Midterm 1: Chapters 2, 3, 4, 5, 8, 9 Flashcards
History of cells:
Hooke coins term “cell”; used early compound microscope
Leeuwenhoek observes animalcules; used spherical lens
Brown discovers nucleus
Schwann proposes that all animals/plants consist of cells that contain a nucleus
Virchow proposes that cells arise from cells
Cell theory (3 tenets):
All organisms consist of one or more cells
The cell is the basic structural and functional unit of life
Cells arise from the division of pre-existing cells
Cell functions: (4)
Organized system of molecules that carry hereditary info and direct production of cellular molecules
Generate energy for activity
Respond to external environment
Cellular reproduction
What is magnification?
Ratio of object as viewed : actual size
What is resolution?
Minimum distance between two points that can still be seen as distinct. The shorter the wavelength, the better the resolution.
Types of microscopy:
Bright field, dark field, phase-contrast, Nomarski/DIC, fluorescence, confocal laser scanning, TEM, SEM
Cell size:
Small to maximize SA-to-V ratio
Volume determines amount of chemical activity, SA determines amount of substance exchange
Some cells flatten or develop folds/extensions to increase SA
Basic parts of cell:
Plasma membrane, central region, cytoplasm
3 common shapes of prokaryotic cells:
Rod, spherical, spiral
Genetic material of prokaryotic organisms:
Info from individual genes is copied to mRNA, which instructs ribosomes to assemble proteins
Prokaryotic ribosome:
Consist of large/small subunits
Each contain 3 types of rRNA and 50+ proteins
Glycocalyx:
Polysaccharide layer around prokaryotic cells
Slime layer vs capsule
Protects from physical damage, desiccation
May help with adhesion
Where is chlorophyll located in photosynthetic bacteria?
Cell membrane
What are lamins?
Protein filaments that line the inner surface of the nuclear membrane
Nuclear pore complex:
Octagonally symmetrical structure composed of proteins called nucleoporins
Controls passage of material in/out
Function of nucleolus:
Ribosome subunit assembly
Eukaryotic ribosome:
2 subunits
May be attached to plasma membrane or be freefloating
Contains 4 types of RNA mcules and 80+ proteins
What kind of cells have large rough ERs?
One that make a lot of proteins for release
Lysosome:
Contains 30+ hydrolytic enzymes to break everything down
Only in animal cells
Derives enzymes from ER, body from Golgi
pH = 5
Tay-Sachs disease:
A lysosomal storage disease - enzyme is missing, substrate builds up
Microtubules:
Wall consists of 13 proteins
Composed of tubulin dimers (alpha and beta bound non-covalently)
1/plus end has alpha, 2/minus end has beta - dimers attach and detach more rapidly at 1 end
What are the motor proteins that walk along microtubules?
Dyneins and kinesins
Intermediate filaments:
Composed of intermediate filament proteins
Have specific protein composition for their tissues (unlike the others)
Size comparison of microtubules, intermediate filaments, microfilaments:
Largest, middle, smallest
Microfilaments:
2 polymers of actin wound in a helical shape
Does more stuff at 1/plus end
Involved in cytoplasmic streaming, muscle contraction, division of cytoplasm during division
What motor protein walks along microfilaments?
Myosins
What is a 9+2 complex?
Structure of flagella and cilia - 9 double microtubules surrounding a central single pair
How do flagella/cilia move?
Dynein slides tubules over each other
Formation of flagella/cilia:
Centriole (ring of 9 triple tubules) move to just under plasma membrane
2/3 of triplets grow to form 9 doubles
2 singles form without direct connection
Basal body:
Centriole that remains at the end of flagella/cilia
Specialized structures of plant cells:
Plastids, cell wall, central vacuole
Plastids:
Chloro, chromo, leuco (includes amylo)
Chloroplasts parts:
Stroma - the inside
Thylakoids - inside stroma, site of photosynthesis, contain chlorophyll
Grana - stacked thylakoids
Where does photosynthesis occur? Where are chlorophyll?
