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CELL 120 Unit 2
| Question | Answer |
|---|---|
| Polymer | A long molecule made of similar building blocks. |
| Monomer | A singular building block |
| Macromolecules | Long polymers |
| Carbohydrates, protein, and nucleic acid are all... | Polymers |
| Dehydration reaction | Two monomers bind with the loss of an H2O molecule |
| Hydrolysis | Two monomers break apart with the addition of a water molecule |
| What are Carbohydrates and their functions? | Sugars. Their function is fuel and building material. |
| Monosaccaride | The simplest carbohydrate. A single sugar. |
| Polysaccharides | Polymers with many sugar blocks. In bacteria, polysaccharides act as shells, so antibiotics break down this barrier. |
| Sugars are made of what atom multipes? | CH2O multiples |
| What is the most common monosaccharide? | C6 H12 O6 |
| How are monosaccharides classified? | By location (Ketose/Aldose) and number of carbons in the skeleton. |
| Ribose | The nucleic acid structure for RNA sugar |
| Deoxiribose | The nucleic acid for DNA sugar (missing an Oxygen) |
| What monomeric unit is in both DNA and RNA | Nucleotides |
| What happens to the body in a fasting state? | The pancreas sends the signal that your blood sugar is low, so it creates glucagon, which goes into the liver for ketogenesis. It transfers the stored energy into ketones, which are released into the bloodstream to be used as energy. |
| What form do saccarides take on in aqueous solutions? | Ring like structures |
| Carbonyl group | C=O Carbon double bonded to Oxygen |
| Hydroxyl group | OH Oxygen and hydrogen |
| Carboxyl group | O=C-OH Carbonyl group + Hydroxyl group |
| Aldose | Carbonyl group on the end of the monosaccharide |
| Ketose | Carbonyl group more central on the monosaccharide |
| Tricose, Pentose, and Hexose | 3, 5, and 6 carbon sugars |
| How is maltose made? | Two glucose molecules come together through a glycosidic linkage for the synthesis of maltose |
| How is sucrose made? | A glucose and fructose molecule come together through a glycosidic linkage for the sythesis of sucrose |
| Glycosidic linkage | Dehydration reaction that takes out a Hydroxyl group (OH) leaving the left-over Oxygen |
| Lipids | A diverse group of hydrophobic molecules. They can't be stacked or create covalent bonds, rather they create aggregates. Not true polymers. Mostly made up of hydrocarbon combinations and glycerol (3 OH's) |
| R'/R"/R''' | Any # of hydrocarbons attatched at the end of the triglyceride (body fat) |
| Fats and their functions | Triglyceride made by 3 fatty acids joined to glycerol. Energy storage. Glucose can enter the creb cycle to make fatty acids if the body needs it. |
| Unsaturated fats | Double bonds to carbon prevent hydrogen from bonding, thus making the chain curve and unable to stack.(stays liquid at room temp) (See pic in notes) |
| Saturated fats | Hydrogen connected everywhere possible. Allows for more fatty acid build up, can be stacked because linear. (Like butter. Solidifies) No double bonds. |
| Functions of Adipose tissue | Insulates and cushions organs, long term energy storage |
| Glycerol | 3 Carbon alcohol with hydroxyl group attached to each carbon |
| Fatty Acid | A carboxyl group with R' |
| Phospholipids | 2 fatty acids and a phosphate group attached to a glycerol. Used in membranes of cells. Hydrophobic fatty acid tails and hydrophilic heads. Self-assemble in water. |
| Steroids | A carbon skeleton of 4 fused hydrocarbon rings |
| Cholesterol | A type of steroid that is a precursor to synthesize other steroids. HCL and LDL. |
| Functions of Proteins | 1. Determine the identity and structure of cells 2. Make up more than 50% of the dry mass of most cells 3. Speed up chemical reactions 4. Defense, storage, transportation, cell communication, movement, structural support |
| Most diseases in the body are caused by this building block misbehaving | Misbehaving proteins |
| The 8 types of proteins | Contractile+Motor, Defensive, Enzymatic, Hormonal, Receptor, Storage, Structural, and Transport |
| Enzymatic proteins | Accelerate chemical reactions Ex. Digestive enzymes catalyze hydrolysis of food molecules |
