells. It is responsible for aerobic energy production. It consists of a permeable outer membrane, a highly-folded and largely impermeable inner membrane, and an interior called the matrix

    • Organic compounds are delivered to the mitochondrion, where they are oxidized, releasing electrons. The electons flow through the inner membrane to combine with O2, transporting protons into the matrix. These in turn flow back out through ATP Synthetase enzymes, generating ATP

    The Living Cell

    • Most drawings and pictures fail to capture the incredibly dynamic and beautiful activity of living cells. A typical cell is packed full of the organelles and macromolecules that we have briefly seen. These structures, while very small in macroscopic terms, are still huge compared to the scale of atoms and molecules

    • Millions of atoms are present within a single macromolecule such as the ribosome. In addition, the molecules are in constant motion, colliding and diffusing throughout the cell. On average, a typical enzyme and small molecule will collide with each other around 1 million times per second

    • The organization and complexity of molecular traffic within the cytosol is only just beginning to be fully appreciated. This organization gives the cell a greater degree control of chemical activity, beyond what is possible through simple solution chemistry

    Questions

    References


    • Book: The Origins of Order, by Stuart Kauffman
      A deep and fascinating investigation of evolutionary mechanisms, including a proposal for 'pre-genomic' autocatalytic metabolic networks

    • Book: The Blind Watchmaker, by Richard Dawkins
      A popular and very readable exposition of evolutionary theory

    • Book: Evo-Devo, by Sean Carroll
      A consideration of evolution in the context of developmental biology, including a presentation of recently-understood mechanisms of morphogenesis and cellular differentiation, and their potential for contributing to evolutionary change

    Next Lecture: Sections 2.1 - 2.3


    • Read Sections 2.1 - 2.3