Cell Biology Notes PDF

Cell Biology Questions for Exam 1 Lecture 1 What is an atom? the smallest unit of matter that retains the properties of an element. What are its basic components? Protons, Neutrons, and Electrons What is atomic number? the number of protons in its nucleus? What is atomic weight? The weighted avera...

Cell Biology Questions for Exam 1 Lecture 1 What is an atom? the smallest unit of matter that retains the properties of an element. What are its basic components? Protons, Neutrons, and Electrons What is atomic number? the number of protons in its nucleus? What is atomic weight? The weighted average mass of the atoms of an element Why are the valence electrons so important? they determine how an atom interacts with other atoms. What are the four most important elements for life? Carbon, Hydrogen, Oxygen, and Nitrogen What are the six most important elements for life? Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, and Phosphorus Why is carbon so important? it serves as the foundation for all organic molecules, which are the building blocks of life. What is a molecule? a group of two or more atoms that are chemically bonded together. What is the electrostatic force? the force of attraction or repulsion between charged particles. What is the distinction between an inter-molecular and intra- molecular bond? Intramolecular bonds hold atoms together within a single molecule, determining the molecule's chemical identity. Intermolecular bonds are the forces between molecules and influence the physical properties of substances. What distinguishes between a strong bond and a weak bond? based on the energy required to break the bond and the strength of the interactions between the particles What is bond dissociation energy? the amount of energy required to break a specific bond in a molecule to separate it into individual atoms. What are covalent bonds? a type of chemical bond where atoms share electrons to achieve a more stable electron configuration. What is the difference between a polar covalent bond and non-polar covalent bond? how the electrons are shared between the atoms involved in the bond, specifically based on the electronegativity Why is the distinction between single bonds and double bonds important? it influences several key aspects of a molecule's structure, stability, and reactivity. What is resonance? some molecules or ions cannot be accurately represented by a single Lewis structure. What are non-covalent interactions? interactions between molecules that do not involve the sharing of electrons. What are van der Waals interactions? weak, non-covalent forces that occur between molecules due to transient or induced fluctuations in electron distribution. What are electrostatic (ionic) interactions? ionic bonds/electrostatic interactions, occur between charged particles or ions. What are hydrophobic interactions? non-polar molecules or molecular regions to aggregate together in an aqueous (water-based) environment, minimizing contact with water. What are hydrogen bonds? non-covalent interaction that occurs between a hydrogen atom covalently bonded to a highly electronegative atom (such as oxygen, nitrogen, or fluorine) and another electronegative atom with a lone pair of electrons. Why are they so important? they play a central role in stabilizing the structure and function of many biomolecules, enabling essential biochemical processes to occur. What are some examples? Water, DNA, Protein, in Alcohols, in Lipids Why is their relative ‘weakness’ so important? essential for their role in biological flexibility, dynamic interactions, and reversibility. What are the four macromolecules? Proteins, Carbohydrates, lipids, and nucleic acid. What are the characteristics and functions of each? Carbohydrates: Provide energy and support cell structure. Proteins: Perform a wide range of functions, including catalysis (enzymes), structural support, and immune defense. Lipids: Store energy, provide insulation, and are key components of cell membranes. Nucleic Acids: Store and transmit genetic information, directing the synthesis of proteins. What are monomers and polymers of each? Carbohydrates: Monomers = Monosaccharides (e.g., glucose), Polymers = Polysaccharides (e.g., starch, cellulose). Proteins: Monomers = Amino acids, Polymers = Polypeptides (e.g., enzymes, hemoglobin). Nucleic acids: Monomers = Nucleotides, Polymers = DNA and RNA. Lipids: Monomers = Fatty acids and glycerol, Polymers = Triglycerides, Phospholipids, Steroids (although lipids are not true polymers, they are made of repeating structural units). Why is water so important to biology? its unique physical and chemical properties, which make it vital for the structure and function of living organisms. What are its important biological roles? regulates blood pressure, digestion, nutrients, regulates temperature. What is the connection between water and hydrogen bonds? fundamental to many of water's unique properties, such