Biology – December Exam
Summary Notes Chapter 4 – Cell Theory
Magnification: image size/actual size.
Resolution (clarity): able to distinguish between adjacent objects.
Contrast: distinguishing different structures (enhanced with dyes).
Light microscope Electron microscope
Uses Light Electron beam
Resolution 0.2μm 2nm
Observes -Mitochondria -Lipids
-Most bacteria -Ribosomes
-Most plant/animal cells -Smallest bacteria
(also same as light microscope)
-Standard light -Transmission electron microscope: thin
Unstained sample: simple, inexpensive slices stained w/ heavy metals some
electrons scattered, others pass
but little contrast.
Stained sample: better contrast. through forming an image.
-Phase contrast: controls path of light to amplify
differences in light transmitted/reflected by -Scanning electron micrograph: sample
sample. Used for living, unstained cells. coated w/ heavy metal & beam scans
-Differential interference contrast: similar to surface to make 3D image.
above but used for viewing whole cells or larger
structures (e.g. nuclei).
-Fluorescence microscope: label particular type
cell/organelle (e.g. proteins).
-Confocal microscope: uses lasers to give 3D
Prokaryotic Cells Eukaryotic cells
Small Much larger
Simple structure Shape, size & organization vary
No membrane-enclosed nucleus DNA housed inside nucleus
Can have a small amount of internal organization. More complex compartmentalization.
Primitive cytoskeleton. Organelles in membrane bound
compartments. Allows rxns to occur that
might be incompatible & interfere with rxns
in other regions.
Bacteria: abundant, mostly not harmful
Archaea: less common, extreme environments Organelle Structure Function
Cell wall (plants) Provides support & protection.
Nuclear Double membrane enclosing nucleus. Helps protect and organize the
envelope Formed from endomembrane system. chromosomes.
Nuclear pore Passageway into/out of nucleus.
Nucleus Inner nuclear matrix proteins form -Contains genetic material (DNA).
meshwork organizing each chromosome -Site for ribosome assembly (nucleolus)
into its own territory.
Endoplasmic Membrane continuous with outer -Protein secretion & sorting (Rough ER)
reticulum membrane of nuclear envelope. -Lipid synthesis (smooth ER)
Membrane of network forming fluid- -Metabolic
filled tubules (cisternae).
Golgi apparatus Stack of flattened, membrane-bound Modification/processing, sorting and
compartments, not continuous with the secretion of proteins. Glycosylation.
Mitochondrion Have outer and inner membranes Site of ATP synthesis
– Intermembrane space
– Mitochondrial matrix
Lysosomes/ -Breakdown of macromolecules,
vacuoles -Autophagy (recycling thru endocytosis)
-Storage, accumulation of water
Peroxisomes Small & found in all eukaryotic cells. Catalyze reactions, breaking down
peroxides and other toxic molecules.
Ribsomes Synthesize polypeptides – involved in
Plasma Phospholipid bilayer. Acts as a barrier. Controls movement of
membrane Semi-fluid mosaic. substances in and out of cell (semi
-Cell signaling and cell adhesion.
Cytoplasm Contains everything inside plasma Contains enzymes for metabolism.
membrane (including organelles).
Cytosol Milieu surrounding organelles inside Site of many metabolic activities of
plasma membrane. . eukaryotes.
Outside plasma membrane:
Pili: attach bacteria to surfaces and to each other.
Flagella: enable movement (locomotion) & swimming.
Cell wall: provides support and protects cell from damage and bursting.
Glycocalyx: outer gelatinous covering that traps water & provides protection.
Cytosol is central coordinating region for many metabolic activities.
Catabolism: breakdown of molecule into smaller components.
Anabolism: synthesis of cellular molecules and macromolecules. Cytoskeleton
Mutations of CS proteins often lead to disease. Three types of protein filaments:
Microtubules Intermediate filaments Actin Filaments
Structure Hollow tube Twisted filament Spiral filament.
Location Attached to Around nucleus. Near cell membrane.
Protein Tubulin Keratin, desmin, lamin… 2 intertwined actin strands.
Function -Cell shape -Cell shape -Cell shape
-Organelle organization -Mechanical strength -Muscle contraction
-Chromosome sorting -Anchorage of cell & -Cell movement
-Cell motility (flagella) nuclear membraines - Animal cell division
Myosin is a motor protein that uses ATP to walk along actin filaments.
What is needed for movement: actin, myosin, ATP!
Use ATP to promote movement.
-Head, hinge and tail.
Three kinds of movement:
– Moves cargo along cytoskeleton.
– Motor protein remains in place and moves filament.
– Motor protein attempts to walk (both the motor protein and filament restricted in
their movement), exerting a force causing filament to bend. Chapter 5 – Systems Biology
Living organisms studied in terms of their underlying network structure to
understand how cell organization arises by complex interactions between various
components and parts.
Genomes, Proteomes and Cell Structure & Organization
Genome: complete collection of organism’s DNA.
Proteome: entire collection of proteins that cell makes, responsible for structure
and function. All cells have IDENTICAL DNA but DIFFERENT proteomes.
o Gene regulation makes proteome dynamic
Amounts of proteins vary in different cells = specialized.
Cells can respond to changes in environment.
o Protein-protein interactions
Guided by sorting signals – direct proteins to correct location.
