BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

BIOL 2030 – In-Class Lecture 1

Cell Biology

CELL BIOLOGY BACKGROUND (Chapter 1)

1. Discovery of Cells

2. Properties of Cells

3. Types of Cells
4. Origin of Cells

5. Cell organelles
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Invention of the Light Microscope led to Discovery of Cells

Robert Hooke (1665)

Electron microscope invented

by Ernst Ruska in 1933
From Karp (2008)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Figure 1-9 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Figure 1-7a Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Figure 1-7b Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Figure 1-8b Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Cell Theory
• Cells - structural compartments
- separate the external environment from relatively
constant internal environment
- macromolecules perform unique functions in cells

• Early “cell biologists” (1800’s) formulated current

Cell Theory stating that:

1. All organisms are composed of one or more cells.

2. The cell is the structural unit of life for all organisms.
3. Cells can arise only by division from a pre-existing cell.
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

2. Properties of Cells
(1) Cells are highly complex and organized
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

2. Properties of Cells
(2) Cells possess genetic program and the means to use it
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

2. Properties of Cells
(3) Cells are capable of producing more of themselves
- mitosis and meiosis

10
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

2. Properties of Cells
(4) Cells acquire and utilize energy

11
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

2. Properties of Cells

(5) Cells carry out a variety chemical reactions

(6) Cells engage in numerous mechanical activities

(7) Cells able to respond to stimuli

(8) Cells are capable of self-regulation

(9) Cells evolve

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Review: Chapters 1 and 4 in Essential Cell Biology

On-Line Lecture # 1 (Chapter 1)

Posted Friday

Next Lecture – Thursday Sept. 16,

2010

13
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

14
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

BIOL 2030 – In-Class Lecture 1

Cell Biology
CELL BIOLOGY BACKGROUND (Chapter 1)

1. Discovery of Cells

2. Properties of Cells

3. Types of Cells
4. Origin of Cells

5. Cell organelles
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

3. Types of Cells
– Prokaryotic – lack membrane-enclosed organelles
– Eukaryotic – have membrane-enclosed organelles

EUKARYOTIC CELL PROKARYOTIC CELL

DNA
(no nucleus)
Membrane
Membrane
Cytoplasm

Organelles
1 µm
Nucleus (contains DNA)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

4. Origins of Cells
Prokaryotic Cells
•are believed to have arisen early in Earth’s history
~ 3 billion years ago (Earth ~ 4 billion years old)
• Most diverse cells
Eukaryotic Cells - unicellular
• are believed to have descended from prokaryotes
~ 1.5 billion years ago
• believed to have arisen from endosymbionts

An endosymbiont is a combination of two cells

living in a symbiotic relationship with one of the
cells resident inside the other one.
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

4. Origins of Cells - Eukaryotes

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

4. Origins of Cells – Eukaryotes (plant)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

4. Origins of Cells
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

4. Origins of Cells - Eukaryotes

Unicellularity vs Multicellularity
- unicellular organisms (e.g. most protists)
- must do everything an organism needs to survive
- multicellular organisms (eg protists, plants, fungi, animals)
- divided and delegated “duties / jobs”
- numerous cells / cell types are organized to function as a
“whole” organism
- are believed to have descended from colonial
eukaryotes (< 1 billion years ago)
- exhibit differentiation
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

4. Origins of Cells - Eukaryotes

Differentiation – process by which a relatively unspecialized

cell becomes highly specialized- expresses “cell specific” genes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Cell structure and cell function are intrinsically

linked
Genes
Enzymes
Components of
Proteins Macromolecules
Gene Activators/
Major Structural
Transcription Factors
Component

Signalling Receptors,
Components Channels

Hormones,
Growth Factors
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

EUKARYOTIC CELLS

Figure 1-24 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

EUKARYOTIC CELLS
• The Nucleus Is the Information Store of the Cell
• Mitochondria Generate Usable Energy from Food to
Power the Cell
• Chloroplasts Capture Energy from Sunlight
• Internal Membranes Create Intracellular Compartments
with Different Functions
• The Cytosol Is a Concentrated Aqueous Gel of Large and
Small Molecules
• The Cytoskeleton Is Responsible for Directed Cell
Movements
• The Cytoplasm Is Far from Static
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

INTRODUCTION
• Overview to wake you up

• Frying eggs = looking at protein structure

26
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Proteins are composed of amino acids

• composed of H, C, O, N and
usually S or P
• basic monomer is amino acid
• amino acid - backbone is asymmetric carbon between
NH3+ (amino) and COO- (carboxyl) groups
R

NH3+ C COO-

20 types of amino acids -

R group is different in each
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

R group determines amino acid

properties
Nonpolar Uncharged polar Charged polar
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

A Useful Reference: Amino Acid Properties

and Abbreviations

• Hydrophilic / Hydrophobic
• Acidic / basic

29
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Proteins are chains of amino acids (polypeptides),

each linked by a covalent peptide bond

peptide bonds form

through condensation
reactions attaching
carboxyl group of one
amino acid to amino
group of another
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Each protein has a characteristic sequence of amino acids aligned

with a N-C-C backbone and R groups forming sidechains

= PRIMARY STRUCTURE
Do small changes in amino acid sequence really matter?
The fundamental importance of primary structure:

Sickle Cell Disease

Video 4.12 32
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Diversity of Protein Structure!

How are these

different 3D
structures formed?
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Further Levels of Protein Structure:

Folding Polypeptide Chains

Secondary Structure:
- folding into regular structures
- results from ‘local”interactions between amino acids in
polypeptide backbone
- involve hydrogen bonds

- two key types:

- α-helix
- β-pleated sheet
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Features of an alpha-helix

• backbone interactions  polypeptide chain

twists itself  spiral
• spiral backbone with side chains (R-groups)
pointing outward
• Regular spiral structure is highly organized:
• the N-H of every peptide bond is H-bonded
to the C=O of a neighboring peptide bond,
located 4 peptide bonds away in the same
chain

35
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

A closer look at an alpha helix

Animation 4.2
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

An alpha helix in action: membrane-spanning proteins

e.g. cannabinoid receptors

In a membrane,
hydrophobic
(nonpolar) R
groups orient
out & interact
with
hydrophobic
phospholipid
tails
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Features of a Beta-Pleated Sheet

Backbone Interactions again:

• H-bonds form between amino acids in separate

areas of a protein
•  protein’s backbone folds into a “zig-zag” shape

• Where are the R Groups?

