Biol 1610 Final

compartmentalization of eukaryotic cells

-Achieved through use of membrane-bound organelles and endomembrane system -Compartmentalization enables specialization

What are two purposes of having multiple steps in the transduction cascade?

-Enables amplification of the signal -Enables fine tuning of the response -It lets different cells respond differently to the same signal.

where are glycoproteins made

glycoproteins are synthesized and modified within two membrane-bound organelles in the cell, the rough endoplasmic reticulum and the Golgi apparatus. •Primary function of glycoproteins is cell-cell recognition -part of the ECM

Entropy

evolution of complex organisms does not violate the second law of thermodynamics -the total entropy of the universe increases (due to breakdown of complex molecules during digestion) even though regions within the system (organized cells) exhibit decreased entropy. -But, Maintaining this order requires a constant input of energy •If the energy is removed the organization is quickly lost -Decay of dead organisms •What is the ultimate energy source driving life on earth? •How is this energy transformed into a useable form?

Glycolysis summary

-Kinase(use ATP to phosphorylate an intermediate) -Isomerase(change shape of a molecule) -Dehydrogenase(remove H's, with e-'s (redox rxn)) Do need to know names of start and end compounds (glucose, G3P, pyruvate), track # of C's generally in process (6C to 3C), track high E e- transfer and generally know when ATP is used and when it is made.

understand why carbon is the backbone of life

-Most common binding partners of carbon are: H,O,N,S,P -has a valence of 4 and forms strong covalent bonds with its binding partners

energy flows through ecosystems

-Nutrients are recycled through organisms (this recycling requires energy) (energy is not recycled, it flows linearly. Life required constant input of new energy) -Energy is a one-way flow from sunlight to producers to consumers (entering as light and exiting as heat) -Cycling of nutrients - nutrients are recycled within the system through catabolic reactions (break things down - releases energy) & anabolic reactions (build complex molecules from simpler components - takes energy to complete) -One way flow of energy - from sunlight to organisms to heat. -Photosynthesis transforms light energy into chemical energy which is used to do cellular work

-reductionism

-Reductionism is a powerful tool for understanding how life works, but it cannot explain all one observes in a complex system because when parts are organized into complex systems, new properties emerge that were not present in the individual components. -Reductionism identified the important parts in a system but may miss emergent properties

membrane fluidity

-Saturated fatty acids make the membrane less fluid (more solid) than unsaturated fatty acids •"Kinks" introduced by the double bonds keep phospholipids from packing tightly together •Most membranes also contain sterols such as cholesterol, which can either increase or decrease membrane fluidity, depending on the temperature ("cholesterol acts as a fluidity buffer") -Membranes are more fluid at warmer temperatures and more solid at colder temperaturses •Cholesterol maintains normal fluidity despite temperature changes •Cold tolerance in bacteria is due to presence of fatty acid desaturases Cholesterol 'buffers' membrane fluidity: It maintains normal fluidity despite changes in temp •As temperatures cool, membranes become more solid (less fluid). The solidification temperature depends on the types of lipids in the membrane. -Membranes with more saturated FA's will harden sooner -Cells can change the ratio of saturated/unsaturated FAs •The cholesterol level also affects membrane fluidity at different temperatures -At warm temperatures (such as 37 C), cholesterol restrains movement of phospholipids (keeps the membrane from "melting") -At cool temperatures, it maintains fluidity by preventing tight packing (keeps the membrane from solidifying too much) •Membranes rich in unsaturated fatty acids are more fluid than those rich in saturated fatty acids (why?) •Membranes must be fluid to work properly; they are usually about as fluid as salad oil. (membrane proteins add structure)

Scientific method

-Scientific method steps: Make an observation, form a question, form a hypothesis (a testable explanation of a phenomenon) (make a prediction based on the hypothesis...if-then), design an experiment to test hypothesis (collect and analyze data), draw conclusion (reject or accept hypothesis) (repeat steps). -Hypotheses must be testable and falsifiable. Science can only answer these types of questions. -Pseudoscience draws conclusions first, and then seeks facts to support it. It uses the the scientific method wrong. -Good science is always open to being disproven. Pseudoscience balks at people questioning it and distorts the process to try to prove a predetermined conclusion. -Controlled experiments to help eliminate alternative hypotheses