Very specific allow organizational structures to be built.
o Continual synthesis/breakdown of molecules
Enzymes break down proteins into their amino acids.
Molecular Machines (e.g. flagella, ribosome)
Moving parts & does useful work
Provide structure & organization to cells
Allow cells to perform complex processes
E.g. ATP synthase
o Forms due to molecular recognition
Subunits recognize each other and bind in a specific way
Attaining Structure in Cells
Cell uses the following to survive by responding to changes in its environment OR
diving into 2 cells:
Genome (provides info. to make mRNA and proteins)
Lipid synthesis in ER
2 fatty acids + 2 activated molecules (CoA) + glycerole-phosphate
o ER nuclear membrane
Transported via vesicles
o Bud of ER, fuse with Golgi
Lipid exchange proteins The Cell is a System with Four Major Components
1. The nucleus
Protects DNA from damage, replicating & packaging DNA for cell division
Using DNA to make RNA and processing RNA
Organization/protection of chromosomes
2. The cytosol
Coordinates response to environment
o Changing expression of genes in the nucleus
Synthesis of proteome (major site of translation)
Organization/movement via cytoskeleton and motor proteins
3. Semi-autonomous organelles (contain own genetic material)
Mitochondria (ATP synthesis) & chloroplasts (photosynthesis)
4. Endomembrane system
Network of membranes enclosing the nuclear envelope, ER, Golgi, lysosomes,
peroxisome, vacuoles & including plasma membrane.
Does not inlclude materials within nucleus.
Very dynamic – structure changes over time
Transport via vesicles amongst various compartments
o ER Golgi plasma membrane
Sorting signals: short stretches of amino acid sequences - direct proteins to correct
Most eukaryotic proteins begin synthesis on ribosomes in the cytosol.
No sorting signal if they are to stay in cytosol (e.g. plant NADHK)
Cotranslational: to ER, Golgi, lysosome/vacuole or plasma membrane.
o ER retention signal recognized by SRP so translation is paused.
o Other proteins transported by vesicles
Coat proteins = specificity & help vesicle bud off.
V-Snares, recognized by t-snares in target membrane.
Post-translational: nucleus, mitochondria, chloroplast, peroxisomes.
SRP – signal recognition particle
1. SRP binds to ER signal sequence, pausing translation.
2. SRP binds to receptor in ER membrane.
3. SRP released and translation resumes. Growing polypeptide threaded into
channel protein directely into ER lumen. 4. Protein completely formed and released into ER lumen.
Large molecules have finite life times (EXCEPT DNA)
Half life: time for 50% of molecules to be broken down)
o Prokaryotic mRNA 5 min.
o Eukaryotic mRNA 30min – several days
Cytosolic enzymes: degrate RNA, polysaccharides & lipids
Proteases: recognize proteins and take them to proteasome
o Ubiquitin directs unwanted proteins to proteasomes
o Degraded by proteases into peptides and amino acids
o Targets misfolded proteins.
o Critical for environmental response.
Provides strength, support, organization and cell signaling.
No sorting Post-
Synthesis halts until
ribosome is bound
to ER After protein is
Stay in cytosol •Lysome/vacuole
•Plasma membrane Sorted to
Polypeptide • Mitochondria
containes ER • Chloroplasts
retention signal • Peroxisome Proteome
Gene Protein- Continual
regulation protein synthesis/b
Amountsof Cells respond to Guided by
proteins environmental sorting Very Enzymes
vary changes signals specific
Chapter 6 – Membrane Structure and Transport
6.1 Membrane Structure and Composition
Lipids Proteins Carbohydrates
Amphipathic Integral Cholesterol found only in
Form basic matrix Peripheral
Hydrophobic, non-polar fatty
acyl tails (faces interior)
Hydrophilic, polar head
-Move laterally relative to
-Rotate freely along axis.
-Only flip with aid of flippase.
Two leaflets of phospholipid bilayer are highly asymmetrical.
More fluid Less fluid
Shorter acyl tail (less likely to interact) Longer tail
Double bond (creates kink) No double bonds (saturated)
Cholesterol: makes membrane more Cholesterol: makes membrane less fluid
fluid at low temps. at high temps. Glycosylation
Involves covalently attaching carbohydrates to:
o Lipid: glycolipid.
o Protein: glycoprotein.
Recognition signals for other cellular proteins
Cell surface regulation (migration of individual cells)
Protective: cell coat (glycocalyx carbohydrate rich zone shielding cell)
TEM (transmission electron microscopy) FFEM (freeze fracture electron microscopy)
Thin sectioned sample Specialized TEM
Stained with heavy metal dyes Analyze interior of bilaryer
Dye binds well to polar head groups Sample frozen then fractured, leaflets
but not nonpolar tails separate
Good 3-D detail.
The Phospholipid Bilayer as a Barrier
Hydrophobic interior prevents hydrophilic molecules from passing freely.
Movement of solute from region of higher concentration to lower concentration
-Passive: w/o transport protein
-Fast (gases and uncharged polar molecules)
Slow (ions, larger polar molecules – sugars & amino acids, macromolecules)
Cells maintain gradients
1. Transmembrane gradient: conc. of solute is higher on one side of membrane.
2. Ion electrochemical gradient: both an electrical AND chemical gradient.