-R groups project above & below the plane of the sheet

38
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Animation 4.4
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Alpha-helices and Beta-sheets bond together to give

a polypeptide chain it’s TERTIARY STRUCTURE
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Tertiary Structure: final level of folding for

individual polypeptide chains
• due to interactions between R groups
• bonds involved:
• hydrogen bonds
• ionic bonds
• hydrophobic interactions
• disulfide bridges between SH groups (strong)
 stabilize
• diverse
• “domains” result: separately folded segment of
the polypeptide chain of a protein
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Some functional proteins are comprised of

a single polypeptide chain

• e.g. opiate
receptor
• 7 alpha-
helices allow it
to sit in the
membrane
and respond
to opioids

42
Many Functional Proteins are Comprised
of >1 Polypeptide Chain

= QUATERNARY STRUCTURE
 • association between 2 or more
polypeptides in a protein
• subunits can be identical or
different
• often symmetrical
• often held together through
common hydrophobic cores

• Advantages?
Hemoglobin • allows construction of large
proteins
• gives proteins complex
Individual polypeptide properties
chains are NOT functional (e.g. cooperativity)

44
 Types of
Quaternary Structure

1. Globular Proteins:
e.g. hemoglobin
- has 4 globular
subunits

2. Fibrous Proteins:
e.g. collagen:
- consists of 3
helices
“supercoiled”

45
 Types of
Quaternary Structure II

46
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Diversity of Protein Structure!

47
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Protein Conformation: the Impact of Water

Polar (hydrophilic)
groups oriented
outward

48
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Protein Conformation Matters: Protein Denaturation

- loss of natural protein structure
- due to relaxation of tertiary and secondary structure
- denaturation  loss of protein’s activity

Denaturation has 2 stages:

1) chain unfolds, extends, exposes new molecules & reactive
groups
2) next, new groups interact  form new bonds
49
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Protein Folding is Crucial to Protein Function

Examples:
• Cystic Fibrosis (CF):
- mutant transport protein cannot fold properly
• Alzheimer’s Disease:
- amyloid protein forms large insoluble fibers that
causes nerve cells to die
• Mad Cow Disease (CJD in humans):
- prion proteins fold incorrectly  aggregates 
damage to nerve cells  fatal

50
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

51
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Summary

• Animation of stages of protein folding from Univ of Wisconsin:

• https://mywebspace.wisc.edu/jonovic/web/proteins/Proteins.swf

52
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Protein Function

Chapter 4

Online Lecture 2
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Structure = Function

• Amino acid sequence determines protein structure

• Amino acids exposed on exterior of final 3D protein
structure determine protein function
• Amino acids are chemically reactive and hence can
bind to other molecules to act as enzymes,
structural support, receptors, motors….
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS WORK

• All Proteins Bind to Other Molecules
• The Binding Sites of Antibodies Are Especially Versatile
• Enzymes Are Powerful and Highly Specific Catalysts
• Lysozyme Illustrates How an Enzyme Works
• Most Drugs Inhibit Enzymes
• Tightly Bound Small Molecules Add Extra Functions to
Proteins
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Binding selectivity
• Selective binding of a protein to a ligand requires
many weak non-covalent bonds simultaneously –
“hand-in-glove”
• Hydrogen bonds
• Electrostatic attractions
• Van der Waals forces
• Protein-ligand interaction occurs at binding site

PROTEIN
FOLDING
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS WORK

• All Proteins Bind to Other Molecules
• The Binding Sites of Antibodies Are Especially Versatile
• Enzymes Are Powerful and Highly Specific Catalysts
• Lysozyme Illustrates How an Enzyme Works
• Most Drugs Inhibit Enzymes
• Tightly Bound Small Molecules Add Extra Functions to
Proteins
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Highly specific protein binding

keeps us healthy
• Antibodies can quickly be made that bind tightly
only to a particular invading foreign molecules
• Y-shaped structure
• 4 chains (H+L)
• 2 variable areas
• VL + V H

• Length and sequence

of loops differ

Movie 4.7
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS WORK

• All Proteins Bind to Other Molecules
• The Binding Sites of Antibodies Are Especially Versatile
• Enzymes Are Powerful and Highly Specific Catalysts
• Lysozyme Illustrates How an Enzyme Works
• Most Drugs Inhibit Enzymes
• Tightly Bound Small Molecules Add Extra Functions to
Proteins
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Different classes of enzymes – each have

unique binding sites to ensure reaction
specificity
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS WORK

• All Proteins Bind to Other Molecules
• The Binding Sites of Antibodies Are Especially Versatile
• Enzymes Are Powerful and Highly Specific Catalysts
• Lysozyme Illustrates How an Enzyme Works
• Most Drugs Inhibit Enzymes
• Tightly Bound Small Molecules Add Extra Functions to
Proteins
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Lysozyme is a natural antibiotic (saliva,

tears) which breaks bacterial cell walls
• Enzyme substrate = molecule that fits its binding
site
• Lysozyme substrate = polysaccharide chains in
bacterial cell wall
• When broken, bacterial wall ruptures
• How does lysozyme work?
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