characteristics and domains of life

-The characteristics of life are: growth (development and reproduction), metabolism (uses energy), sensitivity (responds to its environment), complex organization, maintains homeostasis, adaptable (evolves over time), made up of cells. -Cells are the smallest unit of life. It is the lowest level of organization that can perform all activities required for life. -3 domains that classify life are: Bacteria (prokaryotic - small simple cells, diverse, many kingdoms, most diverse and numerous organisms on earth, essential for life on earth), Archaea (prokaryotic - with some eukaryotic-like characteristics, pseudomurein cell walls, unique phospholipid membranes, live in extreme environments [salty lakes, boiling water, etc.]), Eukarya (eukaryotic - large, complex cells, often complex multicellular organisms[4 kingdoms - plant, animal, fungi, protists]). -Cell theory: 1. All living things are composed of cells, all cells come from preexisting cells, cells are the basic unit of life, cellular structure relates to function. -4 characteristics shared by all cells: enclosed by a membrane, use DNA as their genetic material, contain cytoplasm, contain ribosomes.

How can the same signal cause different responses in different types of cells?

-Transduction pathway -Is the cellular response the same for a particular signal in every cell? No. Response can vary depending on the receptor and the transduction pathway, and interactions with other signaling pathways. Different cells may have different downstream effectors that get turned on, and therefore will show a different response

pH scale

-pH= -log [H+] -Increased [H+] = more acidic -Decreased [H+] = more basic -Neutral solution = [H+]= 1 x 10^-7, [OH-]= 1 x 10^-7 -Example: At pH 6, [H+]= 1 x 10^-6 & [OH-]= 1 x 10^-8 -If pH=12, what is the [OH-]? [OH-]= 1 x 10^-2 -Weak acids make excellent buffers because they can either donate or use up H+ depending on conditions, thus they can prevent large changes in [H+] -Buffers typically consist of a weak acid and its corresponding base

What type of response do membrane soluble ligands (like steroids) usually cause in cells?

-regulate gene expression

The importance of cell membranes

1- they isolate specialized sets of proteins to form organelles (that have specific functions) (sequestration and specialization) •The proteins in each membrane and contained in the lumen are what make organelles different from each other 2- they regulate what comes in and out of the cell(concentration and diffusion) •Since they are semipermeable -Active and Passive Transport mechanisms 3- they determine how cells attach to each other (cell junctions) -What is its purpose? •Selective barrier to keep things in or out: Semipermeable barrier •Membranes allow for Sequestration, concentration, diffusion, specialization

G-protein coupled receptors (GPCRs)

1.G-protein-coupled receptor (GPCRs) are the largest family of cell-surface receptors •work with the help of a G protein (a small peripheral protein that binds GTP) •G proteins act as an on/off switch: for example: the G protein is active when GTP is bound and inactive when GDP is bound (or vice-versa) - GPCRs are a common type of receptor with numerous functions: Embryonic development, sensory (vision, smell, taste.) -GPCRs are Affected in numerous diseases (cholera, pertussis, botulism) -Estimate 60% of pharmaceuticals act through G protein coupled pathways

primary, secondary, tertiary and quaternary structure of proteins

1o protein structure (primary): the sequential order of amino acids in one protein chain (polypeptide) What is this order determined by? The information in the DNA (order of nucleotides in a gene) 2o protein structure (secondary): folding due to interactions of polar groups in the backbone structure of the polypeptide chain. (due to hydrogen bonds b/t backbone groups) α helices, β sheets, disordered regions, turns etc. 3o protein structure (tertiary): 3D folding due to covalent and noncovalent interactions of amino acid R groups in the polypeptide chain. (due to R group interactions) 3o structure is the critical unique 3D shape of each protein"Shape determines function" 4o protein structure (quaternary): the interaction of more than one peptide chain to make the final functional protein All proteins have 1̊ ,2̊ and 3̊ structure, (ex. Actin, keratin, insulin) Some proteins also have 4̊ structure, ex) hemoglobin

Receptor tyrosine kinases (RTKs)

