Cell Biology
- study at the molecular level, of processes that are common to
most cells, including
- replication of the genome
- repair of the genome
- gene expression
- cell energetics
- cytoarchitecture
- transport of molecules within the cell
- transport of molecules in/out of the cell
- cell communication
- cell adhesion, cell migration
- cell division
- methods for studying cell biology
- model systems for studying cell biology
A Yeast Serves as a Minimal Model Eukaryote
Arabidopsis Has Been Chosen Out of 300,000 Species As a Model
Plant
GENETIC INFORMATION IN EUKARYOTES
• The World of Animal Cells Is Represented By a
Worm, a Fly, a Fish, a Mouse, and a Human
C. elegans is the simplest multicellular eukaryotic model system
Drosophila Allows Study of Development in a Complex Animal
Xenopus laevis as a model for embryonic development and for biochemistry
The Frog and the Zebrafish Provide Accessible Models for Vertebrate
Development
The Mouse Is the Predominant Mammalian Model Organism
Divergence of hemoglobulin alpha gene
Tips on how to do well in this course
• Attend all lectures and try to follow.
• Take notes
• Ask questions – in class, after class, by email or office
hours – the sooner the better
• Review the lecture before next class
• If you miss a lecture, get someone’s notes if possible, go
over the powerpoints, and then ask me specific questions
that arise
• Make sure you understand the experiments that we talk
about in class – to the point that you can explain why
each step is done and you can understand how the
results support a specific model.
Lecture 1 - Genetics
A DNA Molecule Consists of Two Complementary Chains of
Nucleotides
Nucleotide
A DNA Molecule Consists of Two Complementary Chains of
Nucleotides
A DNA Molecule Consists of Two Complementary Chains of
Nucleotides
CHROMOSOMAL DNA AND ITS
PACKAGING IN THE CHROMATIN FIBER
• Eukaryotic DNA Is Packaged into a Set of
Chromosomes. Chromosomes Contain Long Strings
of Genes
Eukaryotic DNA Is Packaged into a Set of Chromosomes
Chromosomes Contain Long Strings of Genes
Chromosomes Contain Long Strings of Genes
CHROMOSOMAL DNA AND ITS
PACKAGING IN THE CHROMATIN FIBER
• Each DNA Molecule That Forms a Linear
Chromosome Must Contain a Centromere, Two
Telomeres, and Replication Origins
euchromatin
telomere
centromere
The Nucleotide Sequence of the Human Genome Shows How Our
Genes Are Arranged
All Cells Transcribe Portions of Their Hereditary Information into the
Same Intermediary Form: RNA
All Cells Transcribe Portions of Their Hereditary Information into the
Same Intermediary Form: RNA
Eukaryotic gene
Enhancer
Mutations Can Cause Loss or Gain of Protein Function
Methods for studying gene function
• forward genetics – random mutagenesis
• chemical mutagen
• insertional mutagenesis
• reverse genetics
• site-directed mutagenesis
• homologous recombination
• gene editing – Cas9/CRISPR – lecture 4
• gene knockdown by RNAi – lecture 4
Transgenics
• transfection and transformation – both terms
refer to the same general process:
Introduction of genes into cells or animals
• transfection/transformation can be
• transient (DNA will eventually be lost from
cell)
• stable (DNA integrated into host genome)
if transgene is passed on to germline cells – can
obtain transgenic animals
Using transgenes to study gene
function
• overexpression
• gene reporters (eve reporter – lecture 10)
• epitope or GFP tag (lecture 3)
• structure/function studies – delete specific
domains of protein and test for function
• often these transgenes are placed into a null
background or used for gene replacement
Genes Can Be Cloned Using Bacteria
Genes Can Be Cloned Using Bacteria
Genes Can Be Cloned Using Bacteria
Genes Can Be Cloned Using Bacteria
An Entire Genome Can Be Represented in a DNA Library
Genes Can Be Cloned in vitro Using PCR
Genes Can Be amplified in vitro Using PCR
Genes Can Be amplified in vitro Using PCR
Lecture 2
Proteins
The Shape of a Protein Is Specified by Its Amino Acid Sequence
The Shape of a Protein Is Specified by Its Amino Acid Sequence