Thylakoid membrane inside chloroplasts
Plasmodesmata:
Perforations in cell walls that connects cells to each other to allow transport of ions and small molecules
Cell adhesion molecules:
Glycoproteins embedded in plasma membrane
Bind to specific molecules on other cells
Holds solid tissues together
Types of cell junctions: (3)
Anchoring, tight, gap
Anchoring cell junctions:
Welds adjacent cells together
Common in stretch/shear tissues (heart muscle, skin, organ linings)
Desmosome:
Type of anchoring cell junction where intermediate filaments anchor into cytoplasm
Adherens junction:
Anchoring cell junction where microfilaments anchor to cytoskeleton
Tight cell junctions:
Membranes of cells very close together
Proteins on outer surfaces fuse and form a network
Seals organ linings (stomach, intestine, bladder) - no leaking!
Gap cell junctions:
Hollow protein cylinders line up to form pipes that ions and small molecules travel through
Occur between almost all body tissues of same type
Allow heart muscle, uteran muscle to function as a unit
Extracellular matrix (ECM):
Proteins and polysaccharides secreted by cells in the ECM
Functions to support and protect
Forms the mass of skin, bones, tendons
Components of ECM:
Glycoproteins:
Collagens - high tensile strength and elasticity
Proteoglycans - small proteins attached to polysaccharides
Fibronectins - bind to receptor proteins in plasma membrane to attach cells to ECM
What determines the consistency of the ECM?
Number of interlinks between proteoglycans. The more links, the more water storage, so the more squishy.
Integrin:
Receptor proteins in plasma membrane that communicate between cytoskeleton and ECM
Characteristics of life:
Displays order Harnesses and utilizes energy Reproduces Exhibits homeostasis Responds to stimuli Grows/develops Evolves
Are viruses living or non-living?
NON LIVING. The characteristics of life that they exhibit are dependent on the ability to infect cells. They cannot independently reproduce.
Life is an emergent property.
Arises from simpler interactions
Reducing atmosphere hypothesis:
Oparin-Haldane hypothesis.
Primordial atmosphere consisted of H2O(g), H2, CO2, NH3, CH4 and almost no O2
These molecules have lots of electrons and hydrogens which would react to form larger and more complex organic molecules
UV light provided energy (no ozone layer yet)
Experimental support for reducing atmosphere hypothesis:
Miller-Urey experiment: put hydrogen, methane, ammonia, and water vapour in a closed system and exposed gases to electrode sparks - amino/lactic/formic/acetic acids and urea were formed
Deep sea vent hypothesis:
Hydrothermal vents that release superheated, nutrient rich water
Found near volcanoes and tectonic plates
Surrounded by extremophiles
Extraterrestrial hypothesis:
Murchison meteorite in 1969 found to contain important organic molecules
Clay hypothesis:
Monomers in layered, charged structure of clay allowed for easier polymer formation
Short nucleic acids and polypeptides have been synthesized in clay
3 key attributes of cells:
Membrane-bound compartment
System to store genetic info and to direct protein synthesis
Energy-transforming pathways to bring in energy
Protobiont:
Abiotically produced organic molecules that are membrane-bound
Advantages of membrane-bound compartment:
Allows for more complex metabolic reactions with higher concentration of key molecules
Central dogma of genetic information:
Info stored in DNA -> transcribed to RNA -> translated to production of proteins
Evolution of genetic info transfer:
Before ribosomes evolved, ribozymes could catalyze the formation of v short proteins
Enzymes evolve
DNA evolves after proteins become more complex
Ribozymes:
Thomas Cech discovers a group of RNA molecules that can catalyze reactions on precursor RNA that leads to their own synthesis
They can fold into specific shapes, which is critical for reacting with substrates
Advantages of enzymes over ribozymes:
Enzymes can work much faster
20 types of amino acids vs 4 nucleotides used to build proteins - specificity
Evolution of DNA:
DNA nucleotides formed when oxygen atom is randomly removed from RNA nucleotide. DNA is evolutionarily favoured.
