Biology Notes for the Midterm PDF

**MIDTERM NOTES** **chapter 3** -what are organic molecules? Molecules that contain carbon and are abundant in living organisms. -what are macromolecules? Large and complex organic molecules. -carbon structure. Carbon has 4 valence electrons and needs 4 more to fill its outer electron shell....

**MIDTERM NOTES** **chapter 3** -what are organic molecules? Molecules that contain carbon and are abundant in living organisms. -what are macromolecules? Large and complex organic molecules. -carbon structure. Carbon has 4 valence electrons and needs 4 more to fill its outer electron shell. It can form 4 bonds, single, double, and even triple. Molecules with polar bonds are water soluble(hydrophilic) and nonpolar molecules are not water soluble(hydrophobic) -what are functional groups? Groups of atoms with special chemical features that are functionally important. They exhibit the same properties in the molecules they are found. **EXAMPLES** amino group(NH2), carbonyl or ketone group(CO), aldehyde group(CHO), carboxyl(COOH), hydroxyl(OH), methyl(CH3), phosphate( PO4), sulfate(SO4), sulfhydryl(SH) -what are isomers? Two or more molecules with same chemical formula but different structures and characteristics. There are two types: Structural isomers and stereoisomers. Structural isomers have the same atoms but in different bonding relationships. Stereoisomers have atoms in same bonding relationships but different spatial positioning. Cis-trans isomers involve positioning around a double or triple bond. Enantiomers are mirror-image molecules. -How do organic molecules and macromolecules form and break down? They form through a dehydration or condensation reaction. A water molecule is taken out each time two monomers join. The polymers are broken down through a hydrolysis reaction where a water molecule is inserted, breaking the molecule into monomers. They are both catalyzed by enzymes -what are the types of macromolecules? There are four types of macromolecules. Carbohydrates, lipids, proteins, and nucleic acids. -What are carbohydrates composed of? Carbohydrates contain carbon, hydrogen, and oxygen. The formula for carbohydrates is Cn(H2O)n Most of the atoms In a carbohydrate are linked to a hydrogen atom and a hydroxyl group. -What are the types of carbohydrates? Monosaccharides, disaccharides, and polysaccharides. -What are monosaccharides? Monosaccharides are the simplest form of sugar. They usually contain 5 or 6 carbons. Pentoses(5 carbons) include ribose and deoxyribose. Deoxyribose has 1 oxygen less than ribose(C5,H10,O4) Hexose(6 carbons) include glucose(C6,H12,O6) Can be represented in linear or ring structures. Glucose and galactose are structure isomers. -what are disaccharides? Composed of two monosaccharides joined together by a glycosidic bond. Some examples are sucrose, maltose, and lactose. Disaccharides are broken down by hydrolysis. Sucrose is made up of fructose and glucose joined together by a glycosidic bond. -What are polysaccharides? Long chains of monosaccharides. Two types: Structural: cellulose, chitin, and glycosaminoglycans. Storage(energy): starch and glycogen. Starch is moderately branched, glycogen is highly branched, and cellulose is unbranched -What are lipids? Include four types: fats, phospholipids, steroids, and waxes. Lipids are made predominantly of carbon and hydrogen. Make up 40% of the organic matter in the average human body. Lipids are known to be nonpolar and are highly insoluble in water. -What are fats composed of? Fats are made up of a glyceride group connected to three fatty acids. Fats are also known as triglycerides or triacylglycerols. They are joined together by dehydration reaction and are broken down by hydrolysis. The bond between the glycerol and fatty acid is called an ester bond -What are fatty acids? There are two types of fatty acids: saturated and unsaturated. Saturated fatty acids have carbons linked together by single bonds. Unsaturated fatty acids have at least one double bond. Saturated tend to be solid at room temperature, while unsaturated tend to be liquid(oils) they have low melting points. Cis unsaturated fatty acids are natural while trans are artificial and linked to diseases. -Functions of fats? Fats are an important energy source, providing more energy than starch or glycogen. They can provide cushioning and insulation. -composition of phospholipids? They are made up from glycerol and two fatty acids, and a phosphate group. They are amphipathic molecules(they contain hydrophobic and hydrophilic regions) Tails(fatty acids) are hydrophobic while heads(charged nitrogen containing region, phosphate group, glycerol backbone and end of fatty acids) are hydrophilic. -what are steroids? Four interconnected rings of caron atoms. They are usually insoluble In water and an example is cholesterol. Small changes in structure can lead to profound biological functions. For example, testosterone and estrogen. -What are proteins? Composed of carbon, oxygen, hydrogen, nitrogen, and small amounts of other elements, notably sulfur. Proteins are composed of amino acid building blocks There are 20 different amino acids. Proteins have a common structure with a variable sidechain that determines structure and function. -How are amino acids joined? Amino acids form into a polypeptide through repetitive dehydration reaction. Carboxyl and amino groups join to form a peptide bond. These bonds join amino acids. Polymers of amino acids are known as polypeptides. Proteins can be composed of one or more polypeptides and are broken down by hydrolysis. -What are the types of structures of proteins? Primary structure, secondary structure, tertiary structure, and quaternary structure. Primary structure