Summary from Wednesday

• Physiology - integrative science

that draws from many
disciplines to gain insight into
how animals operate
• Themes
• Structure/Function
• Evolution/Adaptation
• Homeostasis/Feedback
Control
Cellular and Molecular Physiology
Chapter 2
Goal for today and Monday

• Review cell structure and

cell physiology
• Cell theory
• Physiological processes
start at the cellular level.
2.1 Introduction
• Categories of biological
molecules
1) Carbohydrates
2) Lipids
3) Proteins
4) Nucleic Acids
2) These biological molecules are the
components of cells.
2.1 Introduction
• Major subdivisions of eukaryotic
cells
• Plasma membrane = cell
membrane
• Nucleus
• Cytoplasm - organelles plus
cytosol
2.2 Nucleus, Chromosomes, and Genes
• All cells in a multicellular eukaryote
have the same genetic content/DNA.
• Different genes are expressed in different
tissues or at different times.
• Differential gene expression is
accomplished by
• Regulation of individual genes with
promoters and transcription factors
• Regulation of transcription factors in
different tissues and at different stages
• Central Dogma of Molecular Biology
2. Proteins are processed
and segregated in the rER,
and transport vesicles bud
off the rER.

(in some cases)

2.9 Vaults
• Vaults - hollow
structures capable
of docking with
nuclear pores.
• Transport molecules
(e.g. mRNA) from
nucleus to
cytoplasm
2.5 Golgi Complex
• Exocytosis
• Primary mechanism
for secretion into the
extracellular fluid
• Secretory vesicles
bud off of Golgi
complex.
• Vesicle and plasma
membranes fuse,
releasing contents of
vesicle into
extracellular fluid.
2.6 Lysosomes and Proteosomes
1) Pinocytosis - “cell drinking”
• A droplet of ECF is taken up nonselectively
2.6 Lysosomes & Proteosomes cont’d
2) Receptor-mediated endocytosis
• Selective process that enables cells to
import specific, large molecules
• Triggered by molecule binding to specific
surface membrane receptor site
2.6 Lysosomes & Proteosomes cont’d
3) Phagocytosis
• Internalization of large multimolecular particles
• Pseudopodia completely surround a particle and trap it within
an internalized vesicle.
• Lysosome fuses with vesicle and digests its contents.
2.6 Lysosomes & Proteosomes cont’d
• Proteosomes
• Large, tunnel-shaped structures made of
proteins
• Break down internal proteins into
component amino acids
• Unwanted proteins tagged with ubiquitin in
order to be recognized by proteasomes
Protein degradation by
proteasome.
2.8 Mitochondria & Energy Metabolism
• Mitochondria
• double membrane
• Smooth outer
membrane
• Folded inner
membrane - cristae
• Gel-like matrix
contains enzymes.
2.8 Mitochondria & Energy Metabolism cont’d
• Mitochondria extract energy from
nutrients in food and transform it
into a form usable by the cell.
• Produce 90% of energy that cells need
to survive and function
2.8 Mitochondria & Energy Metabolism cont’d
• Aerobic metabolism
• Requires O2
• uses E from food to make ATP
• Anaerobic pathways do not require
O 2.
• Energy released when electrons
transferred from high-energy bonds
to electron acceptors in oxidation-
reduction reactions
2.8 Mitochondria & Energy Metabolism cont’d
• Universal energy carriers
• ATP - high-energy bond in terminal
phosphate
• When terminal phosphate bond is split,
energy is released.
hydrolysis
ATP ADP + Pi + energy
2.8 Mitochondria & Energy Metabolism cont’d
• Universal energy carriers cont’d
• Nicotinamide adenine
dinucleotide (NADH) carries E-
rich electrons that can reduce
other organic molecules.
• Each NADH “is worth” almost 3
ATPs.
• Electrons of NADH are transferred
to O2, the final electron acceptor in
the electron transport chain.
2.8 Mitochondria & Energy Metabolism cont’d
• Glycolysis
• Chemical process -
breaks glucose into
two pyruvate
molecules
• 10 sequential
reactions, each
catalyzed
by a separate
enzyme
2.8 Mitochondria & Energy Metabolism cont’d
• Glycolysis
• takes place in the cytosol
• can proceed in the absence of
oxygen (i.e., under anaerobic
conditions)
• releases two electrons that are
transferred to NAD+ to form NADH
• 2 ATPs are generated for each
glucose consumed
2.8 Mitochondria & Energy Metabolism cont’d
• Citric acid cycle (aka Krebs cycle or
TCA cycle)
• Series of 8 reactions catalyzed by
enzymes in the mitochondrial matrix
• Pyruvate produced from glycolysis enters
the mitochondrial matrix.
• Pyruvate is converted to acetyl CoA by
removal of a carbon and attachment to
CoA; formation of CO2 byproduct
2.8 Mitochondria & Energy Metabolism cont’d
• Citric acid cycle cont’d
• Acetyl CoA enters citric acid cycle by
combining with oxaloacetic acid (4C)
to form citric acid (6C).
• Two carbons are released as CO2.
• One ATP is produced for each turn of
the cycle.
• The key purpose of the cycle is to
produce reduced cofactors to feed
electrons into the electron transport
chain.
2.8 Mitochondria & Energy Metabolism cont’d
• Electron transport chain
• The big energy payoff for the cell.
• Electron carrier molecules are located
in the inner mitochondrial membrane.
• Electrons are transferred through a
chain of reactions with the electrons
falling to lower energy levels at each
successive step.
2.8 Mitochondria & Energy Metabolism cont’d

