MCB Exam 1 Study Guide PDF

Exam 1: Study Guide Concepts: Experimental Model Systems ​ A unicellular simple Eukaryote can make good model organisms (yeast) ​ Model Systems can be manipulated and studied ​ Worms, Fruit Flies, Mice, Yeast, are all good model systems ​ Model systems are chosen based on what you want...

Exam 1: Study Guide Concepts: Experimental Model Systems ​ A unicellular simple Eukaryote can make good model organisms (yeast) ​ Model Systems can be manipulated and studied ​ Worms, Fruit Flies, Mice, Yeast, are all good model systems ​ Model systems are chosen based on what you want to look at so that could be things like unicellular organisms to multicellular organisms ​ Tool used for advancing information in molecular cel biology bc we can use them as parallels. ​ Organelles - Must have a membrane, and specific function within the cell. ​ Animal cells do not have a cell wall ​ Cells need to become differentiated into different structures (Neurons, cells, etc) ​ Mitochondria have an outer phospholipid bilayer and an inner phospholipid bilayer (contains 2 which is not common) ​ Chloroplasts have an outer phospholipid layer and inner membrane and then a series of membranous discs ​ By endosymbiotic theory they were able to develop a relationship with other cells and become the types of cells we know today Biologically Relevant Non-Covalent Interactions ​ Covalent Bonds - Forms when two atoms come very close together and share one or more of their outer-shell electrons. ​ Non-Covalent Bonds: Most of the processes inside of a cell happens due to their interactions with water. ○​ Types: ​ Hydrogen Bonds - Polarized (Partial negative/partial positive charges),electronegativity is what causes this, linkage forms when a hydrogen atom is sandwiched between two electron-attracting atoms (usually oxygen or nitrogen). These are strongest when three atoms lie in a straight line. ​ Electrostatic Interactions (Ionic Bonds) - Occur between fully charged groups (ionic bond) and between partially charged groups on polar molecules. During this type of interaction, the two partial charges fall off rapidly as the distance between charges increases. They are strong in the absence of water. ​ Van Der Waals (Hydrophobic Interactions) - Nonpolar and don’t have a charge. (Ex. Hydrocarbons, equal sharing of electrons). Molecules that are insoluble in water. Water forces hydrophobic groups together in order to minimize their disruptive effects on the water network formed by hydrogen bonds. Aggregating is what keeps oil and water separate. ​ Hydrophilic Molecules - Substances that readily dissolve in water. Include things like ions and polar molecules that attract water molecules  through electrical charge effects. Water molecules surround each ion or polar molecule and carry it into solution. ○​ These types of bonds have a strong cumulative effect. Alone weak, together strong. ○​ The repulsion of hydrophobic groups from water play an important part in these interactions and for the folding of macromolecules. ○​ These can be broken (from folded to unfolded state) through heat, salts, pH, mechanical disruption. From Precursor to Macromolecules ​ Can go from subunits to macromolecules by covalent bonds (condensation) and those macromolecules can then form additional molecules and folding through non-covalent interactions (mostly). Four Macromolecules and Their Significance ​ Polysaccharide ○​ Sugars = small organic building block ​ Sugar form Covalent bonds to go from Monomer to Dimer to Trimer to eventually a polymer (polysaccharide) ○​ Types of Sugars: ​ 3 carbon sugars (trioses) ​ Good intermediates in energy generation. ​ 5 carbon sugars (pentoses) ​ Sugar components of nucleotides ​ 6 carbon sugars (hexoses) ​ Very basic energy course in our cells ○​ Glycogen = most common in us, Starch = most common in plants ○​ Monosaccharides - (CH2O)n, where n can be 3-8, and contain two or more hydroxyl groups. They also contain either an aldehyde or ketone group. ○​ Disaccharides - A carbon that carries an aldehyde or ketone that can react with any hydroxyl group on a second sugar molecule to form this disaccharide ​ Maltose = glucose + glucose ​ Lactose = galactose + glucose ​ Sucrose = glucose + fructose ○​ Oligosaccharides - Short chains of large linear and branched molecules that are made from simple repeating sugar subunits ○​ Polysaccharides - Long chain version of Oligosaccharides ​ Protein ○​ Amino Acids = small organic building block ​ Amino acids form covalent linkages to go from a dipeptide, tripeptide, polypeptide (protein) ○​ Have ionized entities and side groups called R-groups, their nature is dictated by these R groups ​ Nucleic Acid ○​ Nucleotides = small organic building block  ​ Nucleotides form covalent linkages to go from dinucleotide, trinucleotide, to polynucleotide (nucleic acid) ​ Consists of nitrogen containing base, 5-carbon sugar, and one to three phosphate groups, and an organic base (A,T,C,G) ​ The bases are nitrogen containing ring compounds which are either Pyrimidines (1 Ring) (Uracil, Cytosine, Thymine) or Purines (2 rings) (Adenine, Guanine) ​ Phosphates - This is what makes the nucleotide negatively charged ​ Can exist as a mono, di, or triphosphate when they are free as a building block ​ ATP = Adenine Triphosphate ​ Their sugars differ in attachments, hydroxyl = ribose, hydrogen = deoxyribose ​ Hydroxyl (Polar) is more reactive which is the reason why RNA is much more fluid than DNA ​ Hydroxyl at carbon number 3 becomes consumed during condensation ○​ Nucleic Acid Polymers - To form this nucleotides are joined together by phosphodiester bonds between the 5’ and 3’ carbon atoms of adjacent sugar rings ​ Phosphodiester Bonds - A covalent bond between a phosphate group and a sugar molecule. ○​ Nucleotide Functions ​ 1. Nucleoside di/triphosphates carry chemical energy in their easily hydrolyzed phosphoanhydride bonds. ​ 2. They combine with other groups to form coenzymes ​ 3. They are used as small intracellular signaling molecules in the cell ​ These first 3 follow the rule because their covalent linkages is made between two monomers by removal of water. (Condensation reaction or dehydration reaction). ​ Breaking down a polymer can be done through hydrolysis (adding water). ​ Our cells try to hydrolyze nutrients to release energy and make new polymers. Constantly happening ​ Fats and Membrane Lipids ○​ Fatty Acids = small organic building block ​ Long chains of Nonpolar entities ​ Hydrophobic ​ Have carboxyl at one end that forms condensation reaction and covalent linkage with glycerol ​ 3 fatty acid chains through 3 condensation reactions will form a covalent bond with glycerol forming a triacylglycerol ​ They do not like water so they will aggregate within the cell. They act as long term storage for energy. ​ These are major constituents of cell membranes  ​ Contain a carboxyl group at one end and a long hydrocarbon tail at the other ​ They are stored in cells as energy reserve (fats and oils) through ester linkage to glycerol to for triacylglycerols (triglycerides) ​ Saturated - Fatty acids with no double bonds ​ Unsaturated - Fatty acids with one or more double bonds in their hydrocarbon tail ○​ Micelle - Basket of cells that have polar heads and hydrophobic tails, water cannot enter the center of these ○​ Liposome - Similar to micelle but larger and has a round area of polar heads on the inside able to allow water in. Almost like a basket within a basket. ○​ Tricylglycerols - from large, spherical fat droplets in the cell cytoplasm ○​ Phospholipids and Glycolipids - Form self-sealing lipid bilayers which are the basis for all cell membranes ○​ Other Lipids - Lipids are defined as water-insoluble that are soluble in organic solvents. Two other common types are steroids and polyisoprenoids (both are made from isoprene units). Energenetics ​ Condensation is energetically unfavorable, going from smaller to larger molecule creates more order because it needs an input of energy. ​ Hydrolysis or the break down of polymers is energetically favorable bc you are going from order to less order therefore releasing energy ​ Gibbs Free Energy ○​ Molecules are most stable at their lowest state of free energy. ​ Stable conformations are achieved by mostly non-covalent interactions. (Like Micelles and Liposomes) ○​ +G = Endergonic, Applies to products at the end of the reaction, products higher than reactants = +G. This is an anabolic reaction (not energetically favorable) ○​ -G = Exergonic, products lower in energy than reactants = -G. This is a catabolic reaction ○​ These reactions are coupled because once one occurs, the other will take place. ​ Spontaneous Direction of Reactions ​ ATP Coupling ○​ When an endothermic/exothermic reaction takes place we can then have the other reaction take place because it is now in a favorable state for that opposing reaction to take place. ○​ Activated carrier molecules are created as a byproduct of a catabolic reaction an then used to drive an anabolic reaction ○​ Steps: ​ 1. Activation step - ATP transfers a phosphate to produce a high energy intermediate  ​ 2. Condensation step - The