is just a linear polypeptide and is encoded directly by genes Secondary contains certain amino acids that can form hydrogen bonds. These hydrogen bonds lead to a spiral(alpha helix) or beta pleated sheet to form. They are important and define protein characteristics. They are formed by chemical and physical interactions. Tertiary structure is composed of secondary structure and randomly coiled regions that give the polypeptide a 3d shape. Randomly coiled regions are not alpha helix or alpha pleated sheets and are specific and important to function. Folding gives it a 3d shape. It is the last level of structure for a single polypeptide chain. Quaternary structures are when two or more polypeptides come together to form a protein. Individual polypeptides are called protein subunits. Can be formed from several copies of the same polypeptide. Quaternary proteins composed of different protein subunits are known as multimeric. -What bonds exist between protein of secondary structure and above? Hydrogen bonds, disulfide bridge(two cysteine side chains), Van Der Waals forces, ionic bonds, and hydrophobic effect. -What factors promote protein folding and stability? All of the above. -Protein-protein interactions? Many cellular processes involve the interaction of two proteins. Specific binding at surface using the first four factors, leaving out disulfide bridge. -What are nucleic acids? They are responsible for the storage, expression, and transmission of genetic information There are two kinds: DNA and RNA DNA contains the genetic information in the form of nucleotide polymers in different sequences. RNA decodes this information and turns it into code for the synthesis of amino acids. The building blocks of these are nucleotide monomers They are made up of a phosphate group, a five-carbon sugar(deoxy or ribo), a single of double ring of carbon, and nitrogen atoms known as a base. They are joined together into a polymer by a sugar-phosphate backbone -What is the difference between DNA and RNA? DNA has only 1 form and contains thymine instead of uracil DNA contains deoxyribose while RNA contains ribose sugar RNA has multiple forms and contains only one strand while DNA is double stranded and is helix shaped. The bases of opposite DNAs are joined together. **Book Notes:** Carbon allows for a wide variety of molecules to be made from a small number of elements. This is due to its ability to form up to four bonds. It can form single, double, and triple bonds. It can also bond in different structural configurations(linear, ring, and highly branched) Living organisms are carbon based. Carbon is stable and can handle a wide range of temperatures, which allows carbon-based life to prosper as they range a lot In temperature. Carbon forms strong bonds due to its small size and close bonds. Hydrocarbons are nonpolar and are highly concentrated in carbon-hydrogen bonds. Enantiomers have the same chemical properties, but they may not be recognized by the same enzyme or molecule. Organic molecules have many shapes due to bonding properties of carbon Carbohydrates are named so because they are compounds that have carbons and the compound is hydrated Cn,(H2,On)2 Carbohydrate function: Simple carbohydrates or monosaccharides are broken down into ATP. Lipids are a key part of the cell membranes and function as hormones. Also, energy. They also provide insulation and cushioning. Proteins have a wide variety of functions. From gene expression to cell membrane composition to defense mechanisms. Nucleic acid where genetic information is stored in units called genes. Sugars are snall carbohydrates. Monosaccharides are very water soluble so glucose is water soluble Glucose circulates through the blood and enters cells then is broken down by enzymes. The energy in the chemical bonds of glucose is transferred to the bonds in ATP Hydroxyl group is removed and hydrogen is removed in dehydration reaction. High branching of glycogen makes it easily soluble. Starch is less soluble because it is less branched. The bonds between cellulose monomers prevents us from breaking it down and digesting it. A specific enzyme is needed to do so and we do not have it. As such, it is disposed of. Cellulose can form hydrogen bonds with other cellulose chains and form into rigid structure(cell wall) plants break down starch but not cellulose. Chitins form the external structures of insects. Glycosaminoglycans provide support for animals in the joints and cartilage, also in the extracellular matrix, covering the cells. Peptidoglycans form the cell walls in bacteria cross-linked peptide bonds. Lipids are not considered to be macromolecules because they do not contain many covalently bonded monomers. Fatty acids differ with length and bond type(single, double) Saturated = saturated with hydrogen(maximum hydrogens) Double bond gives fatty acid 3d shape. 1 c=c bond is called monounsaturated fatty acid 2 or more c=c bonds is called polyunsaturated fatty acid Essential fatty acids are fatty acids the body needs but cannot produce Fats that contain saturated fatty acids have higher boiling points because they are more packed and intermolecular forces stabilized it. Unsaturated fats have kinks and cannot get very close to each other so the intermolecular forces are less so it is less stabilized and has lower melting point making it a liquid or (oil) The number of C-H bonds determines the amount of energy, so fats(which have a lot of C-H) have a more energy than carbohydrates(C-OH) Phospholipids are different than fats in that the third hydroxyl group is linked to a phosphate group. Charged nitrogen containing group is linked to phosphate. Steroids have four fused rings of carbon and contain one or more hydroxyl groups linked to the