• Any chemical reaction has an activation energy

• Polysaccharide chain break requires hydrolysis Video 4.8
• Will not occur in aqueous environment as activation energy too high
• Lysozyme creates a microenvironment which lowers the
activation energy for the reaction (result = catalysis)
• Multiple weak non-covalent bonds form in lysozyme active
site to hold polysaccharide substrate
• Polysaccharide chain is physically distorted: weakens bonds
• Next random H2O molecule that collides with the distorted
polysaccharide chain  hydrolysis and broken chain  dissolution
of enzyme complex
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Enzymes can catalyze (lower activation energy of) reactions in

various ways

Figure 4-32 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS WORK

• All Proteins Bind to Other Molecules
• The Binding Sites of Antibodies Are Especially Versatile
• Enzymes Are Powerful and Highly Specific Catalysts
• Lysozyme Illustrates How an Enzyme Works
• Most Drugs Inhibit Enzymes
• Tightly Bound Small Molecules Add Extra Functions to
Proteins
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS WORK

• All Proteins Bind to Other Molecules
• The Binding Sites of Antibodies Are Especially Versatile
• Enzymes Are Powerful and Highly Specific Catalysts
• Lysozyme Illustrates How an Enzyme Works
• Most Drugs Inhibit Enzymes
• Tightly Bound Small Molecules Add Extra Functions to Proteins
• Extra tools to enhance protein capabilities
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

• Frequently a metal atom

• Carboxypeptidase (pancreas) has a zinc
ion tightly bound in its active site
• Hemoglobin – four polypeptide
subunits each bound to a heme group
(red blood)
• Central iron atom
• Binds reversibly with oxygen
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence
One Another
• Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
• GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells
• Proteins Often Form Large Complexes That Function
as Protein Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Cells respond to their environment – timing

and strength of protein function is under
negative and positive regulation

= inhibitory
feedback

(positive
feedback
also occurs)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence
One Another and Assist Feedback Regulation
• Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
• GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells
• Proteins Often Form Large Complexes That Function
as Protein Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Most proteins are allosteric

• Allostery = other shape
• Enzymes have an active (binding site) under the
control of a separate regulatory site
• Intramolecular communication between sites
• CONFORMATIONAL CHANGE IN STRUCTURE
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence
One Another
• Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
• GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells
• Proteins Often Form Large Complexes That Function
as Protein Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Rapidly reversible protein phosphorylation is

under the control of two different enzymes

• Direct addition/removal of phosphate group to the protein

(serine side chain)
• Molecular ON-OFF switch
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence
One Another
• Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
• GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells
• Proteins Often Form Large Complexes That Function
as Protein Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

GTP-Binding Proteins form Molecular On-Off Switches

• Indirect phosphorylation control

• GTP = Guanosine triphosphate = ON
• GDP = Guanoside diphosphate = OFF
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence
One Another
• Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
• GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells
• Proteins Often Form Large Complexes That Function
as Protein Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Conformational changes also power

‘motor proteins’
• Unidirectionality achieved by making
‘steps’ irreversible
• ATP hydrolysis releases a phosphate
group and lots of energy from
breaking a phosphate bond
• Myosin and actin function in this way
to contract muscles
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence
One Another
• Phosphorylation Can Control Protein Activity by
Triggering a Conformational Change
• GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to
Produce Large Movements in Cells
• Proteins Often Form Large Complexes That Function
as Protein Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Nucleotide hydrolysis can also power protein complexes

• Video 4.11

Figure 4-43 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

HOW PROTEINS ARE CONTROLLED

• The Catalytic Activities of Enzymes Are Often Regulated by
Other Molecules
• Allosteric Enzymes Have Binding Sites That Influence One
Another
• Phosphorylation Can Control Protein Activity by Triggering a
Conformational Change
• GTP-Binding Proteins Are Also Regulated by the Cyclic Gain
and Loss of a Phosphate Group
• Nucleotide Hydrolysis Allows Motor Proteins to Produce Large
Movements in Cells
• Proteins Often Form Large Complexes That Function as Protein
Machines
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

BIOL 2030 – Lecture 4

Cell Biology
DNA AND CHROMOSOMES (Chapter 5)

• DNA Structure

• Chromosome Structure

82
Nucleus: Home of a (Eukaryotic) Cell’s
“Genetic Library”
• contains most of genes in a cell
• nuclear membrane or nuclear
envelope:
- 2 concentric membranes separating
nucleus from cytoplasm
• nuclear pores:
- “selective channels” through nuclear
envelope

• nucleolus:
- site of ribosomal RNA (rRNA)
synthesis & assembly  ribosomal
subunits
• chromosomes:
- visible as cells prepare
83 to divide
DNA Terminology
• DNA Structure:
- ideal for “accurate and
unlimited replication”
- provides a “mechanism for
heredity”

• Gene Expression:
- process of converting the
gene’s nucleotide
sequence protein’s amino
acid sequence

• The Genome:
- complete set of information
in an organism’s DNA
84
 A DNA Molecule Consists of Two
Complementary Chains of Nucleotides

• What is in a nucleotide?
- 1 pentose sugar
- 1 phosphate group
- 1 nitrogenous base:
(A, G, C, T)

85
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA has a “sugar-phosphate backbone”

DNA has a chemical polarity: a 3’ end (-OH) and a 5’ end (-PO4)

DNA buidling block: Bases in DNA do not pair randomly!

- Pentose sugar
- Phosphate
- Nucleotide
Purine
sugar
complementar
y base pairing

Phosphate

Pyrimidine

A  T
GC
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The two strands of the DNA Strands are

double helix are held together antiparallel
by base pairing
The DNA sequence
of the strands is
complementary
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What is the Structure of DNA?

• covalently bonded sugar–
phosphate backbones
of each strand coil around
outside of helix
• nitrogenous bases point
toward center of helix

• hydrogen bonds between

complementary bases hold
two strands together
• to provide uniform diameter
purine pairs with
pyrimidine
- A always pairs with T
(two H bonds)
- G always pairs with C
(three H 88bonds)
Another look at the DNA Double Helix

• 2 DNA strands twist

 double helix

Video 5.1

89
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What is the Function of DNA?

