1. Chapter 1
1.1. Unity and diversity of cells
1.1.1. Cells come in various shapes, sizes and functions.
1.1.2. All cells have a similar chemical makeup and are made of the same molecules.
1.1.2.1. Ex-Dna and genetic material
1.1.3. Central Dogma- DNA->RNA->Protein
1.1.3.1. Central dogma makes up self replication of catylists. figure 1-4
1.1.3.1.1. Viruses do not have this ability. Ability only found in living cells.
1.1.4. Proteins dictate the appearance/behavior of a cell. (Alberts, 2019, pg 4)
1.1.4.1. Proteins are made of amino acids and there are 20 amino acids.
1.1.5. Daughter cells aren't identical to parent cells due to mutations that take place during the DNA replication process.
1.1.5.1. The struggle for survival- eliminates first-gen, favors second-gen, and tolerates third-gen. (Alberts, 2019, pg 5)
1.1.6. Evolution is the process of organisms changing and adapting to their environments over time in increasingly complex ways. (Alberts, 2019, pg5)
1.1.6.1. Around 3.5-3.8 billion years ago a single ancestral cell with universal instructions for all life existed and all cells evolved from it in their own ways through evolution.
1.1.7. Cells have genomes which are the entire sequence of nucleotides in an organism's DNA and they give the cells instructions on how to behave and what processes to carry out. (Alberts, 2019, pg 6)
1.1.7.1. All cells contain the same DNA however, they express certain parts of the genome which gives certain cells certain tasks depending on the environment they are in.
1.2. Cells under the microscope
1.2.1. Microscopes invented around the 17th century and Hooke used glass lenses to view cork pieces in which he discovered mini chambers which he called cells.
1.2.2. Cell theory states that all living things are formed from the growth and division of existing cells. (ALberts, 2019, pg 7)
1.2.3. There are many types of microscopes each with a different purpose.
1.2.4. Light microscope: views cells (5-20 picometers) and some of their structures. The plasma membrane encloses the animal cells and the nucleus is a round large structure in the cell center. There is also the cytoplasm which is a transparent substance with many smaller undistinguishable molecules in it. The structures less than 0.2 picometers cannot be seen.
1.2.5. Fluorescence microscopes use better methods of imagery and electronic image processing to view fluorescently labeled structures. They can view these structures at sizes around 20 nanometers (ribosomes- structures used to translate RNA to protein).
1.2.6. Electron Microscopes can view structures as small as a few nanometers. There are transmission and scanning electron microscopes. Transmission scopes use a beam of electrons transmitted through the sample to view it. A scanning scope scatters electrons all over the surface of a cell to view the surface detail of cells and small structures.
1.3. Prokaryotes and Eukaryotes
1.3.1. Prokaryotes- No Nucleus; Spherical, rodlike, corkscrew-shaped; Cell wall surrounds the plasma membrane; Plasma membrane surrounds single compartment with cytoplasm and DNA; No membrane-bound organelles; Archaea and bacteria; Monocellular organisms; The most complex and diverse organisms(Alberts, 2019, pgs 11-16)
1.3.2. Eukaryotes-Have nucleus-contains main genetic info in DNA; Cytoplasm-Surrounds all contents inside the cell outside of the nucleus; Mitochondria-Makes ATP and carries out final oxidation of food molecules; Chloroplast-photosynthesis in plant cells and other photosynthetic organisms; Er/Golgi-Synthesis of complex molecules for export/insertion; Has membrane-bound organelles; Cytosol- Made up of many large and small molecules; Multicellular organisms; Cytoskeleton- comprised of protein filaments. Three types of filaments- microtubule filaments, actin filaments, and intermediate filaments.(Alberts, 2019, pgs 16-23)
1.3.3. Endosymbiotic theory- Mitochondria and chloroplasts which have dual membranes are thought to have been originally bacteria that was engulfed by an early eukaryotic cell. They then lived in symbiosis with the host cell since they helped each other reproduce and survive. (Alberts, 2019, pg18)
1.4. Model organisms
1.4.1. Many model organisms were chosen due to the fact that you cannot learn about all organisms just by studying one specific organism.
1.4.2. E.coli has simple DNA and gene expression than other organisms.
1.4.3. Yeast: simple single cell organism that can be grown easily in a dish and can be used to answer more complex questions.
1.4.4. Arabidopsis is a model plant and it is similar to weeds so it is small and can be grown with ease allowing for the study of multiple generations which also allows for a lot of genetic manipulation to be done.
1.4.5. Flies are very cheap and can be grown quickly. They have been used for genetic studies a lot and since they grow quickly they can be studied in multiple generations in the lab.