2. Receptor tyrosine kinases (RTKs) (also called enzyme linked receptors) RTKs are kinases and also membrane receptors. When they bind ligand they first dimerize. This activates their kinase function and they phosphorylate each other. They then phosphorylate molecules to activate the transduction cascade. -What does it mean to phosphorylate? -Which amino acids get phosphorylated? •Those with -OH containing R groups (ser, thr,tyr). RTKs phosphorylate Tyrosine residues. •RTKs activate complex signaling pathways -A receptor tyrosine kinase can trigger multiple signal transduction pathways at once -RTK signaling is often involved in stimulating cell growth (so their ligands are called growth factors) •Abnormal functioning of RTKs is associated with many types of cancers -Abnormal RTK signaling results in abnormal cell growth **Ligands are often growth factors. Often involved in cancer (R is on without a ligand) -The transduction step in RTK signaling often triggers a Phosphorylation Cascade. (MAP kinase cascade) Mitogen Activated Protein kinase) (Mitogens are signals that cause cell dvision) -signals cell growth and cell division -Uses a phosphorylation cascade to transduce the signal -Result is Large signal amplification -(small amount of ligand activates many kinases) -Kinases phosphorylate substrates -Phosphatases dephosphorylate substrates -Insulin receptor is an RTK

Ligand-gated ion channels

3. Ligand gated ion channels -These receptors are ion channel proteins that open when ligand binds them. The change in cytosolic [ion] triggers the response •A ligand-gated ion channel receptor acts as a gate when the receptor changes shape • When a signal molecule binds as a ligand to the receptor, the gate allows specific ions, such as Na+ or Ca 2+, to flow through a channel in the receptor • - very important in nerve signaling and muscle contraction, egg fertilization

difference between Theory and hypothesis

A theory is broader in scope than a hypothesis and are supported by lots of evidence and many different types of experiments. -A long standing hypothesis eventually becomes accepted as a theory -Scientific theories are based on numerous experiments from a wide variety of fields -Inductive reasoning often used to form hypotheses, deductive reasoning used to make predictions to test hypotheses by experiment (if-then statements use deductive reasoning)

The Extracellular Matrix (ECM) of Animal Cells

Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM)made up of proteins such as collagen, fibronectin and proteoglycans. Many of these proteins are modified by adding carbohydrates to them. Review: where are glycoproteins made? How do they get delivered outside the cell?ECM proteins bind to receptor proteins in the plasma membrane called integrins (which connect to the actin cytoskeleton inside the cell) Primary function of glycoproteins is cell-cell recognition-each cell type has specific types of sugars added so cells can recognize each other. Like a "uniform" for other cells to see. •Most cells are required to be attached to ECM in order to live. This connection to the actin cytoskeleton through integrin transmembrane proteins provides feedback that enables cells to live (prevents apoptosis)

Biological hierarchy

Atoms, Molecules, Organelles, Cells, Tissues, Organs & Organ Systems, Organism, Population, Community, Ecosystem, Biosphere

Cell communication steps

Communication between cells requires: -Step 1 (2) Reception: Ligand -signaling molecule (usually from another cell) which binds to a Receptor protein (has a specific shape to bind a particular signal) -Step 2 (3) Transduction: Interaction of ligand+Receptor initiates the process of signal transduction, which uses a series of transduction molecules which amplify the signal and result in -Step 3 (4) Response: the target cell does something new

Linker step

Conversion of pyruvate to Acetyl CoA Input: one 3C pyruvate Output: one 2C Acetyl coA, one CO2, one NADH This is the first formation of CO2 1 C (in each pyruvate) is oxidized to CO2, making NADH, and Acetyl CoA (2C) Occurs in mitochondrial matrix

Lysosomes

Digest: - Old organelles -Other cell structures (like membrane receptors) -Incoming "food" from outside the cell Digested materials can then be reused by the cell •Membrane-bounded digestive vesicles •Arise from Golgi apparatus •Enzymes catalyze breakdown of macromolecules •Digestion and recycling take place here •Destroy cells or foreign matter or food that the cell has engulfed by phagocytosis or endocytosis •Lysosomal enzymes operate best at acid pH •Compartmentalization enables this!!•Taysach's disease (and others) are due to lysosomal defects causing buildup of byproducts and waste in cells

redox rxns

During redox reactions, energy is carried from one molecule to another by movement of electrons This energy transfer via electron flow is what allows cells to extract E from organic molecules (food) and eventually use it to produce ATP (by oxidative phosphorylation)

Endocytic pathway

Incoming vesicles fuse with lysosomes Phagocytic vesicles fuse with lysosomes. Digested materials can then be used by the cell