• Electron transport chain cont’d

• O2 is required.
• O2 = final electron acceptor
of ETC.
• O2 combines with electrons and
hydrogen to form H2O, i.e., O2
is reduced to form water.
2.8 Mitochondria & Energy Metabolism cont’d
• Electron transport chain cont’d
• Some of E released during transfer of
electrons is used to synthesize ATP
(oxidative phosphorylation)
• Total ATP yield is 30 ATPs per molecule of
glucose.

Food + O2 CO2 + H2O + ATP

necessary for produced mainly
produced mainly
oxidative in citric acid
through
phosphorylation cycle
oxidative
phosphorylation
catabolism
2.8 Mitochondria & Energy Metabolism cont’d
• Metabolism under anaerobic conditions
• O2 deficiency forces cells to rely on
glycolysis.
• Pyruvate is reduced to lactate,
regenerating NAD+.
• Lactate accumulates in the tissues and
reduces pH.
• Lactate can be converted back to pyruvate.
Anaerobic conditions produce only 2 ATP per glucose molecule.

Aerobic conditions produce up to 32 ATP per glucose molecule.

2.8 Mitochondria & Energy Metabolism cont’d
• Tolerance of O2 deficiency varies widely
• Obligate aerobes require O2 continuously
for survival (e.g. mammals)
• Facultative anaerobes can adapt to
anaerobic conditions for days or months
(e.g. brine shrimp embryos).
• Obligate anaerobes thrive in anaerobic
environments.
• Inhibited or killed in the presence of O2
• Archaea, bacteria (e.g. Clostridium), and
protozoa (e.g. Entamoeba)
Last time
• Cell Theory
• Physiological processes start at the cellular
level
• Cell parts and their functions
• ATP-generation
• Mitochondria
• Wrap up some concepts and continue
catabolism
2.8 Mitochondria & Energy Metabolism cont’d
• Metabolism under anaerobic conditions
• O2 deficiency forces cells to rely on
glycolysis.
• Pyruvate is reduced to lactate,
regenerating NAD+.
• Lactate accumulates in the tissues and
reduces pH.
• Lactate can be converted back to pyruvate.
Anaerobic conditions produce only 2 ATP per glucose molecule.

Aerobic conditions produce up to 32 ATP per glucose molecule.

Cellular and Molecular Physiology
Chapter 2,
part 2
2.10 Cytosol
• Cytosol - highly organized, gelatinous
mass surrounding organelles
• 55% of cell volume
• Functions:
• Site of intermediary metabolism (e.g.
glycolysis)
• Site of protein synthesis
• Storage of fat and carbohydrates
• Temporary storage of vesicles
2.12 Cytoskeleton: Cells’ “Bone and Muscle”
• Cytoskeleton provides intracellular
scaffolding to support and organize cell’s
components and control their movements.
• Three elements of the cytoskeleton:
1) Microtubules
2) Microfilaments
3) Intermediate filaments
2.12 Cytoskeleton cont’d
1) Microtubules
a) maintain cell shape
b) important in cell movements
c) position organelles
2.12 Cytoskeleton cont’d
1. Microtubules cont’d
b) Coordinate complex cell
movements
• Transport secretory vesicles
using molecular motors
• Dynein
• Kinesin
2.12 Cytoskeleton cont’d
1. Microtubules cont’d
b) Complex cell
movements cont’d
• Cilia and flagella
• “9 + 2”
arrangement of
microtubules
• Sliding of dynein
doublets
• Formation of mitotic
spindle
2.12 Cytoskeleton cont’d
2) Microfilaments
a Fxn in contraction
b)
c)
b Also act as mechanical
stiffeners
2.12 Cytoskeleton cont’d
2) MF cont’d
• Contractile
systems
• Actin/myosin
interactions
• Contraction
of muscle
cells
• Cytokinesis
(shown at
left)
2.12 Cytoskeleton cont’d
2) Microfilaments cont’d
• Complex actin-based assemblies for cell
locomotion
• Amoeboid movement
(e.g. white blood cells)