as its high boiling point, surface tension, and solvent capabilities. What is pH? a measure of the acidity or alkalinity (basicity) of a solution What are the two laws of thermodynamics? First Law of Thermodynamics: Energy is conserved and can only change forms (no creation or destruction). Second Law of Thermodynamics: The entropy (disorder) of an isolated system tends to increase, meaning that energy transformations are never perfectly efficient and lead to a more disordered state. What is the equation for free energy? ΔG=ΔH−TΔS What is the connection between cellular respiration and photosynthesis? They form a biogeochemical cycle, where the products of one process serve as the reactants for the other, facilitating the flow of energy and matter through ecosystems. How do humans get energy from the environment? the consumption of food. What is the difference between an exergonic reaction and an endergonic reaction? Exergonic reactions release energy and are spontaneous. Endergonic reactions require energy and are non-spontaneous. What is entropy? A measure of the disorder or randomness of a system. Why don’t oil and water mix? because of differences in their molecular structure and the way their molecules interact with each other What are enzymes and how do they work? biological catalysts that speed up chemical reactions in living organisms without being consumed in the process. Lecture 2 What is the general structure of an amino acid? Which functional groups are involved? Central carbon (alpha C), Amino Group, Carboxyl Group, An R Group, and a Hydrogen Atom What is the alpha carbon? An Amino Acid (central C atom) with 4 groups attached. What is the R-group? A side chain, A variable group that distinguishes one amino acid from another. What general characteristics does the R group confer on the amino acid? The R group determines the chemical property, the structure, and function. Primary Structure How is it defined? The sequence of amino acids in a polypeptide linked by peptide bonds. What is the N-terminus? The starting end of the chain (amino group) is free and not involved. What is the C-terminus? The ending end where the carboxyl group is free and not involved. What is a peptide bond? A type of covalent bond that links 2 amino acids together. Secondary Structure How is it defined? The local, regular structure of a protein’s backbone (stabilized by H bonds). What are the characteristics of the α-helix? Structure, stabilization, dimension, flexibility. What is a fibrous protein and what are some examples? Proteins, that have fiber-like structures and typically insoluble (collagen, elastin, keratin). What is a β-strand/β-sheet? β-strand is a stretch of the polypeptide chain that is almost fully extended. β-sheet is formed by two or more β-strands that align side-by-side. What is the difference between parallel and anti-parallel β-strands, and Which is stronger and why? The difference lies in their directionality and anti-parallel is stronger due to better alignment. What is silk and what are some examples of silk? Silk is a natural fibrous protein (Spider, Mulberry, Tussah). Tertiary Structure How is it defined? Folding and covalent cross-linking of a protein (3-dimensional) and stabilized by a variety of interactions between R groups. What is a globular protein? What is the general amino acid distribution of globular proteins? What is the exception to the distribution? It is a protein that has a compact, spherical shape. It follows a pattern that helps maintain stable, functional, and water-soluble structure. The main exception is found in membrane proteins. What is a disulfide bond and what is their function? It is a covalent bond formed between -SH groups and 2 cysteine and it plays a role in stabilizing the 3-dimensional structure. What is the role of cysteine in disulfide bonds? Formation What is a protein domain? A distinct, functional, and a stable part that can fold independently into 3-dimensonal. Quaternary Structure How is it defined? the arrangement and interaction of multiple polypeptide chains. What are the components of a eukaryotic cell? (What distinguishes it from a prokaryotic cell?) eukaryotic cells are defined by their compartmentalized structure with membrane- bound organelles, including a nucleus, while prokaryotic cells are simpler and lack such organelles. What are the characteristics of the nucleus? Membrane-bound, chromatin, Nucleolus, Nucleoplasm, contains DNA. What are the characteristics of the rough ER? What takes place there? The rough ER is integral to the synthesis and modification of proteins and is a critical player in maintaining the health and function of the cell. What is a ribosome? Where are they found? What is their job? It is a small complex molecular machine. Found in the rough er, cytoplasm, and mitochondria. Their job is protein synthesis. How do we distinguish between eukaryotic and prokaryotic ribosomes? Based on size, composition, and subunit