1.4.6. Worms are used since the neurons have been mapped and they can be used to better study neuron development.
1.4.7. Fish can be used since they can be studied for genetics and they are clear when larvae so you can see them develop as they grow and you can also study neurons in them.
1.4.8. Mice can be used to study mutations that are phenotypically similar to human mutations. You can also study genes in mice that are similar to humans and they are mammals making them more similar to humans.
1.4.9. Humans are not studied much but their cells are studied in a dish like cancer cells or stem cells.
1.4.10. (Myhr, 2021, ML01-113e )
2. Chapter 3
2.1. The use of energy by cells
2.1.1. Second law of thermodynamics- The law states that the disorder of things in any system will increase which is referred to as entropy.
2.1.2. Energy used by cells is converted from one form t another in order to allow the cell to generate order. the cell generates order by having chemical reactions take place which release that converted energy . The energy released must be great enough to increase the total entropy.
2.1.3. Plants use photosynthesis to obtain energy from the sun by converting sunlight to molecules needed to synthesize larger important macromolecules such as proteins and polysaccharides.
2.1.4. Animals use cellular respiration in order to convert glucose, obtained from eating pants, into energy they can use.
2.1.5. Redox reactions are either oxidation or reduction reactions. Oxidation is when an atom loses an electron while reduction is when an atom gains an electron. Redox reactions always occur simultaneously in order to conserve the number of electrons durng chemical reaactions. (Alberts, 2019, pg 87)
2.2. Free energy and catlysis
2.2.1. Enzymes are catalysts that lower the activation energy of chemical reactions. They do this by binding to substrates in a way that reduces the activation energy.
2.2.2. Chemical reactions always occur in the direction that would cause a loss of free energy. These types of reactions are energetically favorable.
2.2.3. Free energy is referred to as G. The change in free energy during a reaction is delta G. If a reaction has a negative delta G (decreases free energy of the system that the reaction belongs to) it is said to be energetically favorable. if a reaction has a positive delta G (decreases entropy in the system) are energetically unfavorable and must be coupled with a second favorable condition in order to take place. (Alberts, 2019, pgs 91-92)
2.2.4. Equilibrium is reached when the forward and reverse reactions of a chemical reaction have the same rates. At this point, delta G is 0. Cells always attempt to avoid equilibrium because at equilibrium no reactions occur which would lead to the death of the cell.
2.2.5. Delta G cannot be used to compare the free energy of different reactions since it depends on the concentration of the molecules in the reaction. Therefore, the delta G degree is used to represent standard free energy change. This is not dependent on the concentration of molecules. it relies on the characteristics of the reactants and how they behave under ideal conditions. (ALberts, 2019, pg 92-93)
2.2.6. AN equation for calculating delta G is as follows: delta G = delta G degree + RT(ln(x/y)). (Alberts, 2019, pg 93)
2.2.7. The equilibrium constant in a simple reaction is the ratio of substrate to concentration which is K=x/y. (Alberts, 2019, pg 93) The equilibrium constant in complex reactions is the concentration of products over the concentrations of both reactants multiplied: k= [AB]/([A][B]) (Alberts, 2019, pg 97)
2.2.8. The equilibrium constant can also be used to determine the strength of bonds. If the free energy change is negative the reactants will bind together. The free energies of the two reactants can be compared to the free energy of the product and if it's more negative than the free energies of the reactants then the reactants will bind to each other. (ALberts, 2019, pg 97)
2.2.9. There are also sequential reactions in which two reactions are coupled. When this occurs, the free energies of both reactions are summed and if the sum is favorable then both reactions will happen even if the first reaction is unfavorable. As long as the following reaction is favorable and the overall sum is favorable, the reactions will occur. (ALberts. 2019, pg 98)
2.3. Activated carriers and biosynthesis
2.3.1. Coupled reactions are used to produce useful molecules such as activated carries by running a favorable reaction with an unfavorable reaction. Enzymes are used for coupled reactions since they are what couple the reactions together like the paddle wheel example given in the textbook on page 104.
2.3.2. ATP is the most used activated carrier. ATP can be broken down into a phosphate group, which essentially gives provides the energy stored in ATP, and ADP which can be remade into ATP to be used as an energy source once again. This is done through a process called ATP hydrolysis which uses water to break the ATP into ADP and P. The P is then added to another molecule, phosphorylation. The energy stored in the ATP is usually sed when joining molcules together.
