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Lecture Notes on What is Cell - Cell Physiology | BIO 121, Study notes of Microbial Physiology

California State University (CSU) - SacramentoMicrobial Physiology
Prof. Thomas E. Landerholm

Material Type: Notes; Professor: Landerholm; Class: Cell Physiology; Subject: Biological Sciences; University: California State University - Sacramento; Term: Spring 2010;

Typology: Study notes

2009/2010

Uploaded on 03/28/2010

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Outline 1. Introduction to Cell Physiology
Biological Sciences 121 – Spring 2010
The Department of Biological Sciences considers this course to be the “capstone” course of
the B.S. and B.A. degree requirements. As such, we will attempt to bring much of what you have
learned in your other courses into the context of the fundamental unit of organization of life on
Earth – the cell. In this course you will need the prerequisite courses, BIO 1 and BIO 2 and CHEM
161. My primary objective is that you learn to use your knowledge of Biology and not to just
reiterate your short term memorizations of my lectures. In addition, because most of you are
preparing to finish your degrees and become Biologists, our goals in this class are to learn not only
about the physiology of cells but also about the science of Cell Physiology (or Cell Biology).
Lecture Section 1: A. What are Cells?
B. How are Cells Integrated in
Multicellular Organisms?
C. Molecular Biology of the Cell
A. What are Cells?
We hear about them everywhere! Microbiology, Botany, Zoology, Genetics, Molecular Biology – you
name it, everybody mentions them. So what’s the story? Are they all pretty much the same? Or are
there trillions of different kinds with little similarity? How can anyone talk realistically about yeast and
humans as though we had anything in common?!
1. Cell Theory: Cells define the reproducible unit of nearly all living organisms.
a. Life is often defined as any organism that constructs and maintains complex structures from
simpler, externally available resources and has the capacity to reproduce itself.
b. While seemingly obvious and commonplace, this is a relatively recent theory: cell theory in
late 1600’s by Anton van Leeuwenhoek and Robert Hooke. Bacterial pathogenesis by Louis
Pasteur and Robert Koch late 1800’s.
c. What are viruses and prion proteins?
2. What kinds of cells are out there?
a. All cells have some obvious similarities: small size
limiting membrane
cell division
information stored as genes
single-celled vs. multi-celled organisms
b. In multicellular organisms we also see: cell-cell interactions
controlled environments
organ-systems
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Download Lecture Notes on What is Cell - Cell Physiology | BIO 121 and more Study notes Microbial Physiology in PDF only on Docsity!

Outline 1. Introduction to Cell Physiology

Biological Sciences 121 – Spring 2010

The Department of Biological Sciences considers this course to be the “capstone” course of the B.S. and B.A. degree requirements. As such, we will attempt to bring much of what you have learned in your other courses into the context of the fundamental unit of organization of life on Earth – the cell****. In this course you will need the prerequisite courses, BIO 1 and BIO 2 and CHEM

161. My primary objective is that you learn to use your knowledge of Biology and not to just reiterate your short term memorizations of my lectures. In addition, because most of you are preparing to finish your degrees and become Biologists, our goals in this class are to learn not only about the physiology of cells but also about the science of Cell Physiology (or Cell Biology).

Lecture Section 1: A. What are Cells?

B. How are Cells Integrated in

Multicellular Organisms?

C. Molecular Biology of the Cell

A. What are Cells?

We hear about them everywhere! Microbiology, Botany, Zoology, Genetics, Molecular Biology – you name it, everybody mentions them. So what’s the story? Are they all pretty much the same? Or are there trillions of different kinds with little similarity? How can anyone talk realistically about yeast and humans as though we had anything in common?!

1. Cell Theory: Cells define the reproducible unit of nearly all living organisms. a. Life is often defined as any organism that constructs and maintains complex structures from simpler, externally available resources and has the capacity to reproduce itself. b. While seemingly obvious and commonplace, this is a relatively recent theory: cell theory in late 1600’s by Anton van Leeuwenhoek and Robert Hooke. Bacterial pathogenesis by Louis Pasteur and Robert Koch late 1800’s. c. What are viruses and prion proteins? 2. What kinds of cells are out there? a. All cells have some obvious similarities: small size limiting membrane cell division information stored as genes single-celled vs. multi-celled organisms b. In multicellular organisms we also see: cell-cell interactions controlled environments organ-systems

systemic interactions c. Since all organisms are composed of cells, we can start with taxonomic differences

  1. Domain level differences. Eukarya Prokarya Archaea
  2. Kingdom level differences in Eukarya. Animalia Plantae Fungi Protista
  3. Phylum level differences in Animalia (19 total). Chordata Arthropoda Nematoda Echinodermata
  4. Class level differences in Chordata Mammalia Amphibia Reptilia Osteicthyes Aves
  5. Order level differences in Mammalia Primates Rodentia Artiodactyla Perissodactyla
  6. Genus/Species level differences in Primates Homo sapiens Pan troglodytes Macaca mulatta
  7. Organismal level differences Tissue type Age/Development Disease state
  8. Cell type differences based on tissue type Mesenchymal Parenchymal Epithelial

B. Multicellular Environments: We don’t want to get so caught up in discussing

internal organization of cells that we forget the fact that many of our closest friends are

multicellular. The external environment is critical because it is regulated by, and in turn

regulates, the cell’s activity.