fused ring structure. Steroids with one hydroxyl group are known as sterols(cholesterol) All steroid hormones are derived from cholesterol. Estrogen has a hydroxyl group instead of a ketone group and an extra double bond. Testosterone has an extra methyl group. When dissolved in water an amino group accepts an H+ ion and the carboxyl group loses a hydrogen ion and becomes negatively charged. The amino acids are called so because they have an amino group and the carboxyl group functions as an acid. All amino acids except glycine have enantiomers D and L forms. Only L amino acids are found in proteins. D amino acids are found only and only in certain bacteria cell walls. Proteins are functional units composed of one or more polypeptides that have folded and twisted into a precise 3d shape. Nucleic acids account for about 2% of body weight **Chapter 4** -What are cells? Cells are the smallest units of life. All living organisms are composed of at least one cell. New cells can only come from pre-existing cells through cell division What is the difference between eukaryotes and prokaryotes(the two categories of life)? Prokaryotes have simple cell structures and do not contain a nucleus. Eukaryotes are more complex and the dna is enclosed by a double membrane. Internal membranes form organelles. -What are the two types of prokaryotes? Bacteria and archaea Bacteria are small cells: 1-10 micro-meters in diameter. They are very abundant in the environment and the body Many of them are not harmful. Some species cause disease. Archaea are the same size They are less common and are often found in extreme environments. -What is the structure of a bacterial cell? Inside the plasma membrane there is a cytoplasm, nucleoid region, and ribosomes. Outside the plasma membrane there is a cell wall that provides protection, a glycocalyx that traps water; gives protection; and helps evade immune system, appendages; pili(attachment) and flagella(movement) The glycocalyx is a gelatinous covering. The cytoplasm is the site of metabolism. -What is the structure of a eukaryotic cell? DNA is contained within membrane-bound nucleus. Compartmentalized functions with membrane-bound compartments that have specific shapes and functions. Eukaryotic cells vary widely across specialized cells and different species. Different shape, size, and organization. **-What are the components of a eukaryotic cell?** Nucleus: is the area where most of the genetic material is organized and expressed Nuclear envelope: double membrane that encloses the nucleus Nuclear pores: passageway of molecules in and out of the nucleus. Nucleolus: where RNA subunits are assembled(RNA synthesis) Lysosomes: site where macromolecules are degraded. Ribosome: protein synthesis Chromatin: complex of protein and DNA Plasma membrane: membrane that controls movement of substances in and out of the cell; cell signaling. Cytosol: site of many metabolic pathways. Golgi apparatus: site of modification, sorting, and secretion of lipids and proteins Peroxisomes: site where hydrogen peroxide and other harmful macromolecules are broken down. Cytoskeleton: protein filaments that provide shape and aid in movement. Mitochondria: site of ATP synthesis. Smooth ER: site of detoxification, and lipid synthesis. Rough ER: site of protein sorting and secretion. Centrosome: site where microtubules grow, and centrioles are found **-What is the structure of plant cells?** They contain the same things and chloroplast, central vacuole, and cell wall. They also do not have lysosomes or centrioles. Chloroplast is the site of photosynthesis. Cell wall is a structure that provides the cell. Central vacuole is for storage and volume regulation. **-Plant cells vs animal cells?** Plant cells are usually larger than animal cells Aerobic respiration(mitochondria) Plant cells have fixed angular shapes whereas animal cells are round and irregular shaped Plants are autotroph(produce their own energy) animals are heterotroph(consume energy through digestion) The central vacuole can take up 90% of cell space and has a single membrane. They can have digestive functions like lysosomes, store nutrients, and provide space to degrade waste substances. Animal cells also have vacuoles, but they are not as large. There is multiple of them in animal cells. Plants do not have centrioles Flagella in reproductive cells. Cilia in many specialized animal cells. Plant cells don't have cilia. -what is the difference between cytosol and cytoplasm? cytosol includes all areas inside plasma membrane but outside the cell organelles. Cytoplasm includes all areas inside the cell membrane, including the cytosol, endomembrane system, and semiautonomous organelles. -Cell chemical processes? Basically, molecule synthesis and breakdown Catabolism and anabolism Catabolism is the breakdown of a molecule into smaller components. Anabolism is the synthesis of cellular molecules and macromolecules Cytosol is the central coordinating region for metabolic activities of eukaryotic cells -what is the cytoskeleton? Is a network of three types of protein filaments. These types are microtubules, intermediate filaments, and microfilaments(actiin filaments) Microtubules are long, hollow cylindrical structures. They have dynamic instability, meaning that they can change a lot very fast. This allows them to reorganize quickly for different functions. Intermediate filaments are intermediate in size and form twisted ropelike structure. Actin filaments are also known as microfilaments. They are long, thin fibers. -Functions? Microtubules are important for cell shape, organization of cell organelles, movement of cargo, and cell motility(cilia and flagella) Intermediate filaments: cell shape, provide cell with mechanical