structure. What is the smooth ER? What is/are its functions? It is a type of ER that lacks ribosomes, and it plays roles in lipid metabolism, detoxification, calcium storage. What is the Golgi apparatus? What is/are its function(s)? What are cisternae? GA is an organelle in the cell for processing, sorting, and packaging proteins/lipids. Cisternae are the functioning units for the GA. How does it participate in the secretory pathway? GA acts as a key "sorting and distribution center" for proteins and lipids in the secretory pathway. What are the two major components of the cytoplasm? Cytosol and Organelles What are the three major sub-types of the cytoskeleton? Microfilaments, Intermediate Filaments, Microtubules What is the lysosome? What is/are its functions? What are hydrolases? How is the lysosome itself not digested? L is a membrane bound organelle that contain enzymes to break down cellular debris. H are the enzymes within the L. They are protected from digestion due to their acidic environment. What is the peroxisome? Where are they usually found? What is H202? What is catalase? Peroxisome is a membrane bound organelle found in eukaryotic cells (used to break down fatty acids, detoxification, and regulation). H2O2 is a reactive oxygen species and catalase is an enzyme with peroxisome. What are mitochondria? “Powerhouse of cell” What is its primary function? Produce ATP What are its compartments? Inner/outer membrane, cristae, matrix What is the relationship between cell type and ATP production? The number of mitochondria and the type of metabolism a cell uses are closely tied to its energy needs, which are directly related to its function and activity. What are its other functions? Regulation of cell death, Calcium signaling/storage, Heat production What is the relationship between organelle distribution and cell type? The distribution of organelles within a cell is directly related to the cell's type and function. Lecture 3 What are the general characteristics of the plasma membrane? Composition, Function, Dynamic Nature, Key Role What types of organisms/cells have single membranes? prokaryotic cells. What types of organisms/cells have multiple membranes? Eukaryotic cells. How are internal membranes similar to the plasma membrane? They are similar in structure, being composed of lipid bilayers and both play critical roles in selective permeability, compartmentalization, and communication. How are internal membranes different than the plasma membrane? they differ in lipid and protein composition, orientation, and the specific functions tailored to the organelle. What are the general functions of the cell/plasma membrane? protective barrier, gatekeeper for transport, communication hub, and structural anchor. Why don’t oil and water mix? What is the role of energy/entropy? Oil and water don't mix because of differences in their molecular properties and the effects of energy and entropy during interactions. Energy plays a critical role by dictating how interactions between molecules influence the mixing process. Entropy plays a critical role in driving oil and water to separate rather than mix. What is meant by the term amphipathic? How are phospholipids amphipathic? Why is it important that phospholipids are amphipathic? amphipathic refers to a molecule that has both hydrophilic (and hydrophobic parts.Phospholipids are amphipathic because they have both a hydrophilic head and hydrophobic tails. This structure creates a selective barrier, supports membrane fluidity, and enables proper membrane protein function. Why do phospholipid bilayers spontaneously form a sphere? Phospholipid bilayers form spheres because this shape is the most thermodynamically stable configuration. What is the purpose/role of cholesterol in the cell membrane? plays a crucial role in the structure and function of the cell membrane, contributing to its stability, fluidity, and permeability How do individual lipids move within the membrane? Lipid movement is influenced by factors like lipid type, temperature, and membrane composition. How does membrane assembly in the ER work? This organelle contains the enzymes involved in lipid synthesis, and as lipids are manufactured in the ER, they are inserted into the organelle's own membranes. What are scramblases? type of enzyme that play a critical role in the movement of lipids within biological membranes. What are flippases? enzymes that specifically flip certain types of lipids from one leaflet (side) of a biological membrane to the other. What are the four/five major types of membrane proteins? Transporters/Channels, Receptors, Enzymes, Structural Proteins. What are the ways that proteins associated with the lipid bilayer? Integral Membrane, Peripheral Membrane, Lipid-linked, Amphitropic. What is the role of carbohydrates on the cell surface? (What is the glycocalyx) Carbohydrates play a crucial role in various cellular functions, particularly in cell- cell communication, recognition, and