Structure supports Role of DNA in Cells / Organisms

DNA performs at least 4 important roles:

1. it stores all of an organism’s

genetic information

2. it is expressed in the phenotype

3. it is susceptible to mutation

4. it can be precisely replicated

in cell cycle
The Structure of Eukaryotic Chromosomes
• Chromosome = long strand of
DNA + protein
• packaging issues
• 2 m of DNA per human cell
• How big is a cell nucleus?
- 5 mm in diameter!

• challenges for chromosomes:

chromosomes in their • packaging
most compressed form • accessibility
= mitotic chromosomes

91
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA strands are NOT tightly packed unless the cell

is dividing (mitosis)

92
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Cells have an Amazing Ability to Condense their Chromosomes

Interphase Chromosomes M-Phase Chromosomes

Chromsomes
become
condensed
by wrapping
around
specialized
proteins

Condensed a little bit! Super condensed!

93
Figure 5-20
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

How do eukaryotic cells manage to

package DNA molecules into compact
chromosomes – yet still keep it
accessible for replication?

94
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Eukaryotic Chromosome has Successive Levels of Structure

DNA molecule =

• proteins called histones

– responsible for first level of
DNA packing in chromatin
– bind tightly to DNA (ionic bond)
• association of DNA and histones
– remains intact during Cell Cycle

Figure 9.7 from

Purves et al. (2001)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Nucleosomes are Basic Units of Chromatin Structure

Nucleosome = DNA wrapped around histone protoeins
= Basic Units of Chromatin

96
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

So how does DNA wrap around histone proteins to form nucleosomes?

DNA: negative charge due to phosphates in backbone

wraps around protein that have a positive charge

What causes the protein to be positively charged ?

-positively charged amino acids e.g. lysine, arginine amino acids

Figure 5-22 Video 5.2

97
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA strand wraps around histone

octamer TWICE

Histone proteins are formed from

4 different subunits, each with two
copies = 8 total = OCTAMER

Figure 5-22 (part 2 of 2) Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Chromosomes have Several levels of DNA Packing

05_24_Chromatin pack.jpg
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

100
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Eukaryotic Chromosome - Higher Levels of DNA Packing

• form seen at interphase chromosomes (‘uncondensed’)

30
nm

Nucleosome
(b) 30-nm Fiber Figure 19.2 b

• the 30-nm fiber forms looped domains, making a 300-nm fiber

• held on protein scaffold or nuclear lamina
Protein Scaffold Loops

300
Scaffold
nm

(c) Looped Domains

101
(300-nm fiber)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Eukaryotic Chromosome - Higher Levels of DNA Packing

• in a mitotic chromosome
• the looped domains themselves coil and fold forming
the characteristic ‘condensed’ metaphase chromosome

700
nm

1,400
nm

(d) Metaphase Chromosome

102
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What makes Chromatin “Dynamic”?

One Strategy:
- chromatin
remodeling
complexes
(protein
assemblies)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What makes Chromatin “Dynamic”?

Another strategy:
histone tail
modifications

104
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What makes Chromatin “Dynamic”?

• acetyl group added to +ve amino acids in histone tails
= histone acetylation
- charge neutralized – prevents binding to neighbouring nucleosomes
- relaxes chromatin structure and transcription is activated
(transcription enzymes gain access)

• acetyl group removed from histone tails

= histone deacetylation
- becomes charged – permits binding to neighbouring nucleosomes
- chromatin condenses and transcription is inhibited

Unacetylated Histones Acetylated Histones

(not transcribed) (transcribed)

Figure 19.4 b from Campbell and Reese (2005)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What Structures on Chromosomes enable them

to Replicate and Separate ?
(1) Telomere: repeated DNA sequence on the ends of chromosomes that
allows ends to be replicated. Also protects the chromosome

Figure 5-18
106
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What Structures on Chromosomes enable them

to Replicate and Separate ?

(2)Replication Origin: where replication of the chromosome begins

Figure 5-18
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What Structures on Chromosomes enable them

to Replicate and Separate ?
(3) Centromere: DNA sequence that allows attachment to mitotic spindles

Figure 5-18 108

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

REVIEW

• http://www.pbs.org/wgbh/nova/genome/medi
a/journeyintodna.swf

• Animation of chromosomal structure

• NEXT ONLINE LECTURE

• DNA Replication (Chapter 6)

109
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Online Lecture 3

Chapter 6

DNA Replication
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Introduction
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Why is DNA replication important?

• We all start life as one cell

• Adult body contains ~100 TRILLION cells
• 1 cell  100,000,000,000,000 cells
• ~3 billion nucleotides copied / cell division in 8 hrs
• ~50 cell divisions
• ~50 DNA replications
• Accuracy incredibly important
• 1-2 errors / cell division
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a Replication
Machine
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA replicates by each strand acting as a template for complementary binding

GATTACA GATTACA

CTAATGT
GATTACA

CTAATGT GATTACA

CTAATGT CTAATGT

Figure 6-2 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA = Semiconservative replication

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a Replication
Machine
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA ‘Replication Machine’ – proteins cluster at replication origin region

AT rich

: bind to DNA &

break H-bonds
between bases

DNA
Polymerase
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a Replication
Machine
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Replication forks move away in opposite

directions from multiple replication origins in
eukaryotes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA polymerase synthesizes

new DNA in 5’ to 3’ direction

• DNA polymerase needs

paired nucleotides to
function
• New nucleotides always
added to 3’ end of new DNA
strand
• Breaking off (*) 2
phosphates provides energy
for the polymerization
reaction
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a Replication
Machine
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

How are both new DNA strands

synthesized in the 5’ – 3’ direction?
There is no other DNA polymerase that works in 3’-5’ direction

Figure 6-11 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

One DNA strand is synthesized

discontinuously and later joined
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a Replication
Machine
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA Polymerase contains separate sites for DNA synthesis

and proofreadingqq1111111111111111111qq

P = Polymerization site
E = Error-correcting
Proofreading site
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a Replication
Machine
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

