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-“All organisms are made of cells, and cells come from preexisting cells”.
-Scientific conclusion is that the first cell was formed from organic macromolecules in the ancient oceans. Since then, cells divide to generate more cells, supporting the idea that all living organisms have a common ancestry.
Domain Bacteria – bacteria living in normal conditions (prokaryotic, unicellular)
Domain Archaea – bacteria that live in extreme habitats (prokaryotic, unicellular)
Domain Eukarya – organisms with a true nucleus (eukaryotic, unicellular or multicellular)
when one atom pulls electrons stronger due to high electronegativity.
: It is the general idea among scientists, that simple inorganic chemicals reacted gradually to generate more complex organic molecules, finally evolving large molecules that supported the formation of the first cell.
Three long fatty acids are linked to glycerol (a three carbon compound). Fats are solid at room temperature while oils are liquid. This difference depends on the nature of tails. More kinks due to unsaturated carbons make it more liquid.
: Two long fatty acid chains (hydrophobic tails) are linked to glycerol. The remaining carbon on the glycerol is attached to a phosphate. This makes the head region very hydrophilic.
The highly hydrophilic head and highly hydrophobic tail in the same molecule give amphipathic properties to phospholipid molecules. Phospholipids are important components of biological membranes, which are phospholipid bilayers.
is a similar membrane network, but ribosomes are not found on it. It stores calcium for the cell, and produces lipids. Steroid hormones are produced inside smooth ER.
is like a stack of flattened plates. They receive proteins produced on rough ER in ER vesicles that join the cis face of Golgi, where they get tagged, package and shipped out of trans-face to 4 destinations (secreted outside, anchored to plasma membrane, lysosomes, back to ER).
are the centers of photosynthesis in all green plant and algal cells. They have an extensive membrane system carrying chlorophyll pigments to capture light energy that is used to make glucose from CO2. Theory of endosymbiosis explains the prokaryotic origin of chloroplasts.
Molecules require a tag/signal to be able to enter/exit (NLS for nucleus)
Actin filaments (microfilaments) -
-Recycle NAD+ so we don't run out and stop making ATP
-Fermentation produces lactic acid in animals
-Fermentation produces ethanol is single-celled organisms
Continuous with rough ER
Exocytosis is when vesicle membranes fuse with plasma membranes from the interior of a cell—in a way—to expose the inside of the vesicle to the outside environment; the contents of the vesicle are thus released.
Phagocytosis- Plasma membrane of a cell engulfs a “food” molecule or necessary particle
Receptor mediated endocytosis – Receptors bind to particles on the plasma membrane and then fold and pinch inwards creating a vesicle.
Actin filaments (microfilaments) - Movement
Microtubules - Movement
Microfilaments – Myosin (slides actin (microfilaments) like a treadmill/conveyor belt)
Microtubules – Kinesin (like a delivery truck [walks along microtubule] that carry’s vesicles)
Dynein walking- the motor protein Dynein changes shape with ATP, moving it across a microtubule doublet. One side of the doublet moves while the other does not causing the structure to bend, the back and forth of this bending motion is what propels cilia and flagella or has it “swim”
a. The Dynein arms, or “spikes” help bend the microtubule doublets, since they are connected it gives them the ability to “contract” the flagella and cilia’s movement.
fibrous and wound into thick cables. These intermediate filaments are used to maintain cell shape by resisting tension (pull), and are used to anchor the nucleus and some other organelles in place.
Amount of disorder
Polymerization reactions are endergonic and require energy to happen (e.g. Photosynthesis)
Breakdown reactions are exergonic and release energy (e.g. ATP to ADP+Pi)
ATP + H2O --------->ADP +Pi
Main exergonic reactions that provides energy for endergonic reaction.
Lots of energy between 2nd and 3rd phosphate group in ATP.
Enzymes have active sites that only accept specific substrates to facilitate transition states.Enzymes catalyze reactions by lowering the activation energy requirement. (Think about the bell curve)
Enzyme helpers – cofactors (metal ions), Coenzymes (organic molecules), Prosthetic groups (vitamins)*Remember prosthetic groups are irreversible. *
a. Cofactors: Reversibly bind with the enzyme.
b. Coenzymes: Reversibly bind with the enzyme.
i. Vitamin B
c. Prosthetic Groups: Irreversibly attached to the enzyme.
i. Vitamin A in the retina.