activated intermediate reacts with B-H to form the product A-B, a reaction accompanied by the release of inorganic phosphate. ​ Net Result: A-OH + B-H + ATP -> A-B + ADP (activated diphosphate) + P ​ Endothermic vs Exothermic ○​ Endothermic - Similar to Endergonic but only applies to absorption of heat. (needs an enzyme AND ATP). ​ Endergonic (Anabolic) vs Exergonic (Catabolic) ○​ Exergonic - Needs Enzyme but NOT ATP ○​ Endergonic - Needs Enzyme AND ATP ​ What enzymes affect and don't affect in a reaction ○​ Enzymes lower the activation energy to make it easier for things to start. ○​ They are needed in both catabolic and anabolic ○​ They only affect the activation energy ○​ Enzymes interact with their substrates in order to lower this activation energy. They bind with the activation site. ○​ Enzymes are not consumed in the reaction, they come in and bind then leave and start again. ○​ Not all enzymes are proteins, but most are. ​ Activation Energy ○​ Energy requirements that are needed to get the reaction to start. Biomembranes and their Structure/Name ​ Phospholipid bilayer core is hydrophobic Groups of Amino Acids by their Nature ​ Always looking for their lowest state of free energy ​ All 20 amino acids have a backbone, an amino group and a carboxyl group. They differ in their R groups (or side chain). ○​ The R groups can be put into 4 different categories: ​ Acidic - Aspartic Acid, Glutamic Acid ​ Basic - Lysine, Arginine, Histidine ​ Uncharged Polar - ​ NonPolar (Hydrophobic) - Look for evenly shared electrons in the R group ​ Special Amino Acids: ○​ Cysteine - Has SH in R group, this SH can form covalent linkages with another Cysteine SH, they are the ONLY amino acids that can do this. THIS IS IMPORTANT TO REMEMBER. (This is a disulfide bond formation). ○​ Proline - Amine group is covalently engaged with the R group (Triangle looking R group). ○​ Glycine - Doesn't really have an R group just an H. They are seen a lot at the interface of proteins. ○​ The other R groups can interact through NON COVALENT INTERACTIONS. Proteins ​ Primary structure to quaternary structure ○​ Primary Structure - Linear covalently linked macromolecules of single polypeptide chain. Emerges from condensation reactions. Endothermic. ○​ Secondary - Emerges from primary, it is local (happens within the molecule) hydrogen bonding of the backbone rendering alpha helical or beta sheet motifs/shapes. R groups are NOT involved. (not every part of protein will not organize to secondary structure = disorganized regions). Backbone interactions are removed. (Carboxyl and Amino ends are the players here through H bonding) ​ Alpha Helical - R groups are positioned out and exposed while amino acids interact with neighboring amino acids. Intramolecular H bonding (Right handed helix only) ​ Beta Sheets - R groups are positioned out and exposed while amino acids interact with neighboring amino acids. Intermolecular H bonding (Right and Left handed helix) ○​ Tertiary - Maintained by interactions between the R groups, dependent upon their nature and what R groups are (pos or neg = ionic , polar = hydrogen, hydrophobic). Folding is stabilized by R group interactions. Alpha and Beta Interactions. 90% noncovalent interactions. (R groups are the players here through the 4 noncovalent interactions within the single polypeptide chain) ​ Cysteine - Are able to form covalent disulfide linkages between different groups if they have R group cysteines. ○​ Quaternary - These are intermolecular which means it interacts between different polypeptide chains R groups interact between 2 or more polypeptide chains. Engage their R groups and form the same type of R groups as tertiary but form between DIFFERENT polypeptide chains (2 or more). Nonvcovalent and/or sulfhydryl. Once a tertiary structure is formed for each of the monomers, then the monomers will interact to form this structure. ○​ All proteins reach tertiary but not all reach quaternary ○​ Can go beyond the quaternary structure to make large complexes ○​ How they are stabilized ​ Stabilized by other proteins or nonproteins, disulfide bonds ​ Cholesterol stabilizes artificial cells. ○​ Significance of disulfide bonds - aid in stabilization, remember it is formed through the bond of two cysteines. ○​ Can quaternary/tertiary structures be denatured back to primary? How? ​ Denaturation is the breakage of all the noncovalent interactions through salt, heat, mechanical interactions, pH, etc. ​ Disulfide bonds do not break this way because they are covalent. ○​ Can they re-nature?  ​ Theoretically yes, but because many proteins need help going down this energy journey, then they cannot reform. If they used no help to get there then they could be reformed. ​ Peptide chains always grow from the carboxyl end, that's why we say it goes from end terminus to carboxyl terminus. ○​ Polypeptide chain begins its existence as a linear chain of amino acids ​ Phosphorylation ○​ Phosphorylation is the process of adding a phosphate group (PO₄³⁻) to a molecule, typically a protein. This modification can significantly alter the molecule's activity, structure, or function. Phosphorylation is commonly used in cellular signaling to regulate a variety of cellular processes, such as: 1.​ Activating or deactivating enzymes: Adding a phosphate group can change the enzyme's shape, enabling or inhibiting its activity. 2.​ Regulating protein interactions: Phosphorylation can create or prevent binding sites for other molecules, affecting protein interactions. 3.​ Controlling cellular processes: Phosphorylation is essential for controlling processes like cell division, metabolism, and gene expression. 4.​ This process is often catalyzed by enzymes called kinases, which transfer a phosphate group from ATP to the target molecule. Conversely, phosphatases remove phosphate groups from proteins or other molecules, reversing the effect of phosphorylation. ○​ Phosphorylation plays a key role in many biological pathways, including signal transduction and cell cycle regulation. ​ Dephosphorylation - is the process of removing a phosphate group (PO₄³⁻) from a molecule, typically a protein. This process is the reverse of phosphorylation, and it often plays a key role in regulating the activity of proteins and other cellular functions. ○​ Dephosphorylation is usually carried out by enzymes called phosphatases, which catalyze the removal of the phosphate group. This removal can lead to several effects: 1.​ Inactivation of enzymes: In some cases, dephosphorylation can deactivate enzymes that were previously activated by phosphorylation. 2.​ Changes in protein-protein interactions: The removal of a phosphate group can expose or hide specific binding sites on a protein, thus altering its interactions with other molecules. 3.​ Regulation of signaling pathways: Dephosphorylation can switch off signaling pathways that were activated by phosphorylation, allowing for the fine-tuning of cellular processes. 4.​ Cellular processes: It plays a role in processes like cell cycle regulation, gene expression, and metabolism, helping to maintain homeostasis. ○​ In summary, dephosphorylation is essential for turning off or modulating the effects of phosphorylation, helping to maintain balance and control in various cellular activities. ​ Ubiquitylation - Process that attaches ubiquitin to proteins which regulates many cellular functions  ​ Methylation - A chemical process that adds methyl groups to molecules like DNA, proteins, neurotransmitters. ○​ How are these achieved and what are their purposes? ​ Chaperones and other mechanisms that aid protein folding ○​ Proteins that help other proteins fold, they help the protein fold and then they are removed. ○​ ​ ImmunoglobulinG - Antibodies, V shaped structures with a lot of flexibility due to the disorganized regions. ​ Hemoglobin - Oxygen carrier molecule in red blood cells, tetramer. Once a tertiary structure is formed. Globular Protein keeps folding on itself like a ball. ​ Proinsulin/Insulin - Large version of insulin is called PROinsulin bc it is made larger than its final product (insulin). The internal region is removed after it aids. This is also why it cannot be re-natured. ​ Importance of shape and the nature of surfaces of macromolecules to their function ○​ Globular proteins ○​ Coil-coil proteins like collagen (glycine are seen a lot here). ​ Protein Domains ○​ Regions of a protein that often form a functional module for that protein ○​ Proteins can have 1 or more significant domains. ○​ They have distinct structures that often dictate function and they also have unstructured areas ○​ Proteins that are not evolutionarily related but similar function may have the same domain. This is called Kinases (they add phosphates to other proteins). ​ Role of enzymes vs ATP direction vs rate of reactions ​ Characteristics of enzymes and how they affect reactions ○​ (Table 3-1 for some common enzymes) Nucleic Acids ​ Primary sequence to double helix ​ Complementarity - base pairing (A,T,C,G) ​ Directionality - The specific orientation of the nucleic acid strand is determined by the 5’ end which has a free phosphate group, and the 3’ end