The Shape of a Protein Is Specified by Its Amino Acid Sequence
The Shape of a Protein Is Specified by Its Amino Acid Sequence
THE SHAPE AND STRUCTURE
OF PROTEINS
• Protein structure can be defined at 4 different
levels
– 1o structure – amino acid sequence
– 2o structure - α helix and β sheet within a protein
• local 3D structure of the protein
The a Helix and the b Sheet Are Common 2o Structures
b Sheet
THE SHAPE AND STRUCTURE
OF PROTEINS
• Protein structure can be defined at 4 different
levels
– 1o structure – amino acid sequence
– 2o structure - α helix and β sheet within a protein
• local 3D structure of the protein
• both involve H-bonds between non-sidechain
groups on amino acids
The Shape of a Protein Is Specified by Its Amino Acid Sequence
The Shape of a Protein Is Specified by Its Amino Acid Sequence
THE SHAPE AND STRUCTURE
OF PROTEINS
• Protein structure can be defined at 4 different
levels
– 1o structure – amino acid sequence
– 2o structure - α helix and β sheet within a protein
• local 3D structure of the protein
– 3o structure – 3D structure of the protein
• globular form of the protein – determined by
interactions between often distant amino acids
(lecture 14)
– 4o structure – 3D structure of a protein complex
Proteins Fold into a Conformation of Lowest Energy
THE SHAPE AND STRUCTURE
OF PROTEINS
• Proteins Can Be Classified into Families
• Protein families consist of related proteins. They
have the same domains and order of domains
• critical domains will be very similar amongst
family members
• 3o structure is very similar amongst family
members
Proteins Can Be Classified into Many Families
Proteins Can Be Classified into Many Families
Some Protein Domains Are Found in Many Different Proteins
Some Protein Domains Are Found in Many Different Proteins
Some Protein Domains Are Found in Many Different Proteins
Protein domains
• Functional units of a protein
• Each domain confers on protein a specific function – eg
binds to RNA, binds to a specific domain on another
protein, has enzymatic activity
• A given domain may occur multiple times on a given
protein and will be found on many different proteins
• Each domain within a protein can adopt its proper tertiary
structure independent of the other domains
• A protein may have 1 or many domains
• Novel proteins are often the result of addition/subtraction of
domains
• Domains are often named after the first protein that was
found to have that domain
Larger Protein Molecules Often Contain More Than One Polypeptide
Chain
Larger Protein Molecules Often Contain More Than One Polypeptide
Chain
All Proteins Bind to Other Molecules
All Proteins Bind to Other Molecules
The Surface Conformation of a Protein Determines Its Chemistry
Sequence Comparisons Between Protein Family Members Highlight
Crucial Ligand-Binding Sites
Enzymes Are Powerful and Highly Specific Catalysts
PROTEIN FUNCTION
• Many Changes in Proteins Are Driven by Protein
Phosphorylation
• A Eukaryotic Cell Contains a Large Collection of
Protein Kinases and Protein Phosphatases
A Eukaryotic Cell Contains a Large Collection of Protein Kinases and
Protein Phosphatases
A Eukaryotic Cell Contains a Large Collection of Protein Kinases and
Protein Phosphatases
PROTEIN FUNCTION
• Proteins That Bind and Hydrolyze GTP Are
Ubiquitous Cell Regulators
– GTPases (also called GTP binding proteins)
Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cell Regulators
Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cell Regulators
Regulatory Proteins GAP and GEF Control the Activity of GTP-Binding
Proteins by Determining Whether GTP or GDP Is Bound
PROTEIN FUNCTION
• Proteins That Bind and Hydrolyze GTP Are
Ubiquitous Cell Regulators
– GTPases (also called GTP binding proteins)
– GTP vs GDP bound forms have different
conformations, differentially bind to other
proteins
– generally “active” state is GTP-bound
– regulated by
• Guanine Nucleotide Exchange Factors
(GEFs) – promote GTP-bound state
• GTPase Activating Proteins (GAPs) – promote
GDP-bound state
Many Different Covalent Modifications Combine to Regulate Protein
Function