Calvin cycle

Input: 3CO2, and ATP &NADPH from light rxns Output: 1 3C sugar (G3P) every 3 turns(6 turns can make 1 glucose) 1 C is "fixed" each turn: 3 turns incorporate enough carbon to produce a new G3P 6 turns incorporate enough carbon for 1 glucose synthesis step: calvin cycle uses products of light rxns to make sugar by reducing CO2 ATP and NADPH made in light rxns get used to reduce CO2 and form sugar Rubisco is the enzyme that catalyzes addition of CO2 onto RuBP Input: ATP, NADPH, CO2 output: (NADP+, ADP) sugar •Carbon enters the cycle as CO2 and leaves as a 3C sugar named glyceraldehyde 3-phospate (G3P) •For net synthesis of 1 G3P, the cycle must run three times, (fixing 3 molecules of CO2) -Must cycle 6 times to generate 1 glucose •The Calvin cycle has three phases 1-Carbon fixation (catalyzed by rubisco) 2-C Reduction (uses ATP and NADPH) 3-Regeneration of the CO2 acceptor (RuBP) (uses ATP)© 2011 Pearson Education, Inc.

how do integral proteins get embedded in membranes

Integral membrane proteins, also called intrinsic proteins, have one or more segments that are embedded in the phospholipid bilayer. Most integral proteins contain residues with hydrophobic side chains that interact with fatty acyl groups of the membrane phospholipids, thus anchoring the protein to the membrane

Electron transport chain

TAKES PLACE IN INNER MITOCHONDRIAL MEMBRANE NADH donates e-'s to complex I.Which complex does FADH2 donate to? Both complex I and II deliver e-'s to coenzyme Q Coenzyme Q is a hydrophobic molecule (not a protein), diffuses thru the membrane from complex I or II to III. Complex III, IV:Series of cytochromes thatContain Fe (iron)

Kinetic and Potential Energy

Know kinetic energy is energy of motion and potential energy is stored energy (as in energy stored by position like when you are at the top of a hill). Energy stored in chemical bonds is potential energy (because it is based on the position of the molecules with respect to each other). Chemical energy stored in bonds can be transferred thru chemical reactions, such as photosynthesis and cellular respiration. •Kinetic energyis energy associated with motion -Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules •Potential energy is energy that matter possesses because of its location or structure -Chemical energy is potential energy available for release in a chemical reaction -This Potential energy, is stored in the chemical bonds of molecules. When bonds are broken, this E can be used to do work

Citric acid cycle (Krebs cycle)

Kreb's cycle summary:3 phases 1- acetyl transfer to form citric acid 2- oxidation 3-regeneration of oxaloacetate start and stop with ocaloacetate At this point (end of citric acid cycle) Glucose has been fully oxidized to produce: -6 CO2 -4 ATP -10 NADH -2 FADH2

Fluid Mosaic Model

Membranes are about half phospholipids and half proteins. Different membranes contain different types of phospholipids and also different types of proteins.

Emergent properties

New properties emerge at each level as complexity increases -Emergent properties are new functions resulting from organization and interaction of parts within a system. -Both living and nonliving things can exhibit emergent properties. -Life is an emergent property. -Each level of biological organization exhibits new emergent properties that result from interaction or organized parts.

what is reduced and oxidized in cellular respiration

OXYGEN IS REDUCED CARBON IS OXIDIZED During cellular respiration, the fuel (C in glucose) is oxidized (to CO2), and O2 is reduced (to H2O)

Which organelles are part of the endomembrane system?

Organelles with only a single membrane are part of the endomembrane system. ER (smooth and rough) Golgi Lysosomes Peroxisomes Vesicles Organelles with a double membrane are not part of the endomembrane system. (They still contain unique sets of proteins but these proteins are delivered by different mechanisms, not discussed in this class) Nucleus Mitochondria Chloroplasts

Exocytic pathway

Outgoing vesicles fuse with cell membrane This is how cells secrete specific products

Photo step

Photo step: light rxns generate ATP and NADPH (through photosystem I and II) What is the role of water? (The light energy is used to split water and release e-'s, making O2 as a byproduct. The energy in the e-'s is captured by electron transport chains of PSII and PSI) Input: light, water, CO2 output: ATP, NADPH, O2 The final electron acceptor in this ETC is P700+ in PSI -Who is the final electron acceptor in the ETC used in photophosphorylation? -PSI (p700) -How do these low E e-'s become high E to enter the 2nd ETC? -By absorbing a photon of light in PSI (p700) -Who is the final e- acceptor at the end of the second ETC? -NADP+ (becoming NADPH) -Does NADPH deliver its e-'s to an ETC? -NO- it's e-'s will be used to reduce C in the Calvin cycle -How did the low E e-'s in chlorophyll/water become high E e-'s? -By absorbing photon of light in PSII