• DNA polymerase requires

base-paired nucleotides to
start DNA synthesis
• DNA Primase makes a short
region of RNA – DNA
polymerase can then start
• Nuclease breaks up the RNA
primer
• Repair polymerase replaces
RNA with DNA
• DNA ligase joins the nicks in
the DNA backbone
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA REPLICATION
• Base-Pairing Enables DNA Replication
• DNA Synthesis Begins at Replication Origins
• New DNA Synthesis Occurs at Replication Forks
• The Replication Fork Is Asymmetrical
• DNA Polymerase Is Self-correcting
• Short Lengths of RNA Act as Primers for DNA Synthesis
• Proteins at a Replication Fork Cooperate to Form a ‘Replication
Machine’
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

“If I could be an enzyme, I’d be DNA Helicase, so then I could unzip your genes”

DNA polymerase

DNA Helicase – Movie 6.2

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Proteins comprising a Replication

Machine
• DNA polymerase: DNA synthesis
• DNA primase: Creates RNA primer in lagging strand
• Nuclease: Destroys RNA primer in lagging strand
• Repair polymerase: Makes DNA in lagging strand
• DNA ligase: fixes nicks in DNA backbone in lagging strand
• Helicase: Unwinds DNA double stranded helix
• Single Strand Binding Protein:
• Binds unwound single stranded DNA & prevents base-pair
formation
• Sliding Clamp:
• Keeps DNA polymerase attached to template – Movie 6.3
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Figure 6-17a Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Summary
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

BIOL 2030 – Lecture 5

Information flow in cells from DNA to Protein

133
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What makes cells different from each other?

• DNA that a cell contains = GENOTYPE
• Characteristics of a cell = PHENOTYPE
• Within an organism:
• All cells have the same genotype
• Cells have different phenotypes
• Phenotypic differences due to which proteins any given cell
synthesizes
• i.e. nerve cells synthesize a different set of proteins than
muscle cell
• Where, when and how much protein is synthesized
• Control of synthesizing proteins from DNA critical

134
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

How is Genetic Information in DNA transferred

and expressed as Proteins?

Genotype Proteins Phenotype

• Must be able to accurately convert information in DNA

• Amino acid/protein code is dictated by DNA code
• Gene expression control  which proteins are synthesized
 cell phenotype

135
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Cellular Physical Constraints

• DNA is a very large molecule ‘captive’ within the
nucleus
• Proteins synthesized in the cytoplasm
• How does DNA (nucleus) encode new proteins
(cytoplasm)?
• Crick proposed that there must be a carrier molecule –
‘Central dogma’
• Efficient as only a small region of DNA (a gene) may
be necessary for protein x production at any given
time

136
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

CENTRAL DOGMA OF CELL BIOLOGY

Francis Crick’s central dogma stated that:
DNA codes for RNA and RNA codes for protein

DNA Synthesis
(Chapter 6)

transcription translation
Messenger RNA or mRNA Transfer RNA or tRNA
carries instructions for making links the code of mRNA and
polypeptides from DNA in nucleus the code for specifying
into cytoplasm, where it serves as correct sequence of amino
a template for polypeptide acids in polypeptides
synthesis
Protein Synthesis (Chapter
137
7)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

How does Information Flow from Genes to Proteins?

• DNA language is
encoded by nucleotide
sequence
• Copy is made of DNA in
RNA nucleotide
sequence
= TRANSCRIPTION

• RNA is decoded/translated
into the sequence of
amino acids in
polypeptide chains
/proteins
= TRANSLATION
138
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

How does Information Flow from Genes to Proteins?

• RNA is transcribed using the rules of base pairing from the

template strand of DNA
- the information is copied from one strand
• most genes code for proteins
• Some genes code for untranslated functional RNAs used in
protein synthesis
• the nucleotide sequence of the gene determines the order
of amino acids in a protein, which determines shape, size,
and protein function
- the information is translated or deciphered
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Expression of Genes Vary

07_02_Genes express.jpg
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Key concept

• within the DNA sequences of any organism is the

information for each of the gene products that the organism
can make
• not only do these DNA sequences encode the structure of
these products, but they also contain the information for
when, where and how much of the product is made.
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA vs RNA Structure - What is the Difference?

142
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

143
Transcription produces an RNA
Sequence Complementary to
One Strand of DNA • Template Strand = DNA
strand used for
transcription

• Coding Strand = DNA

sequence that is
similar to RNA product

• RNA Transcript = single

RNA strand that is
produced and displaced
from template DNA
strand
144
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Single stranded RNA forms folded structures

07_05_RNA.jpg

Ecb3 animation 7.1 shows RNA structure

145
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Types of RNAs Produced

INFORMATIONAL

FUNCTIONAL
146
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

DNA as a transcription template

• In each chromosome, both strands of DNA are
transcribed
• For any given gene, only one strand is transcribed,
and it is always the same strand for a given gene
• DNA strand always transcribed from 3’ to 5’
• RNA strand always 5’ to 3’
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Transcription is catalysed by RNA polymerase

148
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

07_07_RNApolymer.jpg
RNA polymerase in Action
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

RNA Polymerase Characteristics

Figure 7-8

• RNA polymerase differs from DNA polymerase

• catalyzes ribonucleotide linkage
• does NOT need a primer
• makes more mistakes than DNA polymerase

150
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Overview of Transcription steps

• Initiation
• binding of RNA polymerase to promoter region
• unwinding of DNA
• Elongation
• addition of nucleotides to 3’ end
• rules of base pairing
• Termination
• at 3’ end of transcript
• processing required for mRNA

• Ecb3 Video 7.2

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Transcription - Initiation
• All genes have a promoter region
• Special DNA sequence indicating where
transcription is to begin
• Upstream of the DNA coding region
• RNA polymerase interacts with the promoter to
begin transcription
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