Pseudopodia
2.12 Cytoskeleton cont’d
2) Microfilaments cont’d
• Mechanical stiffeners
• “Not pseudopodia”
• Cellular extensions (e.g. microvilli – next
slide)
Microvilli in small intestine
2.12 Cytoskeleton cont’d
3) Intermediate filaments
maintain cell structure and
resist mechanical stress.
2.12 Cytoskeleton cont’d
3) Intermediate filaments cont’d
• Neurofilaments strengthen
and stabilize axons.
• IFs in skeletal muscle cells
hold sarcomeres in register.
• Keratin filaments in skin
cells form an
interconnected network
among adjacent cells 
cell junctions…
2.13 Cell-to-Cell Adhesions
• Cells are joined by and to
• Cell adhesion molecules in plasma
membranes
• Extracellular matrix
• Secreted by fibroblasts
• Collagen provides tensile strength
• Elastin stretches and recoils
• Fibronectin promotes cell adhesion
• Specialized cell junctions
2.13 Cell-to-Cell Adhesions cont’d
• Specialized cell junctions:
1) Desmosomes
2) Tight junctions
3) Gap junctions
2.13 Cell-to-Cell Adhesions cont’d
1) Desmosomes
(adhering junctions)
• Anchor together two
closely adjacent
cells
• Abundant in tissues
subject to stretching
(e.g. skin, heart and
uterus)
• Associated with IFs
2.13 Cell-to-Cell Adhesions cont’d
2) Tight junctions
permeability
barriers
• Join cells in
epithelial sheets
• Prevent
materials from
passing between
cells
2.13 Cell-to-Cell Adhesions cont’d
3) Gap junctions -
communicating junctions
• Link adjacent cells by
connecting tunnels
(connexons)
• Movement of ions
through gap junctions
transmits electrical
activity
• Enable synchronized
contraction of muscle
(e.g. heart)
2.3 Methodology used to
understand gene regulation
• Molecular biology techniques
• Genome projects
• Deciphering the complete genetic sequence of a
species
• Genomics
• Reveals the connections between genes and cell
function
• Proteomics
• Discovering the functions of proteins
2.3 Methodology
• Immunofluorescence
• Fluorescent antibody is introduced into
an animal or a tissue slice
• Antibody binds to a specific protein
• Location of proteins
can be visualized
using a microscope.
2.3 Methodology
• Gene knockout
• Disruption of a specific gene in laboratory
animals
• Resulting physiological defects are studied
• E.g. MRP4-/- mouse
2.3 Methodology
• DNA Microarrays
• RNA from an organ is isolated and
fluorescently labeled complementary DNA
(cDNA) is generated.
• cDNAs are exposed to a gene chip onto which
thousands of different genes have been bound.
• Binding of cDNA to specific genes on the chip
produces a fluorescent signal and establishes
which genes were being transcribed in the
organ.
DNA microarrays
2.3 Methodology
• Databases
• Nucleotide sequences of related genes in
different organisms are similar.
• Genomic data and nucleotide sequences are
widely available using shared computer data
bases, e.g. Ensembl
2.3 Methodology
• Gene therapy
• Defects arising from mutated genes are
corrected by inserting normal genes.
2.3 Methodology
• Gene therapy
• Transgenic animals carry a gene inserted from
another species
2.3 Methodology
• Cloning
• Nucleus of a fertilized
egg is removed and
replaced with a nucleus
from an adult cell
(nuclear
transplantation)
• Clone is genetically
identical to its parent
2.3 Methodology
• Reprogramming differentiated cells into
pluripotent cells.
• Pluripotent embryonic stem cells have the
ability to become any cell type.
• Adult cells can be reprogrammed to form
induced pluripotent stem cells (iPSCs).