Photosynthesis summary

Photosynthesis takes place in chloroplasts, in the membranes of the thylakoids (light rxns) and in the stroma (calvin cycle)

ΔG =change in free energy

Remember that spontaneous reactions are not necessarily fast reactions. Enzymes are important in biology because they speed up the rate of reactions by lowering the activation energy required (by lining everything up on optimal positions for a reaction to occur)(fig 8.13, 8.15)

importance of surface area to volume ratio

Small cells work best -Volume increases much more rapidly than radius as cells get bigger. V = 4/3 pi(r3) -Diffusion is very efficient over small distances. Not so over large distances-. -Cells need surface area to absorb nutrients and interact with environment Therefore cells are small to maximize surface area, but minimize volume

What is the purpose of cellular respiration

The Purpose Cellular Respiration. Cellular respiration is the process by which cells in plants and animals break down sugar and turn it into energy, which is then used to perform work at the cellular level. The purpose of cellular respiration is simple: it provides cells with the energy they need to function.

cytoskeleton

The cytoskeleton is a network of fibers that organizes structures and activities in the cell The cytoskeleton extends throughout the cytoplasm 1) It organizes the cell's structures and activities Holds organelles in correct place in the cell Provides a network of roads and girders to move things around in the cellAdds strength and maintains cell's shape 2) interacts with motor proteins to produce motility Inside the cell, vesicles travel along "monorails" provided by the cytoskeleton (like cars on a road)- dynein and kinesin move on microtubulesActin/myosin contraction (muscles) Cell crawling: actin is built and degraded to directionally move the cell membrane 3) Recent evidence suggests that the cytoskeleton also helps regulate biochemical activities ( ie, it is participates in cellular communication)

Non-Membranous cellular structures

These cell components are not membrane bound: Ribosomes (in the cytosol) Small molecular machines made up of rRNA and many proteins. (where are ribosomes constructed?) Function to make proteins for the cell (by process called Translation) Cytoskeleton(microfilaments, microtubules, intermediate filaments) (in the cytosol) Function to give cell structure and movement -centrosomes-microtubule organizing centerIn animals: contain 2 centrioles Chromosomes(chromatin-DNA) (in the nucleoplasm)

Why are integral proteins important

They have many functions: -receptors -transporting molecules across membrane -cell adhesion

What are transcription factors?****

Transcription factors bind DNA and turn genes on or off •If the cellular response requires activation of a new gene, then the final activated molecule in a signaling pathway will be a transcription factor (TF) -TF's bind to DNA and turn on (or off) genes which ultimately changes the activity of the cell by changing its proteins. •What is a transcription factor? What is its purpose? -Protein that binds DNA and turns on (or off) specific genes to change cell function

differences between a prokaryotic and eukaryotic cell

Type 1: Prokaryotes •"prenucleus" No nucleus (do have DNA, but no histones) •No membrane bound organelles-Do have ribosomes •Usually have a cell wall made of peptidoglycan •small, simple cells: bacteria and archaea-Even though they are simple, bacteria are the most diverse type of life and are essential for life on earth-Usually unicellular organisms •Divide by binary fission- Type 2: Eukaryotes •Have a "true nucleus." DNA is contained in a nuclear membrane, use histone proteins to package DNA •Also have many other membrane enclosed organelles (lysosomes, mitochondria, etc) •Large, complex cells (ex: mammals, plants) •Often multicellular organisms •Divide by mitosis

ATP is energy currency of cells

Understand that ATP is the energy currency of cells because the potential energy stored in its phosphate bonds can be used to drive other reactions. (ie, the release of energy from cleaving phosphate bonds can be coupled to the requirement for energy in anabolic reactions)

Fermentation

high levels of NADH signal cells that there's not even o2 and switch to fermentation Fermentation: Purpose: to regenerate NAD+ so glycolysis can continue to produce ATP (even in the absence of oxygen) •Fermentation is the process of Reducing organic molecules in order to regenerate NAD+1. Ethanol fermentation occurs in yeast-CO2, ethanol, and NAD+ are produced2. Lactic acid fermentation-Occurs in animal cells (especially muscles)-Electrons are transferred from NADH to pyruvate to produce lactic acid Know that when O2 is limiting, cells can use fermentation instead, to continue to make ATP through the glycolytic pathway. (fermentation recycles the NADH made in glycolysis back to NAD+ so more glucose can be reduced to keep making ATP. IN this recycling process either alcohol (in yeast or bacteria) or lactic acid (in muscle cells) gets made as a byproduct. Explain why the energy yield of this process is low, by explaining how NADH is used in fermentation vs how it gets used in aerobic cellular respiration)