A Closer Look
07_09_2_bacterial at Promoters in Prokaryotes
gene.jpg

TATA box
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

07_09_1_bacterial gene.jpg Steps in Prokaryotic Transcription

1) Initiation

2) Elongation

3) Termination
154
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Prokaryotic
07_09_2_bacterialPromoters
gene.jpg and Terminators
Transcription in Eukaryotes

• Prokaryotes only have one type of RNA polymerase

• Eukaryotes have three RNA polymerases

156
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

RNA Polymerase II
• RNA polymerase II must assemble with other
proteins before transcription can begin
• General transcription factors
• All form transcription initiation complex

RNA polymerase

DNA template
strand

157
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

TATA-binding protein
Distorts DNA – may
attract other
Transcription factor

158
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159
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Transcription Termination

• RNA polymerase II released from DNA at

termination sequence
• Phosphotases remove phosphates from its tail
• Dephophorylated from of RNA polymerase II is now
available for transcription again

160
• Summary of transcription animation for review

161
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Online Lecture 4

Chapter 7

mRNA Splicing
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

FROM DNA TO RNA

• Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus
• Eucaryotic Genes Are Interrupted by Noncoding Sequences
• Introns Are Removed by RNA Splicing
• Mature Eucaryotic mRNAs Are Selectively Exported from the
Nucleus
• mRNA Molecules Are Eventually Degraded by the Cell
• The Earliest Cells May Have Had Introns in Their Genes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

RNA is Processed and Spliced in the

Nucleus

Figure 7-14 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

RNA Processing
Factors

• At the end of
transcription initiation,
phosphorylation of
RNA polymerase tail
causes binding of RNA
processing factors
• These factors are in
position to
immediately act on the
growing RNA strand
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

mRNA is Capped and Polyadenylated

• Stabilizes mRNA and identifies it for export to

the cytoplasm to produce proteins
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

FROM DNA TO RNA

• Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus
• Eucaryotic Genes Are Interrupted by Noncoding Sequences
• Introns Are Removed by RNA Splicing
• Mature Eucaryotic mRNAs Are Selectively Exported from the
Nucleus
• mRNA Molecules Are Eventually Degraded by the Cell
• The Earliest Cells May Have Had Introns in Their Genes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Exons and Introns

• Exons = expressed sequences

• Introns = intervening sequences
• Eukaryotic RNA is radically modified in nucleus
• Introns removed to form ‘mature’ RNA
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

mRNA Transcripts are often Comprised Mainly of

Introns

• Introns can be >10,000 nucleotides

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

FROM DNA TO RNA

• Eucaryotic RNAs Are Transcribed and Processed (5-cap, 3-
polyA tail)Simultaneously in the Nucleus
• Eucaryotic Genes Are Interrupted by Noncoding
Sequences(Introns removed to form ‘mature’ RNA) snRNPs (Small
nuclear ribonucleoprotein particles) recognise the special intron sequences
• Introns Are Removed by RNA Splicing (RNA splicing is performed
by spliceosome)

• Mature Eucaryotic mRNAs Are Selectively Exported from the

Nucleus
• mRNA Molecules Are Eventually Degraded by the Cell
• The Earliest Cells May Have Had Introns in Their Genes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Special Nucleotide Sequences Signal

the Start and End of Introns

• RNA splicing is performed by spliceosome

• Large assembly of RNAs and proteins
• snRNPs (Small nuclear ribonucleoprotein particles) recognise
the special intron sequences
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Introns form Lariats

during Splicing

• Branch point Adenine breaks

the 5’ splice site
• Free 5’ end of intron bonds
with 2’-OH group to form
lariat
• Two exons join together
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

What is the Advantage of Introns?

1. Alternative Splicing

2. Evolution of new proteins

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

FROM DNA TO RNA

• Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus
• Eucaryotic Genes Are Interrupted by Noncoding Sequences
• Introns Are Removed by RNA Splicing
• Mature Eucaryotic mRNAs Are Selectively Exported from the
Nucleus
• mRNA Molecules Are Eventually Degraded by the Cell
• The Earliest Cells May Have Had Introns in Their Genes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Only Mature mRNAs can pass through nuclear pores to the

cytoplasm

Figure 7-22 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

FROM DNA TO RNA

• Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus
• Eucaryotic Genes Are Interrupted by Noncoding Sequences
• Introns Are Removed by RNA Splicing
• Mature Eucaryotic mRNAs Are Selectively Exported from the
Nucleus
• mRNA Molecules Are Eventually Degraded by the Cell
• The Earliest Cells May Have Had Introns in Their Genes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

FROM DNA TO RNA

• Eucaryotic RNAs Are Transcribed and Processed
Simultaneously in the Nucleus
• Eucaryotic Genes Are Interrupted by Noncoding Sequences
• Introns Are Removed by RNA Splicing
• Mature Eucaryotic mRNAs Are Selectively Exported from the
Nucleus
• mRNA Molecules Are Eventually Degraded by the Cell
• The Earliest Cells May Have Had Introns in Their Genes??
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Figure 7-23 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

179
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

BIOL 2030 – Lecture 5

Information flow in cells from DNA to Protein

180
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

181
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Codons – the key to translation

• How is the amino acid sequence of a
polypeptide determined from the nucleotide
sequence of mRNA?
• mRNA nucleotide sequence is read three
nucleotides at a time
• Each triplet of nucleotides is called a codon
−e.g. UCG encodes the amino acid serine
• Each amino acid can be encoded by one or
more codons
−redundancy
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Codons
• mRNA is decoded in sets of 3 nucleotides
• each codes for an amino acid
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

mRNA nucleotide sequence =

C U C A G C G U U A C C A U

• Reading frames
• 3 possible
• Only 1 is correct
• Start codon
sets correct
reading frame
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

tRNA Molecules Match Amino

Acids to Codons in mRNA

• tRNA is a single-stranded functional RNA

(i.e. it’s not translated)
• tRNA has a clover-leaf shape held by
nucleotide H-bonding
• Middle loop contains anticodon of 3
nucleotides
• Complementary to mRNA codon -
antiparallel (3’-5’)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

tRNA Wobble

• permits third nucleotide of anticodon (5’ end) to

hydrogen bond with alternative nucleotide
• permits a tRNA to translate more than one codon
• efficient
 Specific Enzymes Couple tRNAs to
the Correct Amino Acid
• tRNA 3’ acceptor end attaches amino acid by specific
aminoacyl-tRNA synthetases - one for each different amino
acid e.g. tryptohanyl tRNA synthetase binds tryptophan to
tRNAs with anticodon for tryptophan (ACC)