2.3.3. Another example of an activated carrier is NADH and NADPH which are carriers of high energy electrons. The high-energy electrons are accompanied by a proton to make hydride which is passed on to the donor molecule oxidizing the carriers to NADP+ and NAD+. (Alberts, 2019, pg 107) There are also other carriers such as Acytel-coA. Table 3-2 lists the activated carriers on page 109 of the textbook.
2.3.4. Monomers of most macromolecules use enzyme-catalyzed condensation reactions. These reactions are coupled with hydrolysis reactions in order to allow for the condensation reactions to occur. These reactions also use ATP hydrolysis in order to create the final bond that is broken through condensation. (Alberts, 2019, pg 110-111)
3. Chapter 2
3.1. Chemical Bonds
3.1.1. Atoms are made up of a dense nucleus which is made up of protons (positive charge) and neutrons (neutral charge). The nucleus is orbited by electrons (negative charge) that weigh almost nothing compared to protons and neutrons.
3.1.2. 96% of the weight of all living things is made up of Carbon, hydrogen, nitrogen, and oxygen. There are 90 natural elements. (Alberts, 2019, pg 41)
3.1.3. Atoms' electrons are responsible for reactions between atoms. They orbit the nucleus in electron shells that can hold a limited number of electrons per shell. The outermost electrons, or valence electrons, interact with other atoms only when the outer most shell is not full. The atoms with full shells do not react with other atoms.
3.1.3.1. Ex of atoms with full shells: Helium and other noble gasses.
3.1.4. The two types of chemical bonds formed can be Covalent bonds (between atoms sharing electrons) or ionic bonds (between an atom that took electrons from another atom).
3.1.5. 4 types of weak noncovalent bonds: Hydrogen bonds(A positively charged hydrogen in a covalently bonded molecule comes near a negatively charged atom in another molecule and forms a weak bond with it), electrostatic attractions(The positive and negative charge of atoms from different covalently bonded molecules brings the atoms together forming a weak bond.), van der Waals attractions(weak bonds form between atoms when they come into close proximity of each other and can be formed between atoms of molecules that are not nonpolar or cannot form ionic bonds.), and hydrophobic force(Caused when nonpolar surfaces are pushed out of hydrogen-bonded water networks into areas where they would interfere with the interactions between water molecules). (Aberts, 2019, pg 47-48)
3.1.6. Acids are substances that release protons when dissolved in water while bases are substances that accept protons when dissolved in wtaer.
3.2. Small molecules in cells
3.2.1. There are organic molecules that are made using carbon and inorganic molecules like water found in cells. The organic molecules can be separated into four categories: Carbohydrates, Lipids, Proteins, and Nucleic acids.
3.2.1.1. Carbohydrates-Subunit is sugars/monosaccharides. Monosaccharides link together with glycosidic bonds. Two monosaccharides make a disaccharide and multiple monosaccharides make a polysaccharide when boned together using condensation. The glycosidic bonds can be broken apart using hydrolysis. They can be branched and their main use is to store energy. Glucose, a monosaccharide, is used as an eneergy source
3.2.1.1.1. Lipids- Subunit is fatty acids. Fatty acids are amphipathic (have a hydrophobic and hydrophilic region). Can be unsaturated (have double bonds) or unsaturated (no double bonds). Many fatty acids combine to form a lipid. Many lipids form a lipid bilayer which is the basis of cell membranes. Fatty acids are used to store energy (food reserves)
4. Chapter 4
4.1. The shape and structure of proteins
4.1.1. The sequences of amino acids in proteins are what specify the proteins' shape.
4.1.2. Amino acid side chains give a protein its unique properties. The side chains project from the backbone of the protein and do not involve themselves in the peptide bond making process.
4.1.3. The shape of the fold in a protein is determined by the weak noncovalent bond within it. These bonds and attractions are hydrogen bonds, electrostatic attractions, van der Waals attractions, and hydrophobic force. Also, an important factor that determines the shape of the fold is the placement of the polar/nonpolar amino acids in the protein.
4.1.4. Proteins fold into the conformation with the least amount of free energy since this makes the folding energetically favorable. The final structure into which a polypeptide chain folds is called a conformation.
4.1.5. Chaperones are folding helpers that help proteins fold in cells. They do not alter the folding shape since this is determined by the amino acids. They do, however, make the folding process much more efficient and reliable. Some protein shapes are shown on pages 125 and 126 of the textbook.