Understand where/how ATP is made in different steps

some ATP is made in glycolysis(2/glucose) and the citric acid cycle(2/glucose)by substrate level phosphorylation, but most ATP comes from oxidative phosphorylation (26-28/glucose). Where is the energy derived from oxidizing glucose temporarily stored before being harvested to make ATP by oxidative phosphorylation? (NADH and FADH2).

Explain how photosynthesis transforms light energy into chemical energy. Explain how this obeys the first law of thermodynamics.

sunlight drives photosynthesis, roughly 34% of E is used to maintain life through cellular respiration, the rest is lost as heat (entropy)

How is carbon fixed?

through photosynthesis Carbon fixation or сarbon assimilation is the conversion process of inorganic carbon (carbon dioxide) to organic compounds by living organisms.

oxidative vs substrate-level phosphorylation

•2 mechanisms for synthesis of ATP during cellular respiration 1.Substrate-level phosphorylation •Transfer phosphate group directly to ADP •Used during glycolysis and Kreb's cycle •Direct phosphorylation (low ATP yield) -Using E from breaking substrate-P bonds 2.Oxidative phosphorylation •ATP synthase uses energy from a proton gradient •Used during final step cell. Resp. •Indirect phosphorylation (high ATP yield) -Using E from flow of e-'s thru electron transport chain

Glycolysis

•6-carbon glucose molecule is oxidized and broken down into two 3-carbon pyruvic acid molecules .•Glyco-lysis ("splitting of sugar") •Takes place in the cytosol in 10 steps •Anaerobic: does not require oxygen directly in this step •Produces 2 ATP molecules, 2 NADH and 2 pyruvates Glycolysis has two major phases 1- Energy investment phase 2- Energy payoff phase (Glycolysis can occur whether or not O2 is present) In the energy investment phase, 2 ATPs were used to phosphorylate glucose, which then splits into 2 3C p'ated intermediates, called G3P. In the energy output phase NADH is formed from a redox reaction: NAD+ gains a H-, becoming NADH. NADH captures the E released from oxidizing G3P. This E will be used later (in the mitochondria) to make ATP via oxidative phosphorylation. In the E output stage, 4 ATP are produced, a net gain of 2 ATP This ATP comes from substrate level phosphorylation(ATP made directly from the removing a P from the substrate and phosphorylating ADP) In the payoff stage, 4 ATP are produced, a net gain of 2 ATP.(by what process is this ATP made?) substrate level phosphorylation

What are the 4 stages of the cell life cycle

•Cell cycle: the "lifecycle" of the cell -Interphase: cell grows and DNA replicates •Consists of G1, S and G2 phases •All the lifetime of the cell except cell division -Mitosis: division of 1 cell into 2 new cells •Which grow, replicate and eventually divide (or die) 1.G1 (gap phase 1) -Primary growth phase, longest phase 2.S (synthesis) -Replication of DNA 3.G2 (gap phase 2) -Organelles replicate, microtubules organize 4.M (mitosis) -Subdivided into 5 phases 5.C (cytokinesis) -Separation of 2 new cells

Endosymbiosis theory

•Current theory explaining how mitochondria and chloroplasts evolved• Proposes that some of today's eukaryotic organelles (Mitochondria and chloroplasts) evolved by a symbiosis between two cells that were each originally free-living •One small cell, a prokaryote that had developed the ability to use oxygen to do cellular respiration, was engulfed by and became part of a much larger, primitive eukaryotic cell •Instead of being digested, the prokaryotic cell persisted and gave rise to mitochondriaIs it unreasonable to imagine this occurring? Is it common for bacteria to set up symbiotic relationships?