187
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The RNA Message Is Decoded on

Ribosomes
• Ribosomes are complexes of protein & rRNA
• Millions of ribosomes in cytoplasm of each cell
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Ribosomal
Structure

189
Figure 7-31 Essential Cell Biology (© Garland Science 2010)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Initiation 1

191
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Initiation 2

192
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Initiation 3

193
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Step 1

194
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Step 2

195
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Step 3

196
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Step 4

Video 7.8

197
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Translation Termination

198
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Proteins are made on Polyribosomes

Video 7.10

199
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Post-translational
modifications and
protein regulation

Proteasomes

Proteins tagged
with UBIQUITIN
proteases

200
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Online Lecture 5

Chapter 11

Cell Membrane Structure

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Introduction
 A living cell is a self-producing system of molecules held inside a container

 This container is the plasma membrane

 Every cell has a plasma membrane
 Its job is much more than a container for the cell contents
 The plasma membrane must be able to allow the passage of nutrients
back and forth
11_01_Cell.membranes.jpg
 In addition to the plasma membrane the cell has other containers called
internal membranes
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Plasma membrane has many jobs

 The plasma membrane contains proteins that act as sensors to allow
the cell to respond to stimuli
 It can also export and import molecules (endocytosis and exocytosis)
 It can grow when the cell grows and can allow movement
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Plasma membrane is formed by the lipid

bilayer
 The lipid bilayer gives the membrane its basic structure and serves as a
permeability barrier
 The lipid bilayer also has proteins imbedded
 These proteins give the membrane their individual characteristics
11_04_membrane.view.jpg
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Each lipid in the bilayer has a hydrophilic

head and a hydrophobic tail
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The most abundant lipid in the bilayer are phospholipids

 Phospholipids are molecules where the hydrophilic head is linked to the
rest of the molecule through a glycerol group
 The most common phospholipid is the phosphatidycholine (shown below)
 Molecules that contain both hydrophilic and hydrophobic groups are called
amphipathic
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Cholesterol also makes up

animal cell membranes

Cholesterol is also amphipathic

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Other lipids also make up cell

membranes

Both are amphipathic

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Phospholipids and glycolipids are

distributed asymmetrically in the
membrane

Different lipids
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

How is the cell membrane formed?

 Hydrophobic molecules force water molecules to form a
cage-like arrangement
 This is the driving force in the formation of the lipid bilayer
 This arrangement is most energetically favorable
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The properties of phospholipids cause membranes to be spherical?

 For example, any tear in the plasma membrane will expose an edge of
the phospholipid (hydrophobic tails) to water
 This is energetically unfavorable
 Therefore the edges merge and form a spherical shape
11_12_sealed.compar.jpg

This way the hydrophillic head

faces the water and the
hydrophobic fatty-acids are no
longer in contact with water
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

A lipid bilayer can also be observed

experimentally

Liposomes

Video 11.3
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Phosholipids can move within the plane of the membrane

 This gives the plasma membrane fluidity – acts as a 2D fluid

 Fluidity depends on how tightly they are packed together
 How tightly they pack together depends on
1) the length of the hydrocarbon tail
2) their degree of unsaturation (how
many double-bonds they contain)

Fluidity = dynamic cell barrier responds

to changing environment

Proteins must be able to move

within the membrane
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Membrane Fluidity
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Membrane fluidity in animal cells is also modulated by cholesterol

 Cholesterol fills in the gap between phospholipids and provides

stability to the plasma membrane
 In this case cholesterol tends to make the plasma membrane less fluid
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Membrane fluidity allow for functional

membrane proteins
 There are many type of proteins that anchor themselves within the plasma
membrane
 These membrane proteins can give the cell specific functions
 Transporters: membrane proteins that transport nutrients and ions
 Anchors: anchor macromolecules
 Receptors: receive information

 Enzymes: catalyze reactions

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Membrane proteins associate with the

membrane in various ways
11_21_proteins.associ.jpg
 Transmembrane proteins: hydrophobic regions interact with the tails of
phospholipids, while their hydrophilic portions interaction with the cytosol and
extracellular environment.
 Membrane associated: the protein is entirely cytosolic with alpha-helix associated
with inner leaflet of the membrane

 Lipid linked: linked to membrane by covalent bond

 Protein Attached: One protein is held in place with another protein that is associated
with the plasma membrane.
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

A peptide chain can cross the membrane as

an alpha-helix
 the alpha-helix that crosses the membrane has hydrophobic side-
chains that interact with the hydrophobic portion of the membrane
11_23_helix.cross.LB.jpg
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Beta-sheets can cross the membrane as beta-barrel

 This can form an aqueous channel

 The hydrophilic portion of the beta-sheets form the lining of the
aqueous channel
11_25_Porin.proteins.jpg
 The hydrophobic portion interacts with the plasma membrane
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The plasma membrane is reinforced by a cell cortex

 The cell membrane is strengthened by a framework of proteins called a
cortex
 This protein framework is attached by transmembrane proteins
 The cortex of human red blood cell membrane is made up of the
11_31_spectrin.jpg
protein spectrin
 Spectrin forms the meshwork that provide red blood cells with their
shape
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The cell surface is coated with carbohydrates