adhesion. The glycocalyx is a vital structure for maintaining cellular function and ensuring proper interactions. What are integrins? Integrins are a family of cell surface receptors that play a critical role in cell adhesion, signal transduction, and the interactions. Lecture 4 What substances can and can’t cross a plasma membrane? In what order might you expect substances to be permeable? What are the characteristics that drive permeability (of the solute)? Small, nonpolar molecules like oxygen and carbon dioxide can easily cross the plasma membrane; larger or charged molecules like glucose and ions cannot cross easily without assistance. Permeability is driven by factors such as size, polarity, and charge of the solute. What are the two major types of membrane transport proteins? What are the differences between the two? The two major types of membrane transport proteins are channel proteins, which form pores allowing specific ions or molecules to pass through, and carrier proteins, which undergo conformational changes to transport molecules across the membrane. What are the relevant differences between active and passive transport? Active transport requires energy, usually from ATP, to move substances against their concentration gradient, while passive transport does not require energy and moves substances along their concentration gradient. What is membrane potential? What drives it? Membrane potential is the electrical difference across a cell membrane, driven by the distribution of ions like sodium and potassium and their movement through ion channels. What is the Nernst Equation? Calculates the equilibrium potential for a specific ion based on its concentration gradient across the membrane. What is the electrochemical gradient? What are its major components? The combined effect of the concentration gradient and the electrical gradient of ions across the membrane, influencing ion movement. How does water flow across a membrane? Through specialized channels called aquaporins or via osmosis, moving from areas of low solute concentration to areas of high solute concentration. What is osmotic pressure? How is it determined? What is osmolarity? How is it determined? Osmotic pressure is the pressure needed to stop water from flowing into a solution through a semi-permeable membrane. It's determined by the concentration of solutes in the solution. Osmolarity is the measure of solute concentration in a solution. It's determined by counting the number of particles dissolved in the solution. How do we determine if something is hypertonic? Hypotonic? Isotonic? What will happen to a cell in each of those situations? A solution is hypertonic if it has a higher solute concentration than the cell. Hypotonic if it has a lower solute concentration. Isotonic if the concentrations are equal. In a hypertonic solution, a cell will shrink; in a hypotonic solution, a cell will swell; in an isotonic solution, a cell will remain the same size. What are some ways in which cells maintain osmotic pressure? Cells maintain osmotic pressure by regulating ion concentrations via active transport, using contractile vacuoles to expel excess water, and adjusting the production of osmolytes. What is a transporter? A transporter is a membrane protein that facilitates the movement of specific molecules or ions across the cell membrane. What is the glucose transporter? What is its role? How does it respond to insulin and glucagon? The glucose transporter (GLUT) facilitates the uptake of glucose into cells. It responds to insulin by increasing glucose uptake in insulin-sensitive tissues like muscle and fat, while glucagon generally has the opposite effect by promoting glucose release into the bloodstream. What is a pump? What are the different types of pumps? A pump is a type of membrane protein that actively moves ions or molecules against their concentration gradient using energy, typically from ATP. Different types include ATP-driven pumps, light-driven pumps, and gradient-driven pumps. How are pumps different than transporters? How are pumps similar to transporters? Pumps actively transport molecules against their gradient using energy, while transporters typically move molecules down their gradient and can be either passive or active. Both are membrane proteins that facilitate the movement of substances across cell membranes. What is ATP-driven pumps? ATP-driven pumps use energy from ATP hydrolysis to move ions or molecules against their concentration gradients. What is the Na+/K+ ATPase pump? What is its purpose? How does it work? The Na+/K+ ATPase pump maintains the balance of sodium and potassium ions inside and outside the cell by pumping three sodium ions out and two potassium ions into the cell per ATP molecule hydrolyzed. This helps maintain cell volume and membrane potential. What is the Ca2+ pump? How does it work? Why is it necessary? The Ca2+ pump moves calcium ions out of the cell or into the endoplasmic