Ogan Gurel, MD

Biology 301
Review # 2
Roosevelt University

Biology 301
Cellular and Molecular Biology
Spring 2002

Review # 2
 Ogan Gurel, MD
Biology 301
Review # 2

Course Syllabus
Roosevelt University

Text chapter Text chapter

Date Lecture Topics assignments Date Lecture Topics assignments
1/23 Introduction / Molecular Bonding 2,4 3/18 – 3/22 Spring Break
1/28 Water & pH 3 3/25 Transport Channels 8
1/30 Carbohydrates & Lipids 5 3/27 Cell Signaling & Signal Transduction 11
2/4 Proteins 5 3/29 LAST DAY TO WITHDRAW
2/6 Enzymes 6 4/1 Cell Architecture 7
2/11 Nucleic Acids 5 4/3 Cytoskeleton & Cell Junctions 7
2/13 DNA Replication 16 4/8 Mitosis & Cell cycle regulation 12
2/18 Gene Expression I 17 4/10 Meiosis 13
2/20 Gene Expression II 17 4/15 EXAM II (covers lectures 2/25 through 4/3)
2/25 Prokaryotic Gene Expression I 18 4/17 Energy / ATP / Oxidation & Reduction 6, 9
2/27 Prokaryotic Gene Expression II 18 4/22 Glycolysis & Fermentation 9
3/4 EXAM I (covers lectures 1/23 through 2/20) 4/24 The Krebs (Tri-carboxylic acid) cycle 9
3/6 Eukaryotic Gene Expression I 19 4/29 Electron Transport & Chemiosmosis 9
3/11 Eurkaryotic Gene Expression II 19 5/6 Photosynthesis I 10
3/13 Plasma Membrane Structure 8 5/8 FINAL EXAM
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Ten:
Prokaryotic Gene Expression I - Viruses

 Bacteriophages
 The lytic cycle of phage T4
 The lysogenic and lytic reproductive cycles of phage
lambda
 The reproductive cycle of an enveloped retrovirus virus
 HIV, a retrovirus
 Prion replication
 Ogan Gurel, MD
Biology 301
Review # 2

Bacteriophages
Roosevelt University

Bacteriophages are viruses that

specifically infect bacteria.
Though not medically important,
they have served as a useful
experimental system for the
study of basic genetic and
biochemical mechanisms.
 Ogan Gurel, MD
Biology 301
Review # 2

The lytic cycle of phage T4

Roosevelt University
 Ogan Gurel, MD

The lysogenic and lytic reproductive

Biology 301
Review # 2
Roosevelt University

cycles of phage lambda

 Ogan Gurel, MD

The reproductive cycle of an Biology 301

Review # 2
Roosevelt University

enveloped retrovirus virus

(Reverse transcription)
 Ogan Gurel, MD
Biology 301
Review # 2

HIV, a retrovirus
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Prion replication
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Eleven
Prokaryotic Gene Expression II - Bacteria

 Bacterial structure
 Bacterial life cycle
 Detecting genetic recombination in bacteria
 Transduction
 Recombination in E. coli
 Regulation of a metabolic pathway
 The lac operon: regulated synthesis of inducible enzymes
 Positive control: cAMP receptor protein
 The trp operon: regulated synthesis of repressible
enzymes
 Ogan Gurel, MD
Biology 301
Review # 2

Bacterial structure
Roosevelt University

• Prokaryotes are distinguished by

having no membrane-bound
organelles.
• The DNA genome is gathered in a
central region called the nucleoid.
• Bacteria are also uniquely
characterized by a rigid cell wall
which serves to resist osmotic stress.
• Bacteria can be classified in terms
of their cell-wall components and in
terms of their shape.
 Ogan Gurel, MD
Biology 301
Review # 2

Bacterial life cycle

Roosevelt University

• Bacterial growth (generally

exponential) usually involves
asexual reproduction (binary
fission); sexual reproduction via
gene transfer is rarer.
• The resulting semi-log growth
curve involves lag, logarithmic
and stationary phases.
 Ogan Gurel, MD

Detecting genetic recombination in

Biology 301
Review # 2
Roosevelt University

bacteria
 Ogan Gurel, MD
Biology 301
Review # 2

Transduction
Roosevelt University

(during lysis) (during lysogeny)

 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Recombination in E. coli
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Regulation of a metabolic pathway

 Ogan Gurel, MD

The lac operon: regulated synthesis of

Biology 301
Review # 2
Roosevelt University

inducible enzymes

• Regulation of gene
expression often occurs at
the level of transcription.
• The most common strategy
is to control the binding of
RNA polymerase to the
promoter or to block its
precessive activity along the
operon.
• Eukaryotic regulatory
mechanisms are more
complicated and involve a
variety of DNA enhancer
elements and protein
transcription factors.
• The lac operon depicted
here is a prototypical
system.
 Ogan Gurel, MD

Positive control: cAMP receptor Biology 301

Review # 2
Roosevelt University

protein
 Ogan Gurel, MD

The trp operon: regulated synthesis of

Biology 301
Review # 2
Roosevelt University

repressible enzymes
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Twelve
Eukaryotic Gene Expression I

 Levels of structure in chromatin

 Nucleosome structure
 The evolution of human a-globin and b-globin
 Types of repetitive DNA
 DNA rearrangements in immunoglobulin gene
expression
 Ogan Gurel, MD
Biology 301
Review # 2

Levels of structure in chromatin

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Nucleosome structure
Roosevelt University
The evolution of human α-globin
Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

and β-globin
 Ogan Gurel, MD
Biology 301
Review # 2

Types of repetitive DNA

Roosevelt University
 Ogan Gurel, MD

DNA rearrangements in Biology 301

Review # 2
Roosevelt University

immunoglobulin gene expression

 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Thirteen
Eukaryotic Gene Expression II