| Defensive proteins | Protect against disease Ex. Antibodies inactivate/destroy bacteria and viruses |
| Storage proteins | Store amino acids Ex. Milk stores casein, an amino acid for baby mamals |
| Transport proteins | Transport proteins Ex. Hemoglobin transports O2 from lungs to other parts of the body. |
| Hormonal proteins | Coordinates an organisms activities Ex. Insulin secreted in pancreas causes tissues to take up glucose and regulate blood sugar |
| Receptor proteins | Cell response to chemical stimuli Ex. Receptors in nerve cells detect signal molecules from other nerve cells |
| Contractile/Motor proteins | Movement Ex. Actin and myosin proteins are responsible for muscle contraction |
| Structural proteins | Support Ex. Collagen (Keratin) protein for hair cells |
| Enzymes | Catalysts to speed up natural chemical reactions. Build/break down polymers with dehydration or hydrolysis, essential!! |
| The structure of proteins is determined by... | 20 amino acids in a sequence |
| Polypeptide | Polymers without branches, build from amino acids. Can be from 1-more than 1,000 monomers, in a unique sequence. Each has an amino (N-terminus) beginning, and a carboxyl (C-terminus) end. |
| Peptide bond | The covalent bond between the amino acids |
| A protein molecule | BIOLOGICALLY FUNCTIONING consisting of one or more polypeptide chains |
| Amino acids | Monomers made of organic molecules with amino and carboxyl groups. Each amino acid is made unique by the R group (side chain) |
| The 4 groups of amino acids | These determine how amino acids interact 1. Nonpolar (hydrophobic) side chains 2. Polar (hydrophilic) side chains 3. Acidic (negatively charged) side chains 4. Basic (positively charged) side chains |
| How amino acids work | The sequence of amino acids determines the 3D structure, the structure determines how it works, and the function depends on its ability to recognize and bind to another molecule |
| Primary structure | The sequence of amino acids. Order determined by genetic information. (The chain) |
| Secondary structure | The coils (a helix) and folds (B pleated sheet) result from hydrogen bonds between repeating parts of the polypeptide back bone (the waves in a chain) |
| a helix | The coils |
| B pleated sheet | The folds |
| Tertiary structures | Overall shape of the protein, determined by R groupes (rather than the backbone constituents) |
| Types of interactions in proteins | Hydrogen bons, ionic bons, hydrophobic interactions, and Van Der Waals interactions |
| Strong covalent bonds in proteins are also called... | Disulfide bridges. They may reinforce the structure of the protein. |
| Quaternary structure | 2 or more polypeptide chains form 1 macromolecule (ex. collagen is a fibrous protein made of 3 polypeptides coiled like a rope) (another ex. Hemoglobin is a globular protein made of two a helix and two B pleated sheet subunits) |
| Sickle cell anemia | A slight mutation in amino acids. It changes one from a polar hydrophilic RBC to a non-polar hydrophobic cell, which wants to be away from water thus making it change into a sickle. |
| What conditions can cause a protein to unravel? | pH, salt concentration, hot temperatures, and other environmental factors |
| What is the loss of a cell's natural structure called? | Denaturation. The cell becomes biologically inactive |
| Function of nucleic acids | Store, transmit, and help express hereditary information |
| Genes | Program amino acid sequence, consist of DNA, nucleic acid, and monomers called nucleotides. |
| Types of nucleic acid | DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) |
| Functions of DNA | Directions for its own replication, directs synthesis of messenger RNA, and gene expression by controlling protein synthesis through mRNA |
| How does DNA lead to the creation of polypeptides? | DNA--> mRNA interacts with protein synthesizing molecules --> production of a polypeptide |
| What polymers make up nucleic acid? | Polynucleotides, which are made up of the monomer nucleotides. |
| A nucleotide is chemically made up of... | Nucleoside (nitrogen base + pentose sugar) + 1 ore more phosphate groups |