Allosteric inhibitors and competitive inhibitors but, dephosphorylation and other factors can also inhibit enzyme activity.
Feedback Inhibition can help conserve stores of energy when required products are already in abundance.
a. Where the enzyme keeps track of how many products are being synthesized, eventually if too many are detected one of the products will bind to the allosteric site and stop the reaction.
How does it help a cell regulate metabolic pathways?
Glycolysis: C6H12O6--->2ATP, 2NADH, 2Pyruvate
Pyruvate processing: Pyruvate--->CO2, NADH, Acetyl CoA
Citric acid cycle: Acetyl CoA ---> CO2, NADH, FADH2, ATP
Electron transport chain: NADH, FADH ----->NAD, FAD (oxidative the electrons lost are put in the electron transport chain ---->ATP)
Proton Motor Force.
Store high energy electrons in NADPH
2. Light independent reactions (calvin cycle) – Convert CO2 to simple sugar using ATP and NADPH
Photo-excitation is a photo-electrochemical process of electron excitation by photon absorption.
Photosystem II (PSII) fuels Photosystem I (PSI). PSII uses an electron transport chain to produce ATP.
PSI uses the electrons from PSII and stores them in NADPH. Both systems make products that are used in Calvin cycle.
It excites them with photo excitation.
Carbon fixation: RuBP + CO2----> 3-PGA
Reduction Phase: 3-PGA-----ATP+NADPH---> G-3-P
Regeneration Phase: G-3-P + ATP---> RuBP
Photosynthesis – CO2 + H2O ---light energy----> Sugars and O2
Write the net equation for respiration.
Aerobic cellular respiration- C6H12O6 + 6O2 -----> 6CO2 + 6H2O
Plasmodesmata- Plant cells have these direct connections to the plasma membrane and cytoplasm between cells.
Gap Junctions- animal cells connect with these protein that create channels between cells.
Signal receptors and lipid soluble signals. Ligands are molecules that bind to receptors.
. Signal attaches to G-protein.
Receptor changes conformation and binds GTP splitting into two parts.
In response to binding of G protein, Enzyme catalyzes reaction that makes a second message.
1. Hormone binds to cell surface receptor
2. Protein forms dimer; ATP an now bind and enzyme becomes active.
3. activated rec. kin. triggers a protein kin. phosphorylation cas. inside cell activating all
4. phosp. pro. kin. amplify and carry the message to targets where responses happen RAS activates and triggers phosphorylation of another protein.
Activation/inactivation of genes. Activation/inactivation of proteins. Secretion of hormones and enzymes. Opening/closing channels. Breakdown/Synthesis of proteins.
The end of signal transduction or feedback inhibition etc.
Cross talk is the interaction between signaling pathways. The cells integration of diverse signals it receives is cross talk.
Single cell organisms use Quorum sensing to communicate which is a species specific signaling that can diffuse through environments. Bacteria can do number of things with this, e.g. plaque in teeth by bacteria creating biofilms.
a. When a protein enters the ER it is folded, and the ER signal is attached, it is then sent to the Golgi through a vesicle where they will be tagged and transported into different destinations.
a. Reactions don’t occur “Spontaneously”, they require a starting push by an enzyme lowering the activation level for the reaction to occur.
a.Some inhibitors regulate enzymes by competing with substrates for the active sites.
Chromosomes that synapse or pair during meiosis and that are identical with respect to their genetic loci and centromere placement. In other words, a set of one maternal chromosome and one paternal chromosome that pair up with each other inside a cell during meiosis.
1. They use energy (ATP) to do cellular work
2. They are made of at least one cell (unicellular) or many cells (multicellular)
3. They carry genetic information in DNA, and process information (signals) from the environment
4. They support reproduction
5. They evolve as a population
“Species evolve over time, because certain heritable characters of some individuals make them more fitting to the surrounding, and they produce more offspring”.
how species on earth are related with each otherAll species in the world can be fit into branches of a phylogenetic tree.
All molecules are made of atoms.