strength, anchorage of cell and nuclear membranes. Microfilaments: cell shape, cell strength, muscle contraction, intracellular movement of cargo, movement of cell(amoeboid movement) and cytokinesis in animal cells. -what are motor proteins? Proteins such as myosins and kinesins that move across protein filaments. It is a force dependent action and It requires the hydrolysis of ATP. There are three kinds of movements. Motor proteins carry cargo along the filament. Motor proteins remain in place and filament moves. Motor protein and filament both restrained, and action of motor protein exerts a force that causes the filament to bend. -steps of the movement of motor proteins? The head is released from the filament, cocks forward, and attaches to the filament once again. Then, it cocks backwards, bringing the tail forward. -what is the endomembrane system? network of membranes enclosing the nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, and vacuoles. It also includes the plasma membrane. May be directly connected to each other or pass materials via vesicles. -what is the nuclear envelope? Double membrane structure enclosing the nucleus. The outer membrane of the nuclear envelope is continuous with the ER membrane. Nuclear pores provide passageways. Materials within the nucleus are not part of the endoplasmic reticulum What is the nucleus? contains the chromatin(DNA and Proteins) nuclear matrix: filamentous network that organizes chromosomes. Ribosome assembly occurs in the nucleolus What is the endoplasmic reticulum? Network of membranes that form flattened, fluid-filled tubules or cisternae. The er membrane encloses a single compartment called the Er lumen(only one) Types of ER? There are two types: smooth and rough. The rough ER is studded with ribosomes and is involved with protein synthesis and sorting. The smooth endoplasmic reticulum lacks ribosomes. Its function is detoxification, lipid synthesis, carbohydrate metabolism, calcium balance, and modification of lipids. What is the golgi apparatus(body or simple golgi)? And what is its function? Stacks of membrane-bound membranes that form flattened fluid filled compartments or cisternae. Divided into three regions: cis(facing er), medial(in the middle), and trans(facing the plasma membrane) Vesicles transport materials between stacks. Proteins and lipids arrive from the er through vesicles and are incorporated within. Then they go to the medial region and then to the trans region where they are finally packaged for final destination. The golgi apparatus has three overlying functions: secretion, processing. And protein sorting. What are lysosomes and what are their functions? Are membrane-bound organelles that contain acid hydrolases that break down macromolecules. There are a number of acid hydrolases for the breakdown of proteins, lipids, nucleic acids, and carbohydrates. Lysosomes are involved in autophagy(breakdown of worn-out organelles and recycling into building blocks) Materials enter the cell through a process called endocytosis and they are broken down into simpler blocks in the lysosome which are then repurposed for recycling. What are vacuoles? Membrane bound organelles in cell. Their function is extremely varied, and they differ amon cell types and environmental conditions. Central vacuoles in plants regulate volume and can store and have digestive functions. Contractile vacuoles in protists get rid of excess water. This is important because they exist in bacteria that lives in very wet conditions. Phagocytic vacuoles in protists and white blood cells for degradation. They can break down foreign bodies within the human body like bacteria and viruses. What are peroxisomes? Membrane bound organelle that are involved with breakdown of harmful molecules How? They catalyze certain reactions that break down molecules by removing hydrogen or adding oxygen. This forms hydrogen peroxide as a byproduct(H2,O2) Catalase breaks down dangerous hydrogen peroxide into water and oxygen How are they formed? They are formed when vesicles bud off from the golgi and fuse, forming a premature peroxisome. When more materials are imported within the peroxisome, it becomes a mature peroxisome. Peroxisomes can divide to form two peroxisomes through binary fission. What is the plasma membrane? Is the boundary between intracellular environment and extracellular environment. Function? It controls what comes in and goes out with selective permeability Cell signaling Cell adhesion Semiautonomous organelles? Mitochondria and chloroplasts Grow and divide to reproduce themselves. They are not completely autonomous because they rely on the cell for synthesis of internal components(they need proteins and materials from the cell) and membrane maintenance What is mitochondria? Membrane bound organelle that is responsible for ATP synthesis. They are classified into regions: outer membrane, inner membrane, intermembrane space, and mitochondrial matrix. They are also involved in the modification, synthesis, and breakdown of several types of cellular molecules. They have their own DNA and divide by binary fission. The mitochondrial chromosome is in the nucleoid region. what is chloroplast? Membrane bound organelle found in plant cells that is responsible for photosynthesis. How? Capture light energy and use some of that energy to synthesize organic molecules such as glucose. Is found in nearly all plant and algae species. Structure? Outer membrane, inner membrane, intermembrane space, and thylakoid membrane. Stacks of thylakoid are called granum Stroma is the fluid inside the inner membrane. How are proteins sorted in eukaryotes? There are two types of protein sorting: co and post translational sorting Co-translational sorting begins in