Reasons DNA is better than RNA:
More chemically stable
Thymine replaces uracil
Double-stranded backup in case of mutation
Why is thymine better than uracil?
Cytosine often mutates into uracil. By replacing it with thymine, uracil can be recognized as a damaged cytosine.
Evolution of metabolism:
ATP evolves because simple redox reactions are wasteful - electrons removed in oxidizing reactions transferred to substances being reduced
Earliest evidence of life:
Stromatolites, 3.5 billion years
Layered rock that forms when microorganisms bind sediment particles together
Carbon composition of ancient rocks:
Indirect, non-fossil evidence, 3.9 billion years
During photosynthesis, organisms preferred to incorporate carbon-12 over others (carbon-13)
Deposits in sedimentary rocks with low C-13 indicates ancient microbes
Earliest forms of life:
Heterotrophs (obtain carbon from organic molecules)
Anoxygenic autotrophs:
Used compounds such as H2S and Fe2+ for electron donors
Evolution of -trophy:
Heterotrophs, autotrophs (anoxygenic, oxygenic)
Panspermia:
Hypothesis that life originated in space
Life arose too quickly to have been formed solely through abiotic processes
Extremophiles show it’s possible for organisms to survive in a dormant state in space
Fundamental common attributes of life on earth:
Cells made of lipid molecules in bilayer
DNA-based genetic system
System of info transfer
System of protein assembly
Reliance on proteins as major structural/catalytic molecule
Use of ATP as mcule of chemical energy
Breakdown of glucose through glycolysis to generate ATP
LUCA:
Last universal common ancestor.
Major characteristics of eukaryotic cells:
Membrane-bound nucleus, organelles
Chemical evidence of eukaryotes dates back to:
2.5 billion years ago
Evolution of energy-transforming molecules:
Endosymbiont theory.
Mitochondria from aerobic bacteria
Chloroplasts from cyanobacteria
Evidence to support theory of symbiosis:
*** complete for final - chapter 3
Endosymbiosis occurred in stages.
Aerobic respiration was developed first, then some cells went on to eat cyanobacteria
Horizontal gene transfer:
Proto-mitochondria and -chloroplasts lose redundant genes that were already present in nucleic DNA
Genes from both protos relocate to nucleus to centralize the info
Hypothesis for the origin of endomembrane system:
Derived from infolding of plasma membrane. Fused around DNA, made vesicles that would become ER and Golgi.
What allowed eukaryotes to become so large/complex?
They can generate much more energy bc of mitochondria
Aerobic respiration generates much more energy than anaerobic respiration
Fun facts about enzymes:
*** Chapter 4
Types of energy:
Kinetic
Potential
Isolated, open, closed systems:
Isolated does not exchange anything with surroundings
Closed exchanges energy but not matter
Open exchanges matter and energy (ex: ocean)
Living cells and the second law of therm:
Cells bring in matter/energy to maintain low entropy. As they become ordered, they increase the entropy of their surroundings. (Give off heat and less ordered metabolic byproducts)
Living cells are (isolated, closed, open) systems.
Open
Spontaneous reaction:
-ΔG. A rxn that takes place without outside help.
Reactions tend to be spontaneous if:
Products have less PE and are less ordered
Endothermic/exothermic rxns:
Endothermic reactions absorb energy. Products have higher PE.
Exothermic reactions release energy. Reactants have higher PE.
Free energy:
The portion of a system’s energy that is available to do work.
Gibbs free energy equation:
ΔG = ΔH - TΔS
___ G = ___ stability
Higher, lower.
Exergonic reactions reach equilibrium.
At maximum stability, a system has no capacity to do work. The more negative ΔG is, the closer it will go to equilibrium.
At equilibrium, ΔG = …
0
Metabolism:
The sum of all chemical rxns that take place within an organism
Exergonic/endergonic rxns:
Exergonic reactions release energy. -ΔG.
Endergonic reactions consume free energy. +ΔG.