Atom: Has a nucleus containing protons (positive charged) and neutrons (neutral). Number of protons tells the atomic number (what element it is).
. Remember that shell 1 can carry upto 2 electrons, shell 2 carries 8, and shell 3 carries 8. In an atom, the outermost electron shell is known as the valence shell. Valence shells try to share, gain or donate electrons to achieve stability. For example, if the valance shell has only 6 electrons, the atom tries to gain two more electrons to fill the shell to have 8 electrons (maximum number). If the valance shell has 1 electron, the atom tries to donate that electron to achieve stability.
Sharing valence electrons. Each covalent bond has two electrons, one from each atom.
Positive charged ion forms when an atom donates its valence electrons (= reduction)
Weak attractions between slightly positively charged hydrogen and a
slightly negatively charged atom like oxygen in a polar covalent bond.
The polarity of water molecules and hydrogen bonds help keep water as a liquid at room temperature, and also contribute to solubility (mixing) of substances in water.
Ionic compounds and polar molecules mix well with water => hydrophilic
Nonpolar molecules do not mix with water => hydrophobic
- Proteins (polypeptides) : polymers of amino acids joined by peptide bonds
- Nucleic acids : polymers of nucleotides, joined by phosphodiester bonds
- Polysaccharides : polymers of monosaccharides (sugars) joined by glycosidic bonds
- Lipids : small or large molecules with largely hydrophobic regions
Bonds formed by dehydration reactions can be broken down by hydrolysis (splitting and adding water and to break a bond)
– double stranded helix, each strand made of nucleotides A,T,G,C, pentose sugar is deoxyribose. Complementary base pairing is A – T with 2 hydrogen bonds, and G- C with 3 hydrogen bonds. Two strands of DNA double helix are parallel, but run in opposite directions making them “anti-parallel”. DNA is more stable, therefore the ideal material to store genetic information in chromosomes of all living organisms.
- is typically single stranded, contains A,U,G,C (note: U in place of T in RNA), and ribose as the pentose sugar. the molecule can form short double helices, resulting stem and loop secondary structures. Ribozymes are RNA with catalytic activities. The ability to carry genetic information, and the ability to catalyze reactions and to probably self replicate, prompt scientists believe that RNA was the first cell’s genetic material.
All carbohydrates have sugars as the basic unit, with the formula, CH2O.
Monosaccharide sugars are different from each other based on their number of C atoms, the arrangement of groups around these carbon atoms, and the ring or linear structure.
- link by glycosidic bonds to form di-, oligo- or polysaccharides.-like glucose are the major energy resource in cells to make ATP by cellular respiration.
have mostly identity-tag like functions by linking with other molecules like lipids and proteins.
two major functions. Storage (starch in plants and glycogen in animals),
and structural (Cellulose in plant cell walls, Chitin in insects and peptidoglycan in bacteria).
The strength and non-digestability of storage polysaccharides are due to the cross linking between polymers, and the type of glycosidic bond that connects monomers.
have limited functions in cells. DNA stores genetic information, while RNA are copies made to carry this information. RNA can be enzymatic too (ribozymes). DNA and RNA can’t do their expected functions without the help of proteins. To make chromosomes, replicate DNA, copy DNA onto RNA, and to regulate the gene expression, various types of proteins are necessary (think about all the proteins that work during DNA replication and transcription).
Fluid Mosaic Membrane Module
Regulates all materials entering and leaving the cell
All prokaryotes have a cell wall made of peptidoglycan, a structural polysaccharide.Prokaryotes may have flagella for movement, and fimbriae for attaching to surfaces.
is an extensive network of membranes attached to the nuclear envelope. It is called rough, because numerous ribosomes are located on it, producing proteins. (Note that all ribosomes are not attached to rough ER. There are lot of ribosomes floating in the cytosol too)
Cytoskeleton is the fibrous network of proteins inside the cell.
Its functions are 1) provides strength to the cell, 2) maintains and changes cell shape, 3) moves contents inside the cell, and 4) moves whole cells
-Actin microfilaments are the thinnest in diameter, for strength and movement
-Intermediate filaments are medium sized in diameter, just for strength, because they do not have polarity
-Microtubules are the largest in diameter, for strength and movement
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