 Points of regulation
 Transcription & translational level control
 “Action at a distance”
 Protein – DNA interactions mediate regulation
 Carcinogenesis is a multistep process
 Oncogenes can be “activated” in a number of
ways
 Complex pathways cause “downstream”
effects
 Ogan Gurel, MD
Biology 301
Review # 2

Points of regulation
Roosevelt University

• Chromatin

• RNA processing

• Transport

• Translation

• Protein processing
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Transcription & translational level control

 Ogan Gurel, MD
Biology 301
Review # 2

“Action at a distance”
Roosevelt University
Protein – DNA interactions Ogan Gurel, MD
Biology 301
Review # 2

mediate regulation
Roosevelt University

A
 Ogan Gurel, MD

Carcinogenesis is a multistep Biology 301

Review # 2
Roosevelt University

process

Normal
FAP epithelium Metastasis

Hyperprolifer.
epithelium
DNA hypo-
methylation
Early
adenoma
K-ras
Intermediate
adenoma
DCC ?
Metastasis
Late
p53 adenoma

Invasive
Carcinoma

Neoplasia

Sources: Adapted from Ringer & Schnipper, (2001), “Principles of Cancer Biology,” In: Clinical
Oncology – American Cancer Society, p. 30; Fearon & Vogelstein, (1990), “A genetic model of
Other
colorectal tumorigenisis,” Cell, 61: 759; Weinberg (1996), “How Cancer Arises,” Scientific American. alterations
Oncogenes can be “activated”
Ogan Gurel, MD
Biology 301
Review # 2

in a number of ways
Roosevelt University
Complex pathways cause Ogan Gurel, MD
Biology 301
Review # 2

“downstream” effects
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Fourteen
Plasma Membrane Structure & Transport Channels

 Two models of membrane structure

 The fluidity of membranes
 Membrane protein functions
 Membrane topology
 The signal mechanism
 Diffusion of solutes
 Osmosis
 Osmotic regulation in cells
 Kinetics of facilitated diffusion
 A model for facilitated diffusion
 Active transport: the Na-K pump
 Active & passive transport compared
 Types of endocytosis
Two models of membrane Ogan Gurel, MD
Biology 301
Review # 2

structure
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

The fluidity of membranes

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Membrane protein functions

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Membrane topology
Roosevelt University
 Ogan Gurel, MD
Biology 301

The signal mechanism for the synthesis of Review # 2

Roosevelt University

membrane-bound & extracellular proteins

 Ogan Gurel, MD
Biology 301
Review # 2

Diffusion of solutes
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Osmosis
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Osmotic regulation in cells

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Kinetics of facilitated diffusion

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

A model for facilitated diffusion

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Active transport: the Na-K pump

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Active & passive transport compared

 Ogan Gurel, MD
Biology 301
Review # 2

Types of endocytosis
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Fifteen
Cell Signaling & Signal Transduction

 Local and distant cell communication

 Overview of cell signaling
 The structure of a G-protein-linked receptor
 The functioning of a G-protein-linked receptor
 The structure and function of a tyrosine-kinase receptor
 Ligand-gated ion channels
 A phosphorylation cascade
 Calcium ion concentrations in the cell
 Calcium and inositol trisphosphate in signaling pathways
 Cellular responses: Stimulation of glycogen breakdown
 Nuclear response to a signal: The activation of a specific
gene by a growth factor
 Ogan Gurel, MD

Local and distant cell Biology 301

Review # 2
Roosevelt University

communication
 Ogan Gurel, MD
Biology 301
Review # 2

Overview of cell signaling

Roosevelt University
The structure of a Ogan Gurel, MD
Biology 301
Review # 2

G-protein-linked receptor
Roosevelt University
The functioning of a G-protein-
Ogan Gurel, MD
Biology 301
Review # 2

linked receptor
Roosevelt University
 Ogan Gurel, MD

The structure and function of a Biology 301

Review # 2
Roosevelt University

tyrosine-kinase receptor
 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Ligand-gated ion channels

 Ogan Gurel, MD
Biology 301
Review # 2

A phosphorylation cascade
Roosevelt University
Calcium ion concentrations in
Ogan Gurel, MD
Biology 301
Review # 2

the cell
Roosevelt University
 Ogan Gurel, MD

Calcium and inositol trisphosphate in

Biology 301
Review # 2
Roosevelt University

signaling pathways
Cellular responses: Stimulation
Ogan Gurel, MD
Biology 301
Review # 2

of glycogen breakdown
Roosevelt University
 Ogan Gurel, MD
Biology 301

Nuclear response to a signal: The activation of a

Review # 2
Roosevelt University

specific gene by a growth factor

 Ogan Gurel, MD
Biology 301
Review # 2
Roosevelt University

Lecture Sixteen
Cell Architecture: Cytoskeleton & Cell Junctions

 Structure & Function of the Cytoskeleton

 Motor molecules and the cytoskeleton
 Ultrastructure of flagella and cilia
 Microfilaments and motility
 The extracellular matrix
 Intracellular junctions
Structure & Function of the Ogan Gurel, MD
Biology 301
Review # 2

Cytoskeleton
Roosevelt University
Motor molecules and the Ogan Gurel, MD
Biology 301
Review # 2

cytoskeleton
Roosevelt University
Ultrastructure of flagella and Ogan Gurel, MD
Biology 301
Review # 2

cilia
Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Microfilaments and motility

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

The extracellular matrix

Roosevelt University
 Ogan Gurel, MD
Biology 301
Review # 2

Intracellular junctions
Roosevelt University