reticulum using ATP. It is crucial for regulating intracellular calcium levels, which affect various cellular processes including muscle contraction and neurotransmitter release. What are light driven pumps? Light-driven pumps use energy from light to move ions or molecules across the membrane. What is Bacteriorhodopsin? Bacteriorhodopsin is a light-driven pump found in some microorganisms. What is retinal? Retinal is the light-sensitive molecule that absorbs photons and drives the pump's function. What are gradient-driven pumps? Gradient-driven pumps use the energy from existing ion gradients to drive the transport of other molecules against their gradients. What is a symport? What is an example? How does it work? Symport is a type of gradient-driven pump where two or more ions or molecules are transported in the same direction across the membrane. Example: sodium- glucose symporter What is antiport? What is an example? How does it work ? Antiport is a type of gradient-driven pump where ions or molecules are transported in opposite directions. Example: Na+/Ca2+ exchanger Why isn’t uniport considered a pump? Uniporters facilitate passive transport without the use of energy, unlike pumps which require energy to move substances against their gradient What are ion channels? Ion channels are proteins that form pores in the membrane, allowing specific ions to flow down their concentration gradient. What are the important characteristics of ion channels? Selectivity: They allow specific ions (like sodium or potassium) to pass through. Gating: They can open and close in response to signals (like changes in voltage or molecule binding). Permeability: How easily ions can pass through the channel. Conductance: How much current the channel can carry by letting ions flow. Voltage Sensitivity: Some channels open or close based on changes in the cell’s electrical charge. Kinetics: How fast the channels open and close. Inactivation: Some channels stop working after being open for a while. Regulation: Ion channels can be controlled by other factors, like proteins or environmental changes. How are they different than transporters? Ion channels facilitate passive ion flow, while transporters can actively move substances using energy What are the four (three) ways that ion channels close? Voltage-dependent inactivation: Channels close when the membrane potential changes. Ligand binding: Channels close when the activating molecule (ligand) unbinds. Mechanical force: Channels close in response to physical changes, like pressure or stretching. Desensitization: Channels stop responding to a stimulus even if it's still present, causing them to close. What is an example of a mechanically gated ion channel? (audition, hearing) An example of a mechanically gated ion channel involved in hearing is found in the hair cells of the inner ear. These cells have stereocilia that bend in response to sound vibrations. What is an example of a voltage-gated ion channel? (the action potential) An example of a voltage-gated ion channel involved in the action potential is the sodium (Na⁺) channel. During action potential, when the membrane potential becomes more positive (depolarization), these sodium channels open. What is an example of a ligand-gated ion channel? (acetylcholine receptors) An example of a ligand-gated ion channel is the acetylcholine receptor at the neuromuscular junction. When the neurotransmitter acetylcholine binds to the receptor on the muscle cell membrane, it causes the ion channel to open. Lecture 5 What are chromosomes? Chromosomes are long strands made of DNA and proteins. They carry genes, which are instructions for making proteins or RNA. In eukaryotic cells (like in animals and plants), chromosomes are in the nucleus, while in prokaryotic cells (like bacteria), they're in the cytoplasm. Who are the primary players in the discovery of DNA structure? James Watson and Francis Crick (1953) are known for discovering the double. helix structure of DNA, where two strands twist around each other with base pairs in the middle (A pairs with T, C pairs with G). Rosalind Franklin took X-ray images, like the famous Photo 51, which provided key data that helped Watson and Crick figure out the structure of DNA. Her work was important, though she didn’t get enough recognition during her life. Maurice Wilkins worked with Franklin and helped study X-ray images of DNA, which also contributed to understanding its structure. What are nucleic acids? What are the basic components? Nucleic acids (DNA and RNA) are made of nucleotides, which are composed of a nitrogenous base, a sugar molecule, and a phosphate group. These molecules are vital for carrying and expressing genetic information in cells. What is a base? What is a nucleoside? Nucleotide? How are the component parts labeled/numbered? Base: A nitrogen-containing molecule (A, T, C, G, U). Nucleoside: A nitrogenous base + a sugar (no phosphate group). Nucleotide: A nucleoside + a