Types of metabolic pathways:
Catabolic - energy is released when complex molecules break down.
Anabolic/biosynthetic - energy is consumed to build complex molecules.
Hydrolysis of ATP reaction:
ATP + H2O -> ADP + Pi (HPO4 2-)
ΔG = -7.3 kcal/mol
High free energy of ATP is due to:
Negative charge of products encourages hydrolysis (repulsion)
Releasing Pi allows more solvation, which is energetically favoured
Releasing Pi increases entropy because Pi has many resonance forms that are not available when bonded
Energy coupling:
Enzyme brings ATP to reactant mcule
Phosphate group is transferred to reactant
(ATP does not hydrolyze because water is not accessible)
Exergonic ATP breakdown and endergonic biosynthesis are coupled to produce an overall exergonic reaction
Regeneration of ATP:
Exergonic breakdown of complex mcules provides energy to combine ADP and Pi for an overall endergonic reaction
Enzyme terms from 4.4
*** Chapter 4
Induced-fit hypothesis:
Just before substrate binding, enzymes change their conformation (shape) to become even more precise in its binding
How do enzymes work?
Increase # of substrate mcules that attain transition states by:
bringing reacting molecules together
exposing reactant molecules to charges that promote catalysis (active site may contain ionic groups)
changing the shape of the substrate to mimic transition states
Conditions that affect enzyme activity: (5)
Concentrations, inhibitors, need, temp, pH
Enzyme and substrate concentration:
In the presence of excess substrate, LR = enzyme
Changing substrate concentration from low to high increases the rate at first (LR = substrate) but increase stops when enzyme is saturated (LR = enzyme)
Enzyme inhibitors:
Nonsubstrate mcules that bind to enzymes. Competitive/noncompetitive, reversible/irreversible
Competitive enzyme inhibitors:
Binds to active site and blocks substrate
Noncompetitive enzyme inhibitors:
Binds to enzyme (not on active site) and changes conformation, reducing its ability to bind to a substrate
Reversible inhibitors:
Binds weakly, function can return to normal
Irreversible inhibitors:
Binds covalently, completely disabled enzyme function
Can only be overcome if cell synthesizes more enzyme
Types of metabolic regulation:
Allosteric regulation, covalent modification regulation
Metabolic regulation:
Metabolites act as reversible activators and inhibitors to match cell’s needs
Allosteric enzyme regulation:
Regulatory mcules binds to allosteric site (not active site) to control enzyme activity.
High-affinity state (active) - enzyme binds strongly
Low-affinity state (inactive) - enzyme binds weakly or not at all
Feedback inhibition:
Product of reaction inhibits enzymes earlier on
Covalent modification enzyme regulation:
Some enzymes are completely active/inactive and need to be chemically modified by adding/removing phosphate groups through the action of protein phosphatases, protein kinases, and proteolytic cleavage.
Phosphorylation/dephosphorylation:
Adding/removing phosphate groups to regulate enzyme activity
Protein kinases:
Regulatory phosphate groups derived from ATP/nucleotides
Protein phosphatases:
Enzymes that carry out dephosphorylation
Proteolytic cleavage:
Some proteins are synthesizes in dormant, slightly longer states so they must be activated. Protease (enzyme) shortens proteins to activate them. (Ex: pancreas doesn’t want to be damaged by digestive enzymes)
Temperature’s effect on enzyme function:
Heat speeds up all chemical rxns.
High temps can cause denaturation - enzymes lose 3D structure and dies under excessive heat
pH’s effect on enzyme function:
Each enzyme has a pH optimum where efficiency peaks, usually when the external pH is near the pH of cellular contents
Fluid mosaic model (for membrane structure):
Membranes are not rigid - instead, they consist of proteins within a mixture of lipids with the consistency of olive oil.
Fluid - each half of the bilayer can wiggle and exchange parts with its half
Mosaic - membranes contain a variety of proteins
Integral proteins:
Suspended individually. They span across the membrane.