| The different nitrogen bases in nucleotides | Pyrimidines: (6 membered ring) cytosine, thymine, uracil Purine: (6 membered ring fused to 5 membered ring) Adenine, guanine (C, T, U, A, G) |
| Phosphodiester linkages | A phosphate group that links the two pentoses in a polynucleotide. Creates a sugar-phosphate backbone with the nitrogen bases coming off as appendages |
| Structure of DNA | 2 polynucleotides spiraling in a double helix with antiparallel backbones. Adenine=Guanine, Thymine=Cytosine through hydrogen bonds! |
| Structure of RNA | Single strand, more variable in form, Uracil replaces Thymine. |
| LM (Light microscope) | Light passes though a lens to refract the light and magnify. |
| The 3 principals of good microscopy | 1. Magnification (enlarged ratio) 2. Resolution (Clarity of the image to distinguish two separate points) 3. Contrast (visible differences in brightness/color) |
| Electron microscopes (EM) | Two types: 1. Transmission electron (TEMs) electrons go through the cell 2. Scanning electron (SEMs) electrons bounce off the cell |
| Cell Fractionation | Blend up a cell, then use high speeds to separate the parts into centrifuges. Helpful to determine the function of organelles |
| What are microscopes used to study? | Cell and organelle structure |
| Eukaryotic cells examples | Protists, fungi, plants, and animals |
| Prokaryotic cells examples | Only bacteria and archaea |
| What 4 things do all cells have? | 1. Plasma membrane 2. Cytosol/cytoplasm 3. Chromosomes to carry genes 4. Ribosomes to make proteins |
| Prokaryotic cells | Much smaller than eukaryotic cells. No nucleus, all free floating in cytoplasm, some condensed in regions. All organelles interact. |
| Eukaryotic cells | DNA in a nucleus bounded by a double membrane. Membrane bound organelles, and cytoplasm between the membrane and nucleus. |
| Plasma membrane | Selective barrier that: allows sufficient passage of oxygen, nutrients, waste removal, and determines volume of cell. |
| The nucleus | HQ. Contains DNA (23 pairs of chromatins like spaghetti until division), makes mRNA to make proteins, contains most genes. Nucleolus within is site of rRNA synthesis (ribosomal RNA) |
| Ribosomes | Made of rRNA and protein. Build protein in cytosol (free floating), outside of rough ER, and nuclear envelope (bound). |
| The endomembrane system | Consists of nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane. Work as a strand or via vesicles. |
| Endoplasmic reticulum | Factory. A big membrane continuous with the nuclear envelope. Smooth: Synthesis of lipids, detoxifies poisons, stores calcium ions for muscle function. Rough: secrete glycoproteins, membrane factory, distributes vesicles |
| Vesicles | Secretory proteins surrounded by membranes, carry stuff around the cell. |
| Golgi apparatus | Shipping and receiving. Flattened membranous sacs called cisternae. Modifies ER products, makes some macromolecules, sorts and packages stuff into vesicles. |
| Lysosomes | Digestive guys. Membranous sacs of hydrolytic enzymes that break down macromolecules like vacuoles by fusing with it. Made by rER, transferred to Golgi, digest with phagocytosis. |
| Mitochondria | Is the powerhouse of the cell. Site of cellular respiration, the metabolic process oxygen becomes ATP energy. (plant version is chloroplasts) |
| Perioxsosomes | Oxidative organelles |
| What theory suggests that chloroplasts and mitochondria come from a common ancestor? | Endosymbiont theory, supported by double membrane, circular DNA, free ribosomes, and that these organelles reproduce somewhat independently from the cell. |
| Mitochondrial matrix | Formed by the inner membrane of the cristae, cellular respiration is catalyzed here. |
| Cytoskeleton | Scaffolding. Support and mobility. Interacts with motor proteins and helps travelling organelles move along. Made of microtubules, intermediate filaments, and microfilaments. Separate chromosomes. |
| Centrosome | Centrioles only in animals. 9 sets of 3 triplets of microtubules for cell division formed in a ring. |