phosphate group. The sugar in nucleotides (ribose or deoxyribose) is numbered 1' to 5', where the base attaches to 1', and the phosphate attaches to 5'. What is meant by antiparallel? In which ‘direction’ does DNA run? What is meant by the term complementary? Antiparallel: DNA strands run in opposite directions (5' to 3' and 3' to 5'). DNA Direction: The strands run from 5' to 3'. Complementary: Bases pair in a specific way: A with T and C with G. What is the role of covalent bonding? What is the role of hydrogen bonding? Covalent bonding: Holds the sugar-phosphate backbone of each strand together. Hydrogen bonding: Holds the two DNA strands together between complementary bases. Which base-pairs have how many hydrogen bonds? Why is that important? A-T pairs have two hydrogen bonds. C-G pairs have three hydrogen bonds, making them stronger. What is gene expression? Gene expression is how a gene's information is turned into a functional product. It involves two main processes: transcription (DNA to mRNA) and translation (mRNA to protein). Gene expression allows cells to produce proteins or RNA molecules that control cell structure, function, and response to the environment. What are the characteristics of chromosomes? What is a karyotype? Structure: Chromosomes are made of DNA wrapped around proteins. They are tightly packed during cell division but longer and relaxed when the cell is not dividing. Location: In eukaryotic cells, chromosomes are in the nucleus; in prokaryotes, they’re in the cytoplasm. Number: Different species have different numbers of chromosomes. Humans have 46 chromosomes (23 pairs). Types: There are autosomes (non-sex chromosomes) and sex chromosomes (determine gender—XX for females, XY for males). Function: Chromosomes carry genes, which are instructions for making proteins and controlling cell activities. ell Division: During cell division, chromosomes help ensure genetic information is copied and passed on. A karyotype is a picture of all the chromosomes in a cell, arranged in pairs. It shows: The number of chromosomes. The size and shape of each chromosome. It can help identify any extra or missing chromosomes or other abnormalities. What is chromosome painting? How does it work? Chromosome painting uses fluorescent dyes attached to DNA probes to “paint” chromosomes with specific colors. This technique helps scientists visualize chromosome structure, identify abnormalities, and study genetic information in detail. What is a chromosomal translocation? What role does chromosome painting detecting it? A chromosomal translocation is when a chromosome piece breaks off and attaches to another chromosome. Chromosome painting detects translocations by using fluorescent colors to mark chromosomes, allowing scientists to visually identify rearranged chromosomes and pinpoint the involved regions. This is helpful in diagnosing genetic disorders and cancers caused by translocations. What is the relationship between genome size organismal complexity? What is ploidy? Genome size and organismal complexity don’t always correlate directly. Larger genomes may not always mean more complexity, as much of the genome can be non-coding DNA. Ploidy refers to the number of chromosomes sets in a cell. Organisms can be haploid, diploid, or polyploid, and polyploidy can lead to larger genomes but not necessarily greater complexity. What are genes? What is a genome? What are exons? What are introns? Genes are segments of DNA that provide instructions for making proteins or RNA. The genome is the complete set of genetic material in an organism. Exons are the coding parts of genes, while introns are non-coding parts. Are introns ‘junk’ DNA? Introns are not "junk" DNA; they have important roles in gene regulation, alternative splicing, and evolutionary processes. What are the requirements for a functional chromosome? A centromere for proper cell division. Telomeres to protect chromosome ends. Origins of replication to allow DNA duplication. Genes and regulatory elements to control cellular functions. A well-organized chromatin structure for DNA packaging. Mechanisms for DNA repair to maintain chromosome integrity. What is an interphase chromosome? What is a m phase chromosome? Interphase Chromosomes: Uncoiled, relaxed chromatin during interphase (non- dividing phase), where the DNA is actively transcribed and replicated. M Phase Chromosomes: Tightly condensed chromosomes visible during mitosis (or meiosis) that are necessary for accurate separation of genetic material during cell division. What are the roles for important sequences for DNA replication? In which type of chromosome are they important (interphase vs. m phase) The important DNA sequences involved in DNA replication play crucial roles in ensuring that the genetic material is accurately copied and properly distributed during cell division. These sequences are active during different phases of the cell cycle (interphase vs. M phase), where their