Peripheral proteins:
Attached to integral proteins or to cytoplasm-side membrane lipids.
Different types of cells contain different amounts of proteins/lipids.
Insulators have more lipid, less protein Electron transporters (protein complexes) have more protein, less lipid
Membrane asymmetry reflects differences in function.
yeah. that’s the whole card.
Evidence supporting fluid mosaic model:
Fluid: Frye and Edidin tagged membrane proteins of mice and men then fused them - colours mixed, indicating that proteins moved around
Mosaic: asymmetry indicated by freeze-fracture technique
Freeze-fracture technique:
Freeze membrane in liquid nitrogen (-196ºC)
Fracture with teeny knife
Observe split bilayer with electron microscopy
Bumps in the layers are proteins???***
Phospholipid:
Head group attached to 2 fatty acid chains (hydrocarbons)
Phospholipid head:
Glycerol linked to an alcohol or amino acid by a phosphate group
Which parts of phospholipids are polar/nonpolar? hydrophobic/hydrophilic?
Head group is polar and hydrophilic
Tails are nonpolar and hydrophobic
When added to aqueous solution, phospholipids assemble into:
Micelles, liposomes, bilayers
Which phospholipid formation is most likely and why?
Bilayer.
Hydrophobic effect causes tails to interact with each other and heads to associate with water
This arrangement is favoured because it has the lowest energy state
Effect of temp on bilayer fluidity:
When temp cools and lipid mcule movement lessens, phospholipids form a semi-solid gel. The more unsaturated, the lower the gelling temperature.
Effect of composition on bilayer fluidity:
Fully saturated fatty acids pack tightly - less fluid
Unsaturated acids are kinky (hehe) - more fluid
The more unsaturated, the lower the gelling temperature.
How do ectotherms maintain membrane fluidity?
Action of enzymes: regulating the abundance of denaturase through gene transcription controls fluidity
Denaturase:
Enzyme that catalyzes the removal of 2 hydrogens and the establishment of a double-bond between carbons, creating an unsaturated fatty acid. Controls membrane fluidity.
Sterols’ effect on membrane fluidity:
At high temps, they restrain lipid mcule movement
At low temps, they slow the transition to gel state
Cholesterol:
The best example of a sterol. It is only found in animals.
What happens when membrane fluidity is disturbed?
Low temps: changes permeability, inhibits function of membrane-bound enzymes
High temps: Ions (K+, Na+, Ca2+) leak and disrupt ion balance which leads to cell death
Function of membrane proteins:
Transport
Enzymatic activity
Signal transduction
Attachment/recognition
Integral membrane proteins:
Embedded in bilayer - includes trans-membrane proteins
Contain stretches of non-polar amino acids inside the membrane and polar ones on the exposed ends
Most span the membrane more than once
How can you tell if a protein is a transmembrane protein?
If a protein has stretches of 17-20 non-polar amino acids linked by polar ones, it’s probably transmembrane
Peripheral membrane proteins:
Do not interact with internal hydrophobic part of membrane
Held to membrane surface by non-covalent bonds
Can be part of cytoskelly
Composed of mixture of polar/nonpolar amino acids
Are peripheral membrane proteins polar/nonpolar?
A mixture of polar/nonpolar amino acids!
Passive transport is driven by:
Diffusion, which is driven by an increase in entropy.
High concentrations have ___ entropy.
Low
At maximum entropy:
Mcules release free energy
Define simple diffusion.
Movement of mcules across a membrane without a transporter
Rate of diffusion depends on:
Size, lipid solubility.
What kinds of molecules are more/less likely to diffuse?
Small, nonpolar molecules and amphipathic mcules diffuse easily and quickly
Small uncharged mcules (water, glycerol) diffuse quite quickly
Ions can’t even
Facilitated diffusion:
Transport with aid of transporter
Rate of facilitated diffusion depends on:
Concentration gradient
Channel proteins:
*
Rate of facilitated diffusion depends on:
Concentration gradient
Channel proteins:
*