 Membrane proteins with sugars (oligosaccharides) attached are called
glycoproteins
 Lipids with carbohydrates attached are glycolipids
 These carbohydrates help protect the cell from mechanical and chemical
damage 11_32_sugar.coated.jpg
 Carbohydrates here can absorb
water giving the cell a slimy
surface

This slimy surface

allows white-blood cells
to squeeze between other cells

And prevents cells

from sticking together

Carbohydrates also allow for

Cell-cell recognition
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Carbohydrates on the surface of neutrophils recognize sites of infection

 Oligosaccharide on the neutrophils bind to lectin proteins on

endothelial cells at the site of infection
11_33_neutrophils.jpg
 This allows neutrophils to migrate through the blood vessel at the
correct location to the site of infection
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Neutrophils in Action

• Video 11.6
Summary
225
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

BIOL 2030 – Lecture 6

Cell Biology

MEMBRANE TRANSPORT (Chapter 12)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Lipid bilayers are differentially

permeable
1. Small nonpolar
molecules are readily
permeable
2. Uncharged polar
molecules diffuse
relative to size
3. Ions and charged
molecules are highly
impermeable

Figure 12-2 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Ionic concentrations vary

Table 12-1 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Membrane transport proteins are needed

to allow cells to take up nutrients, excrete
waste and respond to the environment

Figure 12-1 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Two Classes
• Channel
Transporters of Membrane Transport
Proteins
• Discriminate
Ligand binds on
to specific
size and site
ionic charge
Proteins
• Conformational change allows passage

Figure 12-3 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Solutes Cross Membranes by Passive

or Active Transport

Figure 12-4 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Passive Transport: Driven by

Concentration Gradients and Electrical
Forces

Figure 12-6 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Active Transport Moves Solutes

Against Their Electrochemical
Gradients

Figure 12-7 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The energy source for active

transport is from 3 possible
mechanisms

Figure 12-8 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Na+-K+ Pump plays a central role in

membrane transport

Figure 12-9 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Na+-K+ pump cycle is driven by

de / phosphorylation

Figure 12-11 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The Na+-K+ Pump Helps Maintain

the Osmotic Balance of Animal Cells

Figure 12-12 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

The energy source for active

transport is from 3 possible
mechanisms

Figure 12-8 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Different types of Coupled

Transporters

Figure 12-16 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

• Glucose – Na+ symport protein uses the Na+

Coupled Transporters Exploit Gradients
electrochemical gradient tom import glucose
to Take Up Nutrients Actively

Figure 12-17 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Glucose transport in the gut

epithelia
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Two Classes
• Channel
Transporters of Membrane Transport
Proteins
• Discriminate
Ligand binds on
to specific
size and site
ionic charge
Proteins
• Conformational change allows passage
3 Critical properties

Figure 12-3 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

1. Ion Channels Are Ion-selective

• K+ ions selected
by size and
negative charge
of carbonyl
oxygens
• Ion channels are
not simple pores

Figure 12-20 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

2. Ion Channels Randomly Snap

Between Open and Closed States

Transient ion channel

openings can be
recorded in real time

Figure 12-21 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

3. Ion channels are gated

e.g. neurons e.g. auditory hair cells

Figure 12-25 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Voltage-gated ion channels underlie

cell resting membrane potential
• Cell electricity • Resting membrane
carried by ions not potential can be
electrons anywhere between
-20 to -200 mV

Figure 12-28 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Membrane potential is determined by

permeability to K+ ions
K+ leak channels

Charge separation
results in resting
membrane potential

Membrane potential
can be calculated
using the Nernst
equation if K+
concentrations are
known

Figure 12-29 Essential Cell Biology (© Garland Science 2010)

BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Neurons use voltage-gated ion channels to

transmit signals quickly over long distances
• To transmit a signal a stimulus initiates a small change in membrane
potential in the cell body
• This triggers a wave of electrical excitation, called an action potential
• Action potentials travel up to 100 m/s
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Action potentials are usually mediated by voltage-

gated Na+ channels
An action potential is triggered by a sudden depolarization of the plasma membrane
Depolarization means the membrane potential shifts to a less negative number

1) A stimulus causes a sufficient depolarization to pass to a threshold value

2) This causes voltage-gated Na+ channels to open at that site
3) This allows Na+ ions to enter
the cell further depolarizing
the membrane
4) A cascade of voltage-gated Na+
channels openings  action potential
5) Voltage-gated Na+ channels
inactivate at peak of action potential
6) Voltage-gated K+ channels opening
return the cell to the resting membrane
potential
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Depolarization in the axon leads to propagation

of depolarization
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Neurons transmit electrical signals through ion

channels
12_30_neuron .jpg

Video
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Action potential must be converted to a chemical

signal to reach the target cell
•Action potential releases neurotransmitters at synapses
•Neurotransmitters are stored in the presynaptic cell in synaptic vesicles which are released
during an action potential
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Neurotransmitters are released due to opening

of voltage-gated Ca 2+ channels
• Neurotransmitters are stored in the presynaptic cell in synaptic vesicles which are released
during an action potential
• The arriving action potential opens Voltage-gated Ca 2+ channels
• The rush of Ca 2+ ions causes the synaptic vesicles to fuse with the plasma membrane of the
presynaptic cell releasing the neurotransmitter
12_40_nerve_terminal.jpg
BIOL 2030 – Fall 2010 – Lecture 1– INTRODUCTION AND CELL BIOLOGY BACKGROUND (Chapter 1)

Neurotransmitters then bind to

neurotransmitter receptors
• Neurotransmitter receptors are also called transmitter-gated ion channels
• The binding of neurotransmitter changes the conformation of the channel causing it to open

• This causes ions to flow into the postsynaptic cell, changing the membrane potential.
• Therefore, the original electrical signal is converted to a chemical signal back to an electrical
signal

• Neurotransmitters can be
excitatory or inhibitory

Figure: 12. 41