| Cilia and flagella | Microtubules that help cell move. Cillia lots, flagella only one or a few, like sperm. |
| Dynein | The walking feet that make microtubules bend. |
| Microfilaments | Form a cortex in a membrane. The microvilli in the intestines are bundles of this. Actin and myosin, which uses pseudopodia to walk along the actin. |
| Intermediate filaments | More permanent features that fix organelles in place. |
| Extracellular Matrix (ECM) | Covers cell. Made out of: glycoproteins (like collagen), proteoglycans, and fibronectin. They bind to membrane proteins called integrins, which can control communication and influence genes. |
| Cell junctions | Cell touch. How cells interact. Tight: prevent leakage (skin). Desmosomes are anchoring which fasten cells together, and gap junctions are for communication (cytoplasm channels) |
| Integrins | Integrated proteins in membrane. |
| Plasma membrane | Barrier, regulate by bringing things out/in with diffusion, active transport, or exo/endocytosis. MUST BE FLUID TO WORK!!! Not too solid, not too liquid. |
| Ampihtpathic | Hydrophilic and phobic, like phospholipid bilayers and certain proteins |
| The fluid mosaic model | Shows how like proteins gather together and bob around like buoys on the membrane, and how the hydrophobic regions keep the membrane in tact. |
| Fluid vs viscous membranes | Like saturated/unsaturated fats: the fluid has curves, so there are gaps, whereas the viscous the tails are uniform and can pack really tight. |
| Role of cholesterol in the membrane | Restrains movement at hot temps when cells want to move a lot, keeps reigned in. When cold, prevents tight packing to maintain fluidity. |
| Major types of membrane proteins | Peripheral- bound to surface of the membrane Integral- Penetrate the hydrophobic core, even a little. Transmembrane- type of integral. Spans the whole up and down of membrane. |
| Roles of surface proteins | Transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining/junctions, and attach cytoskeleton and ECM |
| These molecules identify cells: | glycoproteins and glycolipids |
| Selective permeability | Regulates membrane traffic by letting only certain things through-- like the border. |
| How do different molecules pass through the membrane? | Hydrophobic non polar: quick and easy (oxygen and carbon dioxide) Hydrophilic is impeded by the interior phobic membrane, so sugars and water pass through slow, if at all. There are specific channels for these. |
| Channel proteins | Transmembrane hydrophilic passage, like aquaporins for water! |
| Carrier proteins | Bind to the molecule and change its shape to get it in the cell-- only works on certain substances. Glucose carrier proteins only work on glucose. |
| Passive transport | No energy required. Diffusion, osmosis. |
| Diffusion | Movement to spread out evenly down a concentration gradient from high to low for equilibrium. |
| Osmosis | movement of water to dilute another substance. Like making the substance's density even. |
| Tonicity | Ability to gain/lose water |
| Isotonic | Equilibrium, equal solute concentration. Water moves at same rate. |
| Hypertonic | Solute greater OUTSIDE the cell, water rushes OUT and the cell shrivels (note, this different in plant cells w/ a cell wall |
| Hypotonic | Solute grater INSIDE the cell, water rushes IN, and the cell swells, and bursts (lyse). |
| Osmoregulation | Control solute concentration |
| Facilitated diffusion | Transport proteins speed up passive transport, like the channels and carrier proteins. Gated channels open/close to a stimulus (potassium ion channel opens w/ electrical stimulus) |
| Active transport | Uses ATP to go against the concentration gradient (sometimes). Ex. potassium is higher in the cell and sodium is higher outside the cell for animals. |
| Ion pumps | Na K pump in animals, why membranes have a voltage/potential. |
| Membrane potential | Necessary disequilibrium for the cell to do work. Created by distribution of +/- ions across the membrane. - inside and + outside makes passive transport of cations in and anions out of the cell. |