1. In plants and animals most cells create their immediate environment

a. They secrete the extracellular matrix (ECM) composed of four types of molecules

  1. Ground substance glycosaminoglycans

2. Cell-cell communication and cell-matrix communication

a. Gap junctions – transmit molecules directly from cell to cell

  1. cells that are not electrically linked act as synctitium b. Chemical synapses – transmit chemical signals to receptors
  2. require appropriate receptors and second messengers c. Cadherins – transmit binding information and physical changes
  3. have direct nuclear signal through -catenin d. Delta-notch – non-homophilic cell types can identify each other e. Ephs-ephrins – different cell-types separate during development f. Integrins – binding info and physical changes with cells and ECM
  4. probably also have direct nuclear signal g. Plasmodesmata – plant “gap junctions”

3. Systemic and local controls reside within the matrix

a. The vascular system reaches tissues and cells through their ECM b. The nervous system reaches tissues and cells through their ECM c. Cells involved with systemic immunity d. Matrix-bound growth and survival factors

C. The Molecular Evolution Revolution has taught us more about cells.

1. Everyone knows the first work that showed that plants and animals transfer their

characteristics to their offspring (Mendel and Darwin 1800’s).

a. All known cells store their hereditary information in double-stranded DNA.

  1. DNA structure in the 1950’s. Watson and Crick (Linus Pauling).
  2. Nearly all of the cells in an organism have exactly the same DNA.

a. The sex cells are different from the somatic cells.

  1. Modern cell biology is dominated by molecular biology: a. Duplication, transcription and translation by templated polymerization. 1. DNA  RNA  PROTEIN. 2. The Central Dogma: one gene – one protein. b. Life’s genetic complexity is less than you might think.
  2. The least complex genome: M ycoplasma genitalia has 477 genes
  3. The most complex: Homo sapiens have 30,000-50,000 genes (only 100 fold!)

2. Basic Molecular Biology

a. We Probably Need a Quick Review of DNA Structure.

  1. Nuclear DNA is called Chromatin. a. Euchromatin demonstrates very active transcription. 1. Only visible by electron microscopy. b. Heterochromatin is so highly condensed as to be visible. 1. Far less active than euchromatin. 2. Includes the inactivated female x-chromosome. b. Nucleic Acid Polymerization
  2. DNA replication occurs during the cell cycle when new cells are made a. occurs in the 5’ to 3’ direction…. So, the template strand is being read from 3’ to 5’ in order to synthesize the new strand in the 5’ to 3’ direction. b. Prokaryotic cells
  3. DNA is a small circular double helix (150,000-200,000 base pairs)
  4. One origin of replication; One termination site
  5. Replication is bidirectional c. Eukaryotic Cells
  6. DNA is organized into linear molecules called chromosomes.
  7. Smallest chromosome in humans is 2 million base pairs in length.
  8. Hundreds of origins of replication spaced to terminate at same time.

c. Cryptic Splicing Sites: these can be found within exons and can cause partial removal of exons. So, only a portion of an exon would be removed. d. Cis-splicing: splicing that occurs within mRNA from a single gene. e.Trans-splicing: splicing that occurs within mRNA from two different genes and then the products are ligated together.

f. Intron-Exon borders recognized by small nuclear RNA (snRNA)

  1. snRNA-protein complexes function as enzymes.
  2. Different compleses catalyze cleavage of the 5’ and 3’ Splicing Sites.
  3. Ligase enzymes then join 3’ end of one exon to the 5’end of next 1 2. Polyadenylation signals the end of transcription. a. Poly A polymerase synthesizes a poly A tail on 3’ end of transcript b. Length of the Poly A tail determines length of translation time
  4. Slows down digestion of the mRNA by exonucleases in the cytosol.

3. DNA Mutation and Repair

a. Types of mutation.

  1. Point mutations: change in a single base pair. a. Transitions: Change from a pyrimadine to another pyrimadine or change from a purine to another purine. Causes mismatch. b. Transversion: change from a purine to a pyrimadine or a pyrimadine to a purine. c. Insertion: addition of an extra nucleotide. d. Deletion: deletion of a nucleotide. e. Causes. 1. Electrophilic attack of negatively charged molecules 2. UV radiation Causes the formation of pyrimadine dimers. 3. Gamma rays indirectly causes single or double stranded cleavage 4. Deamination of an amino group from the nitrogenous base.
  2. Hypermutations: multiple base changes, including chromosamal deletions, additions a. Double stranded breaks can drift apart and religate with other chromosomes b. Regions of microhomology can match up and reanneal to rejoin the two broken ends. This causes hypermutation because some DNA is lost.

a. Example 1: More complex organisms don’t necessarily have more transcription factors, just more members of a family like the MADS-box family.

  1. Flies and humans share MEF-2, we just have more of them! c. Gene structure and gene expression in higher organisms produce greater complexity.
  2. Let’s quickly review eukaryotic gene structure.
  3. The difference between cells is in their “hard-wiring” or phenotype. a. Which genes a cell expresses make it the type of cell that it is. b. Cell specialization is the hallmark of multicellular organisms.
  4. Splicing variation and the proteome