4.1.6. Two structures within proteins are alpha and beta helices. Alpha helices are formed when a single polypeptide chain coils around itself making a rigid cylinder. A hydrogen bond is then made between every fourth amino acid. Beta helices are formed when hydrogen bonds form between side by side polypeptide chains. If the chains are parallel, its called a parallel beta helix and if they are anti parallel it is called an antiparallel beta helix. (Alberts, 2019, pgs 128-129)
4.1.7. A misfolded protein can cause problems that can lead to disease. Amyloid structures are formed by proteins, however, when proteins fold incorrectly, they can form amyloid structures that harm cells such as those in Alzheimer's disease. (Alberts, 2019, pg 129)
4.1.8. Proteins have multiple structural levels. They include primary (amino acid chain), secondary (alpha and beta helices), tertiary (3-d structure formed by polypeptide that includes the helices and loops/folds between the terminuses), and quaternary structures (Protein is made up of more than one polypeptide chain interacting with one another).
4.1.9. Proteins are classified into families. Each family has its own unique amino acid sequence and 3-d shape that is found among all members of the family.
4.1.9.1. Ex-serine proteases: family with some digestive enzymes and same blood clotting proteases that are all similar in the amino acid sequences. (Alberts, 2019, pg 132)
4.2. How proteins work
4.2.1. Proteins can bind to other molecules. The molecules that each protein binds to are very specific ranging from one to a few molecules. The substance that binds to the protein is called a ligand. The part of the protein that bonds to the ligand is called the binding site.
4.2.2. An example of proteins that bind to other molecules are antibodies. They are produced by the immune system and bind to specific antigens, or target molecules, that they target for destruction.
4.2.3. Enzymes are proteins that catalyze reactions. they bind to substrates (ligands) and convert them to chemically modified products. They increase the speed of reactions by binding to substrates.
4.2.4. Michaelis constant- the concentration of substrate at which an enzyme works at half its maximum speed. This is denoted by Km. The smaller the Km, the stronger the enzyme and substrate are bonded. The larger the Km, the weaker the enzyme and ligand are bonded. (Alberts, 2019, pg 143)
4.3. How proteins are controlled
4.3.1. Cells control the concentration of proteins within them. Another type of control done on proteins is feed back inhibition in which a product of an enzyme in a metabolic pathway later inhibits that enzyme when too much of that product is produced. This is called negative regulation. The opposite affect can also occur and that is called positive regulation.
4.3.2. Allosteric proteins can change their conformation to multiple slightly different shapes. A ligand stabilizes the conformation that it binds to strongest. Thus, the substrates, at high concentrations, can switch the type of protein to the population that it prefers. Protein phosphorylation occurs when a phosphate group is added to a protein's amino acid chain. The negative charge of the phosphate group can ultimately cause a conformational change which can alter the binding site. (Alberts, 2019, pg 152)
4.3.3. Some proteins can be modified at multiple amino acid chains such as p53 protein. This checks for any damage in DNA before the cell enters mitosis. The p53 protein has 20 sites at which it can be modified. Thus, the p53 protein can be altered in a multitude of ways.
4.3.4. GTP is another way to control proteins. GTP binds various types of GTP-binding proteins tightly. The proteins are like a switch that are activated when bound to GTP and inactivated when they hydrolyze the GTP releasing a phosphate group. Motor proteins control muscle movement. In order to achieve this, proteins must undergo irreversible conformational changes through the coupling of ATP hydrolysis to one of the conformational changes. (Alberts, 2019, pg 154-155)
4.4. How proteins are studied
4.4.1. Proteins are studied in various ways. They first must be purified from cells or tissues through processes such as: Homogenization and centrifugation, chromatography, and electrophoresis.
4.4.2. Homogenization is when you break apart the protein and other intercellular contents from the cell through ultrasound, mild detergent, forcing cells through small holes using pressure, and shearing cells between a rotating plunger and the walls of a glass tube.
4.4.2.1. Centrifugation separates the contents from the broken cell, homogenate, into a pellet (more dense components) and supernatant (less dense components).
4.4.3. Column chromatography uses a large amount of solvent to separate a mixture of proteins along a permeable solid matrix. The proteins can be collected separately along the matrix based on their size, charge, or hydrophobicity.
4.4.4. Gel electrophoresis separates proteins based on their size. The proteins are coated in negative charge and they must travel through a gel like substance since they are attracted to the positive buffer at the other side of the gel. This separates proteins based on their size and net charge.
4.4.5. Immunocytochemistry uses the binding of specific antibodies to their specific antigens to pinpoint specific proteins.
4.4.6. To study the finer details of proteins, such as their amino acids, you will need to use a method like mass spectrometry. Mass spectrometry determines the exact mass of peptide fragments from the amino acid chain which allows for the protein to be identified from a database. (Alberts, 2019, pg 159)
4.4.7. Alberts, 2019, pgs 158-161, panel 4-3 pg 164-169