| Cotransport | Animals: Coupled active transport of glucose to the diffusion of Na+ into intestine cells Plants: proton pumps H+ downhill, as a side effect sucrose is brought in the cell. |
| Electrochemical gradient | Drives diffusion down the membrane. Chemical: ion concentration gradient. Electric: membrane potential on ion movement. |
| Exocytosis | Bulk transport out of the cell. Vesicle migrates to membrane, fuses with membrane, releases contents outside. Used for secretory cells like the pancreas secreting. |
| Endocytosis | Membrane forms pocket, deepens and pinches to form a vesicle with the contents inside. 3 types: Phagocytosis (eating big, like vacuoles), pinocytosis (drinking small, coated vesicle), receptor mediated (triggered by proteins) |
| Low Density Lipoproteins | LDL Cholesterol |
| What can be a cause of heart damage/stroke relating to cholesterol? | When receptors that take in LDL into the cell are missing or defective, the LDL builds up in blood vessels, narrowing them or even blocking passages. |
| What are the 2 laws of thermal dynamics? | 1. Energy can be transferred or transformed, but never destroyed. 2. Energy transfer increases entropy |
| Entropy | Disorder of the universe |
| Metabolism | Totality of an organism's chemical reactions, a significant quality of life forms. |
| Metabolic pathway: | Molecule is altered in steps to produce a product. Each step is catalyzed by a specific enzyme. |
| Catabolic pathway | Release energy by breaking things down from complex to simple |
| Anabolic pathway | Use energy to build complex things from simple things |
| Energy | Capacity to cause change and do work |
| Kinetic energy | The energy of movement |
| Potential energy | Potential to do work |
| Chemical energy | The potential energy for a chemical reaction to take place. Because of the arrangement of electrons making their bonds (covalent, ionic) |
| Thermal energy | random movement of molecules. When it is transferred it releases heat |
| Open system | Organisms need to be open systems that can interact with their environment. |
| Spontaneous reactions | Can occur without energy, quick or slow, increases ENTROPY |
| Non-spontaneous reactions | Require energy. Decrease entropy |
| Gibbs free energy | Occurs in systems with uniform temperature and pressure, like cells. Change in free energy is because of temperature changes in entropy and enthalpy. |
| How to calculate free energy | G = H - T * S (Free energy = Change in Enthalpy (total energy) - Temperature in Kelvin times change in Entropy) |
| What does it mean if the change in free energy is positive or negative | Positive: Reaction was non-spontaneous endergonic and USED energy, INCREASING FREE ENERGY Negative: reaction was exergonic spontaneous reaction, RELEASED energy, and DECREASED free energy because spontaneous reactions USE free energy. |
| How does free energy effect the stability of a thing? | More free energy, then less stable so greater work capacity. Less free energy, then more stable. |
| Exergonic reactions | Energy Exit. Release of free energy to surroundings. Spontaneous. Products have less energy than reactants. |
| Endergonic reactions | Energy inward. Absorb free energy. Non-spontaneous. Get energy to perform reaction from exergonic reactions. Products have more free energy than reactants. |
| Why do metabolic reactions have to be open systems? | If living cells reach equilibrium they die, because they need to do work. |
| Types of metabolic work | Chemical work- push endergonic Transport work- pump substances across the membrane non-spontaneously. Mechanical work- beating cillia/contracting muscles |
| What powers cellular work? | ATP Hydrolysis |
| What is ATP and what is it made of? | Adenosine triphosphate: A ribose sugar, adenine nitrogen base, and 3 phosphate groups |
| Energy coupling | Exergonic reactions drive endergonic reactions. Overall, the coupled reactions are exergonic. |
| Phosphorlyation | The transfer of one of the 3 phosphate groups on ATP to other molecules. This powers endergonic reactions. |
| Phosphorylated intermediate | The recipient of the extra phosphate molecule, causing it to have more free energy and become less stable. |