functions are especially important. Replication origin Located in the DNA where replication starts; important during interphase (especially in S phase) for copying the DNA. Telomeres Protect the ends of chromosomes from damage and prevent fusion, important during interphase for DNA replication and during M phase for chromosome stability. Centromeres Essential for attaching spindle fibers during cell division, ensuring proper chromosome segregation; important in M phase during mitosis and meiosis, but structurally present during interphase. What are the characteristics of interphase chromosomes? What is the nuclear lamina? Interphase chromosomes are less condensed and exist as chromatin, which includes both euchromatin (active) and heterochromatin (inactive). They are organized into chromosomal territories within the nucleus. The nuclear lamina is a fibrous protein mesh beneath the nuclear membrane that provides structural support to the nucleus and helps organize chromatin and regulate processes like DNA replication and cell division. What is the nucleolus? How does it ‘work’? How is rRNA synthesized? The nucleolus is a part of the nucleus where ribosomes are made. It creates rRNA (ribosomal RNA) by transcribing rRNA genes. This rRNA is then processed and combined with proteins to form ribosome subunits. These subunits leave the nucleolus and join together in the cytoplasm to make full ribosomes, which are responsible for protein synthesis. What is chromatin? What is heterochromatin? What is euchromatin? Chromatin is a complex of DNA and proteins (mainly histones) found in the nucleus. It helps package the DNA into a more compact, organized structure and plays a role in regulating gene expression. Heterochromatin is a tightly packed form of chromatin, which is usually inactive or less transcriptionally active. It often contains genes that are not expressed and is found at the periphery of the nucleus. Euchromatin is a looser, more relaxed form of chromatin that is actively involved in transcription. It contains genes that are being expressed or are ready to be expressed. What is chromosomal density so important? Chromosomal density is important because it helps balance DNA packaging with accessibility for processes like gene expression and replication. DNA is tightly packed but needs to be accessible when required. Why does chromosome structure need to be dynamic? Chromosome structure needs to be dynamic to allow for different functions: relaxed during interphase for gene activity and more condensed during mitosis for proper cell division. This flexibility ensures both stability and proper functioning of the genome. What is the nucleosome? A nucleosome is a structure where DNA is wrapped around proteins called histones. It helps organize and pack the DNA in the nucleus, making it more compact. Nucleosomes also play a role in controlling gene activity by making the DNA more or less accessible. What are histone proteins? What are non-histone proteins? Histone proteins help package and organize DNA. Non-histone proteins assist with gene regulation and other cellular processes. What types of amino acids make up a histone protein? What are the proteins that make up a histone? Histone proteins are made up of basic amino acids such as lysine, arginine, and histidine. These amino acids have positive charges, which help the histones interact with the negatively charged DNA, allowing them to tightly bind and organize the DNA. The proteins that make up a histone are: H2A / H2B / H3 /H4 These four histone proteins come together to form the core of the nucleosome, around which the DNA is wrapped. What is linker DNA? What histone proteins are present in linker DNA? Linker DNA connects nucleosomes and is not wrapped around histones. Histone H1 binds to linker DNA, helping to organize and stabilize the chromatin structure. What is the relevance of a histone tail? Histone tails are the flexible ends of histone proteins that stick out from the nucleosome. They are important because they can be chemically modified (like adding acetyl or methyl groups) to control how tightly or loosely DNA is packaged. These modifications help regulate gene activity and allow other proteins to interact with the chromatin, affecting gene expression and cell functions. Are histone proteins conserved? Why is that important? Yes, the conservation of histones ensures that essential processes like DNA packaging and gene regulation remain consistent and efficient across organisms. What is chromatin-remodeling complexes? groups of proteins that use energy (often from ATP) to modify the structure of chromatin, making it more or less accessible for processes like gene expression, DNA replication, and repair. How do they work? What do they do? How they work: These complexes can move, slide, or eject histones from the DNA, changing how tightly or loosely the chromatin is packed. By doing this, they make certain regions of DNA more or less accessible