which has a free hydroxyl group. ​ Types of DNA sequences found in eukaryotes and their function ○​ Each DNA molecule that forms a linear chromosome must contain a centromere, two telomeres, and multiple origins of replication. ​ Introns/Exons ○​ Intron - Non Coding segments of DNA/RNA that are removed during protein synthesis ○​ Exons - Segment of DNA/RNA molecule that contain information coding for a protein or peptide sequence ​ Regulatory Sequences ​ Centromeres - regions of a chromosome that are a point of attachment for the kinetochore. It is also the main site for the attachment of the spindle fiber. Help with proper alignment. ○​ Kinetochore - a protein structure that attaches chromosomes to spindle fibers during cell division. ​ Telomeres - Protective caps at the ends of chromosomes that are made of DNA and proteins. This is a repetitive DNA sequence. ​ Origin of Replication - a specific sequence of the DNA molecule where the process of DNA replication begins. ​ mRNA vs functional/non coding RNA ○​ mRNA - is a coding RNA that carries genetic info to be translated into proteins ○​ Functional/noncoding RNA - Does not code for proteins but instead performs various regulatory roles within the cell WITHOUT being translated. ​ Purpose and role of chromatin compaction state ○​ Regulated by chemical modification upon DNA sequences and histone proteins, such as DNA methylation, histone acetylation, and methylation ○​ Chromatin is made of DNA and histone proteins ○​ It helps regulate transcription, DNA replication, damage, and repair. ​ Heterochromatin vs Euchromatin ○​ Heterochromatin - A tightly packed form of DNA in chromosomes that regulates gene expression and genome integrity. Helps make sure chromosomes separate properly during cell division. Functions spanning from gene expression silencing to constraining DNA replication and repair. ○​ Euchromatin - A loosely packed form of chromatin within the nucleus of eukaryotic cells, gene-rich, and more easily transcribed. Marked by histone mods via methylation and acetylation to facilitate gene expression. DNA is more accessible here. ​ Facultative vs Permanent Heterochromatin ○​ Facultative Heterochromatin - A genomic region in a cell’s nucleus that can switch between open and compact states. Can become transcriptionally active under certain conditions. ○​ Permanent Heterochromatin - A condensed form of DNA that is permanently present in chromosomes. It is found around the centromeres of chromosomes and is transcriptionally inactive. ​ Histones - Proteins that condense DNA into chromosomes and regulate gene expression. Found in the nucleus and provides structural support to the chromosome. They are abundant in lysine and arginine residues. They act as spools around which DNA winds to create structural subunits called nucleosomes ​ Nucleosomes - A section of DNA that is wrapped around histone proteins forming the basic unit of chromatin. Its job is to tighten and condense the packaged DNA. ​ DNA Loops - Forms when proteins bind to two different sites on DNA. They can activate or repress transcription. Occur in nucleus of eukaryotic organisms and cytoplasm of prokaryotic.  ○​ In DNA replication, loops formed in the lagging strand allow the polymerase to synthesize in the same direction. ​ Condensed/Compacted State of DNA and transcription; Relationship ​ Making of histones and their significance: methylation and acetylation ○​ Tell These Compete Stories ​ The Story of DNA Replication (Where, How, Molecules Involved, Why it is how it is) ​ The Story of Chromatin Compaction(Naked DNA to euchromatin or heterochromatin: process and proteins involved) ​ The story of how we go from amino acids to a given functioning protein (key interactions, levels of organization, specific characterization, bonds, interactions, player at each level, mods, roles of coenzymes and chaperones) ○​ A string of polypeptide chains begins its existence as a 2D linear string of amino acids, as they emerge with their different side chains (polar, nonpolar, etc), These R groups will look for the lowest state of free energy by folding certain ways until it is achieved, at the end when it is fully folded it will fold so it is interacting in a way with its neighbors and aqueous environment to achieve lowest state of free energy. This means the inside will be hydrophobic, while the outside will be hydrophilic (neg charge, pos charge). Techniques and Technical Concepts and Tools ​ Spectral Karyotyping ​ Prob/Tag ​ Fluorescently tagged probes for visualization ​ Subcellular Fractionation ​ Metabolic Labelling