2 laws of thermodynamics

•First law of thermodynamics: the energy of the universe is constant-Energy can be transferred and transformed, but it cannot be created or destroyed -also called the Law of conservation of energy •Second law of thermodynamics: Entropy (disorder) always increases. Every energy transfer or transformation increases the entropyof the universe. (in biological systems entropy is often heat) `- in other words, During every energy transformation, some energy becomes unusable to do work

Golgi apparatus

•Flattened stacks of interconnected membranes (Golgi bodies) •Functions in packaging and distribution of molecules synthesized at one location and used at another within the cell or even outside of it •Vesicles leaving the ER are delivered to the golgi •Vesicles leaving the golgi are delivered to their final destination (another organelle or the membrane) •Has cis(receiving side) and trans (delivery side) faces •Vesicles transport molecules to destination •Vesicles move along cytoskeletal "roads" (also by diffusion) •This delivery is ATP driven and used motor proteins

Anaerobic respiration and fermentation

•In Aerobic respiration-Final electron acceptor is oxygen (O2) •In Anaerobic respiration-Final electron acceptor is a different inorganic molecule (Such as S2, but not O2) •In Fermentation-Final electron acceptor is an organic molecule

Competitive vs noncompetitive inhibitors

•Inhibitor - substance that binds to enzyme and decreases its activity •Competitive inhibitors bind to the active site of an enzyme, directly competing with the substrate for binding •Noncompetitive inhibitors bind to an allosteric site, causing the active site of the enzyme to change shape and "turn off" the enzyme •toxins, poisons, pesticides, and antibiotics often work by inhibiting enzymes •Noncompetitive inhibitors bind to an allosteric site - chemical on/off switch -Allosteric inhibitor - binds to allosteric site and reduces enzyme activity -Allosteric activator - binds to allosteric site and increases enzyme activity

Vacuoles

•Membrane-bounded structures in plants (also some fungi and protists) •Various functions depending on the cell type •Maintain tonicity •Increase/decrease cell size •Store both useful and/or waste products •There are different types of vacuoles: -Central vacuole in plant cells -Contractile vacuole of some fungi and protists -Storage vacuoles

Mitochondria and chloroplasts

•Mitochondria sites of cellular respiration, a metabolic process that uses oxygen to generate ATPFound in (almost) all eukaryotes •Chloroplasts sites of photosynthesis found in plants, algae, photosynthetic protists (plankton) •not part of the endomembrane system Most of their Proteins are made by cytosolic ribosomes (not bound ribosomes) and are delivered by pathways other than the endomembrane delivery system. These organelles also contain their own ribosomes and their own circular DNA (evidence they evolved from independent prokaryotic cells)

Peripheral vs. Integral Proteins

•Peripheral membrane proteins -Are proteins associated with the membrane but not embedded in it -Anchoring molecules attach membrane protein to cell surface Peripheral proteins attach loosely to the membrane surface but do not penetrate into the membrane.They can also attach to integral proteins embedded in the membrane. •Integral Membrane proteins-Proteins embedded in the membrane -protrude into the hydrophobic portions of the membrane. •Transmembrane proteins cross the membrane -transmembrane proteins are integral proteins that completely cross the membrane. (so they are exposed to both the extracellular fluids (ECF) and the cytosol) •Nonpolar regions of the protein are embedded in the interior of the bilayer •Polar regions of the protein protrude from both sides of the bilayer -The Transmembrane domain •Spans the lipid bilayer •Contains Hydrophobic amino acids arranged in α helices

Membranes are fluid

•Phospholipids in the plasma membrane can move within the plane of the bilayer •Most of the lipids, and some proteins, drift laterally (easily) •Rarely does a molecule flip-flop transversely across the membrane. Why? TAKES A LOT MORE ENERGY

Connections between cells

•Plasmodesmata are the only type of cell junctions in plant cells (since the wall already holds the cells together. These provide communication channels between adjacent plant cells Tight Junctions, Desmosomes, and Gap Junctions occur in Animal Cells At tight junctions, membranes of neighboring cells are pressed together, prevents leakage of extracellular fluid make a band of connection around the top of cells in layer Allow coordinated movement of cells and formation of epithelial sheets of cells (all organs are bound by epithelial cells) Desmosomes(anchoring junctions) fasten cells together into strong sheets (act like rivets) Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells (similar to plasmodesmata in plants) Plasmodesmata (communicating junctions in plants) •3 categories based on function: 1.) Tight junction-Connect the plasma membranes of adjacent cells in a sheet - no leakage -Provide a barrier to prevent leakage and have differential functions on apical and basal cell faces 2.Anchoring junctions-Mechanically attaches cytoskeletons of neighboring cells (desmosomes- act like rivets between cells, connect to intermediate filaments -Adherens junctions- attach cells tightly together, interact with actin cytoskeleton 3.Communicating junctions-Channels between cells enabling direct communication through cytoplasm. Chemical or electrical signal passes directly from one cell to an adjacent one (gap junctions) -Only junctions in Plant cells are plasmodesmata (similar to gap junctions, they allow for cell-cell communication through cell walls)