to the cellular machinery that needs to read or copy the DNA. What they do: Regulate gene expression: By changing the chromatin structure, they allow or prevent access to specific genes, controlling whether they are turned on or off. Facilitate DNA repair and replication: They help make the DNA accessible to the proteins needed for these processes. Change chromatin structure: They can make DNA more relaxed (euchromatin) or more tightly packed (heterochromatin), affecting gene activity. What is a histone modifying enzyme? a type of enzyme that adds or removes chemical groups (such as acetyl, methyl, phosphate, or ubiquitin) to or from histone proteins. These modifications can alter the structure of the chromatin and, in turn, influence gene activity. Some common histone modifications include: Acetylation: The addition of an acetyl group (COCH₃) to lysine residues on histones. This modification generally loosens chromatin, making DNA more accessible for transcription and often leading to gene activation. Methylation: The addition of a methyl group (CH₃) to histones. Methylation can have different effects depending on the specific histone and the number of methyl groups added, but it often results in chromatin condensation and gene silencing. Phosphorylation: The addition of a phosphate group (PO₄) to histones, which can influence chromatin structure during processes like cell division and DNA repair. Ubiquitination: The addition of a small protein called ubiquitin to histones, often linked to gene silencing or DNA repair processes. These modifications act like signals that can either promote or inhibit gene expression, depending on the context. They play a key role in regulating how DNA is packaged and accessed in the nucleus. Why are histone-modifications important? How can they alter chromatin structure/function? Histone modifications are important because they control gene activity and how DNA is packed. By adding or removing certain chemical groups on histones, these changes can make DNA more or less accessible, affecting whether genes are used for things like making proteins, copying DNA, or fixing damage. DNA Accessibility: Acetylation loosens the DNA, making it easier for genes to be turned on. Methylation can either tighten the DNA, turning genes off, or open it up for certain functions, depending on where it happens. Gene Regulation: Adding or removing chemical marks on histones decides if genes are turned on or off. For example, acetylation activates genes, while methylation can silence them by compacting the DNA. Chromatin Compaction: Modifications like methylation and phosphorylation make the DNA more compact and inactive (heterochromatin). Acetylation helps loosen the DNA, making it more active (euchromatin). DNA Repair and Replication: Some histone changes help signal when DNA needs repairing or assist in copying DNA during cell division. Which types of amino acids are altered by modification? The amino acids most commonly modified in histones are those with basic side chains, as they are positively charged and interact with the negatively charged DNA. These include Lysine (K) – Can be acetylated, methylated, ubiquitinated, or sumoylated. Arginine (R) – Can be methylated. Serine (S) – Can be phosphorylated. Threonine (T) – Can also be phosphorylated. Histidine (H) – Can be methylated, though this is less common. These modifications alter the properties of histones, affecting their interaction with DNA and other proteins, and play a major role in regulating chromatin structure and gene expression. Why do interphase chromosomes contain both heterochromatin and euchromatin? both heterochromatin and euchromatin are needed to balance gene activity and genome stability during interphase. How can heterochromatin lead to more heterochromatin? What are the barrier sequences? Heterochromatin spreading occurs when heterochromatin proteins spread and convert neighboring DNA into more heterochromatin. Barrier sequences are DNA regions that stop this spreading, protecting euchromatin and ensuring proper gene regulation. What is gene-silencing? Why is it important? What is a major example of it? (X-inactivation) Gene-silencing is when certain genes are turned off, so they aren't expressed. It’s important because it helps control which genes are active in different cells and at the right times, ensuring proper development and function. A major example of gene-silencing is X-inactivation, which happens in female mammals. Since females have two X chromosomes, one is randomly turned off in each cell to balance gene expression between males (who have one X) and females (who have two X chromosomes). This silencing happens through changes in DNA and histones, turning the inactive X into a tightly packed, inactive form. What is X-inactivation? What is a Barr Body? X-inactivation ensures that only one X chromosome is active in each cell of a female. The Barr body is the visible form of the inactive X chromosome.