the cytosol. This sorting is for the ER, Golgi, Lysosomes, Vacuoles, plasma membrane, and secretion. This one involved vesicles and sorting signals. They start in cytosol then when the ribosome encounters an ER sorting signal it pauses translation and the whole thing travels to the rough ER, hence the RER is studded with ribosomes. The signal is recognized and the polypeptide is synthesized into the ER lumen. They may stay due to an ER retention signal or may be taken to the golgi through vesicles. In the er and golgi, they undergo modification. They may stay in the golgi due to a retention signal or are sorted elsewhere depending on signal. They may also be secreted outside the cell. Post translational sorting happens after translation and it is for nucleus, peroxisome, and semiautonomous organelle. Some proteins-known as cytosolic proteins- stay in the cytosol because there is no signal. how is the ER sorting signal recognized? It is recognized by an SRP and taken to the ER, where it attaches to a receptor in the ER membrane. The receptor recognizes the RER sorting signal and opens the channel for entry. A protein called signal peptidase cleaves the RER signal. How do vesicles form and transport materials? A coat of proteins helps a vesicle form from the ER membrane, and V snares are incorporated into the vesicle. After being released from the membrane, the coat of proteins is shed and the v snares connect to the t snared of the golgi, which allows the material to be incorporated inside the membrane. How are post translational proteins sorted? Chaperone proteins keep protein unfolded, signal is recognized by protein receptor, incorporated in cell, chaperone proteins are released then bound to the sequence once it Is inside, the sequence is taken to location then chaperones are released, allowing the polypeptide to fold. **BOOK NOTES:** Some species of bacteria are pathogenic-they cause diseases. The plasma membrane is a double layer of phospholipids and embedded proteins that acts as barrier between inside and outside. Glycocalyx keeps the bacterium from drying out. Some species of bacteria produce a very thick gelatinous glycocalyx called a capsule Eukaryotic: protists, plants, animal, and fungi cells. Prokaryotes include bacteria and archaea. Compartmentalization Is in eukaryotes but not in prokaryotes. This allows eukaryotes to carry out specialized chemical reactions in different locations within the cell. divided biochemistry. Cells can become compartmentalized due to mechanisms: membrane or liquid-liquid phase separation( solutes such as proteins and rna molecules form a droplet) The environment of the droplet allows the molecules inside to be closer together and assemble more easily. Also, it creates a different chemical environment inside which can affect chemical processes. Nucleolus is an example of a droplet organelle Why is it important for cells to be small? As cells get larger, the ratio of volume to surface area gets larger, making it less suitable for import and export of substances. This makes cells take on smaller sizes for maximum efficiency and plasma membrane surface area. \- Metabolism is defined as the sum of chemical processes by which cells synthesize the materials utilize the energy they need to survive. Metabolic pathways = series of steps for metabolism with each step being catalyzed by a specific enzyme An enzyme is a protein that accelerates the rate of a chemical reaction. All chemical reactions that happen in cells can be summed up by synthesis and breakdown of molecules. Some pathways involve: Catabolism: breakdown of a molecule into smaller components for energy or building blocks. Anabolism: synthesis of cellular molecules and macromolecules(formation of proteins, DNA, Polysaccharides, etc. \- Each type of protein filament is constructed from many protein monomers. Cytoskeleton is primarily found in the cytosol and in the nucleus along the inner membrane. Microtubules are about 25nm in size. They are formed from a tubulin and b tubulin. This results in a structure with a minus and positive end. Animal cells contain a region from which microtubules grow. It is called the microtubule organizing center(MTOC) In nondividing eukaryotic cells, the MTOC is located near the nucleus-the centrosome. The microtubule plus end is at the centrosome. Microtubules only grow from the positive terminus, but can get shorter from both termini Microtubules can change rapidly from growing to shrinking. This is called dynamic instability and is important for cellular processes, like chromosome sorting and cells orientation. Centrosomes also contain centrioles. In contrast, plant cells do not contain an MTOC(centrosome) or centriole. In plants, microtubules are created at many sites scattered throughout the cell, especially along the nuclear membrane. Golgi apparatus is connected to microtubules Intermediate filaments are 10nm Length of intermediate filaments is permanent and does not change like microtubules and microfilaments. Keratins form intermediate filaments. Keratinocytes are cells that synthesize a lot of keratins Dead keratinocytes= hair, nails, and surface of skin. Actin filaments are 7nm in diameter and are the smallest protein filaments They have plus and minus ends Made up of actin monomers. Throughout cytosol but are concentrated near plasma membrane. Motor proteins are a category of proteins that use ATP as energy to promote various types of movements. The hinge and tail make up a structure called the lever arm. The head is the site where ATP binds and hydrolyzes to ADP This causes the tail to bend and results in movement Cilia and flagella contain an internal structure called an axoneme. The axoneme contains microtubules, linking