| ATP Hydrolysis | Addition of a water molecule to break off the terminal phosphate group off of ATP, turning it into ADP. Energy comes from the change from a state of higher free energy to lower free energy when the phosphate bond breaks. |
| Why is ATP the most effective molecule for cell energy? | ATP releases more energy when it loses a phosphate than most other molecules. The repulsion between the 3 phosphate groups creates a lot of potential energy, the equivalent of a compressed spring. |
| ATP cycle | Energy from catabolism (exergonic) powers the transition of ADP to ATP. ATP Hydrolysis happens, releasing energy for cellular work, then the ADP re bonds to the phosphorylated intermediate, turning it back into ATP |
| Catalyst | Speeds up a reaction without being consumed in it |
| Enzyme | A macromolecule (usually protein) that is a catalyst by lowering the energy activation barrier for a reaction to occur at normal temperatures |
| Activation Energy | Ea. How much energy is required to break bonds. Mostly supplied by heat. |
| Transition state | When enough energy is absorbed, so the bonds get all excited and ready to break. |
| Exergonic reactions and BONDS | New bonds forming releases more energy than it took to break the old bonds. |
| Endergonic reactions and BONDS | Absorb energy to break bonds, then release energy once new bonds form. |
| Substrate | The reactant an enzyme acts on |
| Most enzyme names end in | -ase |
| Active site | The part of the enzyme where the substrate binds. Creates an induced fit that modifies the shape of the substrate, and lowering the activation energy for the reaction to occur at normal temps |
| Enzyme activity is affected by... | Temperature, pH, and chemicals that influence the enzyme |
| Substrate concentration | When enzymes have their active sites engaged |
| What temperature do enzymes in the body like? | 37 degrees celcius |
| Cofactors | Non-protein helpers that bind to enzymes to help them do their job better. |
| Inorganic cofactors | Zinc, iron, copper |
| Organic cofacters | Coenzymes. Most vitamins act as these. |
| Inhibitors | Selectively inhibit action of enzymes. Irreversible if covalently bond. |
| Competitive inhibitors | Similar to the substrate and compete to the active site. Makes it so the real substrate can't come in. This can be overcome by substrate concentration, which just makes more enzymes. |
| Non-competitive inhibitors | Bind to a different part of the enzyme to change the shape of the active site so the substrate can't bond. Irreversible ones are antibiotics, toxins, and poisons. |
| Allosteric regulation | Inhibitor binds to one site, which effects the active sites everywhere else by either stabilizing or making the enzyme inactive. |
| Feedback inhibition | The end of the metabolic pathway that shuts down the enzyme so that it doesn't make more product than needed. |
| Cellular respiration | Take the potential energy from glucose bonds to create ATP and perform metabolic functions. Can also be break down of lipids and stuff. Sugars ferment with Oxygen, Aerobic process consumes organic molecules and O2, yielding ATP |
| Chemical representation of cellular respiration | C6 H12 O6 --> 6CO2 + 6H20 + energy (as heat and ATP) |
| Redox/Reduction reactions | Chemical reaction where molecule gains electrons, making it MORE negative. Positivity reduced! |
| Oxidation | Chemical reaction where molecule loses electrons, making it more positive. |
| The stages of cellular respiration | 1. Glycolysis 2. Pyruvate oxidation and citric acid cycle 3. Oxidative phosphorylation |
| Glycolysis | Catabolism (break down) of glucose into 2 molecules of pyruvate |
| Pyruvate oxidation and citric acid cycle | Complete the break down of glucose to CO2 |
| Oxidative phosphorylation | The electron transfer chain and chemiosmosis facilitate the synthesis of ATP. |
| Chemiosmosis | Energy from the H+ gradient drives cellular work (ATP synthase protein complex) A proton motive force. |
| Flow of cellular respiration products | glucose --> NADH --> electron transport chain --> proton motive force --> ATP (around 32 ATP) |
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