Nucleus

•Repository of the genetic information •Most eukaryotic cells possess one nucleus •Muscle cells are multinucleated •Contain a Nucleolus - dark region where ribosomal RNA synthesis takes place •Synthesis of Ribosomal subunits takes place here •Nuclear membrane is called the Nuclear envelope -Has 2 phospholipid bilayers (it is a double membrane) -Contains Nuclear pores - control passage in and out •the DNA is contained in multiple, linear chromosomes -Chromosomes are DNA wrapped around proteins, fully coiled -Chromatin is partially uncoiled DNA

Ribosomes

•Ribosomes are cellular machines that build proteins •Found in all cell types in all 3 domains of life •Made of Ribosomal RNA (rRNA) and proteins •Complex of about 50 proteins with rRNA •2 subunits (large and small) •Protein synthesis also requires messenger RNA (mRNA) and transfer RNA (tRNA) •Ribosomes occur free in the cytoplasm or associated with ER membranes •Rough ER has attached ribosomes, smooth ER does not

Endoplasmic reticulum

•Rough endoplasmic reticulum (RER) -Attachment of ribosomes to the membrane gives it a rough appearance (dynamic) -Processes proteins whose final destination is secretion or delivery to an organelle that is part of the endomembrane system. -Performs modifications to the protein -Forms vesicles containing the protein •Smooth endoplasmic reticulum (SER) -Relatively few bound ribosomes -Variety of functions - lipid synthesis, store Ca2+, detoxification •Ratio of RER to SER depends on cell's function •Secretory cells have more RER •Liver cells have more SER

what are second messengers?

•Second messengers are small, nonprotein, water- soluble molecules or ions that spread throughout a cell by diffusion -cAMP, Ca++, IP3 and DAG are all second messengers -Second messengers participate in pathways initiated by GPCRs and RTKs •Cyclic AMP, calcium ions, and IP3 and DAG are common second messengers **cAMP is the second messenger used in epinephrine cascade (causes large rapid response throughout cell)

Endomembrane System

•Series of membrane bound organelles that function to deliver proteins to their appropriate destinations •Divides cell into compartments where different cellular functions occur •This system is one of the fundamental distinctions between eukaryotes and prokaryotes

Water

•Unique characteristics of water: -only common substance existing in all three physical states of matter: solid, liquid, and gas -6 Unique properties •All Due to H2O's polarity -Water is involved in most biol. rxns Properties of water: 1.Water is cohesive and adhesive- It forms H bonds with itself and other polar molecules 2.Water moderates temperature due to its high specific heat-A large amount of energy is required to change the temperature of water-Thus earth (and our bodies) have relatively stable temperatures and its high heat of vaporization-The evaporation of water from a surface causes cooling of that surface (we can cool by sweating) 3. Solid water is less dense than liquid water-Bodies of water freeze from the top down (so the has lots of liquid water instead of frozen oceans) 4. Water organizes nonpolar molecules (hydrophobic interactions)-Hydrophilic "water-loving"-Hydrophobic "water-fearing"-Water causes hydrophobic molecules to aggregate or assume specific shapes or locations in cells 5. Water is a good solvent-Water dissolves polar molecules and ionic substances easily 6. (AND pH) Water can dissociate into ions-pH is a measure of [H+] in an aqueous solution

Microbodies

•Variety of enzyme-bearing, membrane-enclosed vesicles •Peroxisomes -Contain enzymes involved in the oxidation of fatty acids -Hydrogen peroxide produced as by-product - rendered harmless by catalase

Hydrogen bonds

•polarity of water allows water molecules to be attracted to one another (Cohesion) •This attraction produces hydrogen bonds •Each individual H bond is weak and transitory •Cumulative effects of H bonds are enormous and very important in biological reactions •H bonds are Responsible for all of water's important physical properties •polarity of water allows water molecules to be attracted to one another (Cohesion) •This attraction produces hydrogen bonds •Each individual H bond is weak and transitory •Cumulative effects of H bonds are enormous and very important in biological reactions •H bonds are Responsible for all of water's important physical properties