proteins, and the motor protein dynein. Flagella is usually longer than cilia and less abundant. The microtubules in the flagella and cilia emanate from basal bodies that are anchored to the cytoplasmic side of the plasma membrane. Nuclear pores are formed when the outer and inner nuclear membranes make contact with each other. Proteins compact dna to fit inside the nucleus. The primary function of the nucleus is the protection, replication, organization, and expression of genetic material. The nuclear lamina is responsible for the organization of chromosomes to the chromosome territory Lumen is the internal space of an organelle. Functions of the rough ER include protein sorting, synthesis, and attachment of carbohydrates to lipids and proteins in a process called glycosylation. Important processes that happen in golgi apparatus are glycosylation and proteolysis(through proteases enzymes) In proteolysis, polypeptides are cut into smaller goups. Materials to be secreted through secretory vesicles that go through the secretory pathway and outside the plasma membrane. Lysosomes use a molecule of water to break a covalent bond(hydrolytic enzymes) What prevents significant damage from happening in the case of lysosome membrane breakage? The cytosol PH is neutral and buffered, preventing the enzymes from becoming active(the enzymes need an acidic environment. The PH inside the lysosome is usually 4.8 \- Vesicles in animal cells are sometimes called storage vacuoles because they temporarily store or transport materials. Most vacuoles are made from the fusion of many smaller membrane vesicles. The central vacuole exerts pressure on the cell wall called turgor pressure Turgor pressure is important for cell shape and health. It also helps the cell grow through cell wall expansion. Food vacuoles(phagocytic) and contractile vacuoles. A typical eukaryotic cell contains hundreds of peroxisomes Peroxisomes break down harmful molecules and especially hydrogen peroxide. They also serve in metabolism of fats and amino acids. Glyoxysomes are specialized organelles like peroxisomes that are found in plant seeds. They contain enzymes that break down fats in the seeds. Chloroplasts are also known more generally as plastids. Types of plastids: Chloroplast, chromoplast, and leucoplast Chromoplasts synthesize and store color pigments known as carotenoids Leucoplasts for starch production. Mitochondrial genome is smaller than nuclear and chloroplast genome and codes for less proteins. I think chloroplasts are usually bigger than mitochondria. **Chapter 5** What is the membrane made up of? The framework of the membrane is a phospholipid bilayer. Membranes also contain carbohydrates and proteins. The two leaflets of the bilayer are asymmetrical as they are composed of different amounts of each component Fluid-mosaic model? the membrane is considered a mosaic of lipids, proteins, and carbohydrates membranes resemble a fluid because lipids and proteins move relative to each other within the membrane. Types of proteins in membrane? Integral or intrinsic membrane proteins. Two of them: transmembrane proteins where regions are physically imbedded in the hydrophobic portion of the phospholipid bilayer. Lipid-anchored proteins where an amino acid of a protein is covalently attached to a fatty acid within the membrane Peripheral or extrinsic membrane proteins: Noncovalently bound to either integral membrane proteins projecting out of the membrane or to polar head groups of phospholipids. Membranes are semifluid? Most lipids can rotate freely around their long axis and move laterally within the membrane leaflet. Flip-flop of lipids from one leaflet to another does not occur spontaneously and requires ATP. What are lipid rafts? Certain lipids associate strongly with each other to form lipid rafts. A group of lipids floats together as a unit within the larger sea of lipids in the membrane Composition of lipid rafts is different than rest of the membrane. -high concentration of cholesterol -unique set of membrane proteins. What factors affect membrane fluidity? Length of fatty acyl tails -shorter fatty acyl tails are less likely to interact, making the membrane more fluid. Prescence of double bonds -double bonds create a kind in the fatty acyl, making it more difficult for neighboring tails to interact. -Prescence of cholesterol -cholesterol tends to stabilize the membrane -effects vary with temperature( higher fluidity at lower temperatures and lower fluidity at higher temperatures) SYNTHESIS OF MEMBRANE COMPONENTS. Synthesis of lipids: In eukaryotic cells, cytosol and endomembrane system work together to synthesize lipids Fatty acid building blocks are made via enzymes in cytosol or taken into cells by food. Process occurs at cytosolic leaflet of the smooth ER. Transfer of lipids to other membranes: Lipids in the ER membrane diffuse laterally to the nuclear envelope or are transported to golgi, vacuoles, plasma membrane or lysosomes. Lipid exchange proteins extract lipids from one membrane to be inserted into another. Synthesis of transmembrane proteins: Except for semiautonomous organelles, most transmembrane proteins are directed to the ER membrane first. From the ER, membrane proteins can be transported to other membranes via vesicles. What is glycosylation? It is the process of covalently attaching a carbohydrate to a lipid or protein. Glycolipid: carbohydrate to lipid Glycoprotein: carbohydrate to protein Function of carbohydrate? Recognition signal for other cellular proteins and cell surface. Helps protect proteins from damage. Types of glycosylation? N-linked glycosylation: addition of carbohydrate to nitrogen atom of asparagine side chain. O-linked side chain: addition of sugars to oxygen atoms of serine or threonine side chains(occurs only in golgi) Sugar is built onto lipid first then is transferred to proteins by oligosaccharide transferase. **Membrane transport** the plasma membrane is selectively permeable(some ions and molecules enter/leave but not others) why? so that essential molecules enter, metabolic intermediates remain, and waste products ex how do molecules pass through the membrane? Two ways: passive and active. Passive transport: no energy needed(down or with gradient) Active transport: requires energy(up or against gradient) uses ATP Phospholipid bilayer barrier: Barrier to hydrophilic molecules and ions due to hydrophobic interior Rate of diffusion depends on the chemistry of the solute and its concentration. Diethyl urea\>urea due to ethyl sidechains \- Gases and very small uncharged molecules have high permeability. Water and urea have moderate permeability Polar organic molecules have low permeability Ions and charged polar molecules have very low permeability Types of gradients: Transmembrane gradient and ion electrochemical gradient. Cells maintain gradients(environment inside is constant and different from outside) Transmembrane is chemical gradient while ion electrochemical is chemical and electrical gradient. What is tonicity? Tendency of cell to take in water. Three types: Isotonic: equal water and solute concentrations on both sides. Hypertonic: solute concentration is higher, and water concentration is lower on one side. Hypotonic: solute is lower, water is higher on one side. What is osmosis? Process of water diffusion from higher to lower concentration across membrane. If the solutes cannot move, water movement can make the cells shrink or swell as water leaves or enters. Osmotic pressure: the tendency of water to move into any cell. Animal cells must maintain a balance between extracellular and intracellular water and solute concentrations to maintain their shape and size. If not, then Crenation: shrinkage of a cell in a hypertonic solution. Osmotic lysis: swelling of cell in hypotonic solution. In plant cells, The cell wall prevents major changes in cell size and shape(expansion) Turgor pressure pushes plasma membrane against cell wall. Plasmolysis: plants wilting in hypertonic solution. In freshwater protists: Example: paramecium Must live in strongly hypotonic environment. Use contractile vacuoles to prevent osmotic lysis by getting rid of excess water. **Transport proteins:** for ions and hydrophilic molecules. two types: channel and transporters. Channels are open passageways. Most of them are gated. Aquaporins for water. Transporters(carriers) do a conformational change. Is used for organic molecules Tyes of transporters: Uniporter: one ion or molecule in one direction Symporter or cotransporter: 2 or more ions or molecules in same direction. Antiporter: 2 or more ions or molecules in opposite directions What is active transport? Up or against gradient Requires energy Two types: Primary active transport: uses pump with ATP directly Secondary active transport uses a pre-existing gradient for transport. **EXOCYTOSIS AND ENDOCYTOSIS:** Use to transport large molecules such as proteins and polysaccharides Exocytosis: excreted into extracellular matrix Endocytosis: folds inwards to form a vesicle, bring stuff inside. Three types; receptor-mediated endocytosis. Pinocytosis Phagocytosis **Chapter 5 book:** The two primary components of membranes are phospholipids and proteins. A third component is carbohydrate that attaches to lipids and proteins. Phospholipid bilayer: consists of two layers of phospholipids(amphipathic) Membrane is a mosaic of lipid, protein, and carbohydrates. Leaflet(half of a phospholipid bilayer) The two leaflets are asymmetrical, especially with glycolipids and glycoproteins only being on the extracellular leaflet. The nonpolar part of the transmembrane that is in the middle is called transmembrane segments, and are nonpolar amino acids that span from one leaflet to another Integral membrane proteins cannot be removed from the membrane unless the membrane is dissolved or damaged. Peripheral membrane proteins are usually bound to the membrane by hydrogen and/or ionic bonds. The membrane has fluidity(the individual molecules remain in close association but can readily move within the membrane) Membranes are considered semifluid because its components can only move in two dimensions( a fluid can move in three dimensions) Unlike rotational and lateral movements, flip-flop of lipids from one leaflet to another does not occur spontaneously because it is energetically unfavorable(hydrophilic phosphate group travels through hydrophobic interior) Requires flippase enzyme Double bonds= unsaturated Cholesterol in animal cells and phytosterols in plant cells. If the membrane is too fluid, it may become leaky. If it is too solid, it may inhibit the function of membrane proteins. How do cells maintain the membrane's fluidity? They insert more cholesterol in the membrane in lower temp and lengthen lipid tails or reduce double bonds in higher temperatures Transmembrane proteins can be restricted in place because of being bound to cytoskeleton filaments in cytosol or large fibers in extracellular matrix. Transmembrane proteins care capable of lateral and rotational movement. The building blocks of phospholipids are made in the cytosol by enzymes or taken into the cell by food. Two fatty acid tails are activated by the binding of a coenzyme that makes them attach to a glycerol-phosphate molecule. Carbohydrates at the outer leaflet protect proteins from protases that digest proteins. For N-linked glycosylation to occur, first, 14 sugar molecules are connected to a lipid, then oligosaccharide transferase transfers the carbohydrate tree to an asparagine in the polypeptide. O-linked glycosylation is important for the secretion of proteoglycans that organize extracellular matrix and forms mucus which coats cells. Membrane transport: the movement of ions and molecules across biological membranes. Important molecules such as glucose and amino acids remain in cell(selective permeability) Types of passive transport: Simple diffusion(pass through phospholipid bilayer) Facilitated diffusion(through membrane proteins) Do not need energy. Active transport: Lower to higher concentration. Needs energy. Ions and molecules are solutes, and they dissolve in water which is the solvent. What four factors affect the permeability of solutes? Size: smaller crosses faster Polarity: nonpolar crosses faster Charge: noncharged crosses faster Concentration: lower crosses faster. \- Transmembrane gradient= concentration gradient(concentration of solute) also called chemical gradient. An electrochemical gradient is a dual gradient-electrical and chemical gradient. It occurs for solutes with net positive or negative charge. The formation of a gradient requires an input of energy. Plasmolysis: cell membrane pulls away from cell wall. Gated channels are controlled by the noncovalent bonding of small molecules called ligands(like hormones and neurotransmitters) Transporter proteins are slower than channel proteins. Antiporters are also called exchangers A pump is a type of transporter that directly uses energy(primary active transport) Secondary active transport where a pre-existing gradient drives the transport of another solute. H+/solute transporters in fungi, algae, plant, and bacteria cells. Na+/solute transporters in animal cells. K+ is higher inside, Na+ higher outside in animal cells. Na+/K+ - ATPase uses ATP to make Na higher outside and K+ higher inside(important for electrochemical gradient maintaining) Electrogenic pumps generate an electrical gradient. E1 and E2 E1: higher affinity Na+ inside, lower affinity K+ inside. E2 lower affinity Na+ outside, higher affinity K+ outside. ATP turns to ADP in a process called phosphorylation Types of endocytosis: Receptor mediated: specific to certain molecules Pinocytosis: for absorption of nutrients and is not specific. Takes in whatever. Phagocytosis: engulf a large particle such as a bacterium and is specific to certain cells. Creates a phagosome that fuses to a lysosome that breaks down what's inside. Kill bacteria with phagocytosis. **Chapter 6** Types of energy? First, energy is the ability to promote change or do work. There are two types: Kinetic(movement) and potential(due to location or structure) energy Chemical energy is the energy found in molecular bonds. It is a form of potential energy. What are the two laws of thermodynamics? First law is the law of conservation of energy. It states that energy cannot be created or destroyed but can be transformed from one kind to another. Second law of thermodynamics states that transfer of energy from one kind to another increases entropy(degree of disorder) of the system. As entropy increases, less energy is available for organisms to use to promote change. \- Total energy(enthalpy) is sum of useable and unusable energy. Entropy is disorder that cannot be harnessed to do work Free energy(G) is the amount of energy available to do work. It is also called Gibbs free energy. H = G + TS H = enthalpy G = free energy T = temperature(K). S = entropy What is a spontaneous reaction? Does not require energy(happens on its own) Is determined by free energy change(G~2~-G~1~) delta G Spontaneous does not mean fast. Formula for free energy change? **ΔG = Δ H -- T Δ S** If **ΔG** is negative, then the process is exergonic, releasing energy. Is spontaneous If **ΔG** is positive, then the process is endergonic, requiring energy. Not spontaneous Example of exergonic reaction: hydrolysis of ATP. It favors formation of products(ADP) released energy is used for exergonic processes. Endergonic is coupled with exergonic. The reaction will be spontaneous if the net free energy change for both processes is negative. ATP? Each ATP undergoes 10k cycles of hydrolysis and resynthesis. Particular amino acids bind to ATP. Thus, we can predict whether a protein will bind to ATP or not. On average, 20% of all proteins bind ATP. However, this is likely an underestimate due to other possible unknown ATP-binding sites. This means ATP is an important energy source in the body. \- How is ATP resynthesized? ATP synthesis is an endergonic process, needing energy. It is driven by exergonic processes like cellular respiration. What are catalysts? A catalyst is an agent that speeds up the rate of a chemical reaction without being consumed during the reaction. Enzymes are protein catalysts Ribozymes are RNA molecules with catalytic properties. Activation energy? Is needed to drive chemical processes, even exergonic. It is an initial input of energy to start reaction How? Allows molecules to get close enough to cause bond rearrangement. Transition state where bonds are stretched. Method? Large amounts of heat. Enzymes to lower activation energy. How do enzymes lower activation energy? By straining bonds in reactants to make it easier to reach transition state Positioning reactants together to facilitate bonding. Changing local environment: direct participation through very temporary bonding Enzyme terms? Active site-where reaction takes place. Substrates-reactants that bind to active site. Enzyme-substrate complex-formed when enzyme and substrate bind. Chapter 7: Number of ATP synthesized by the metabolic pathways of mitochondria Steps for each process, 3 for ex. Dehydrogenase Oxoacetate No need to know the enzymes of citric acid cycle Midterm only until slide 18