Biology Midterm I Study Guide PDF

Functional Groups There are seven: Hydroxyl Group (-OH) - Carbonyl Group (-C=O) - Carboxyl Group (-COOH) - Amino Group (-NH3) - Sulfhydryl Group (-SH) - Phosphate Group ← - Methyl Group (-CH3) Monomers→ Polymers → Macromolecules Monomers can make an immense variety of polymers P...

Functional Groups There are seven: Hydroxyl Group (-OH) - Carbonyl Group (-C=O) - Carboxyl Group (-COOH) - Amino Group (-NH3) - Sulfhydryl Group (-SH) - Phosphate Group ← - Methyl Group (-CH3) Monomers→ Polymers → Macromolecules Monomers can make an immense variety of polymers Polymers make up 3 out of the 4 classes (Lipids do not form polymers) of life’s organic molecules: 1. Carbohydrates 2. Proteins 3. Nucleic Acids Examples of Mono-, Di-, and Poly-s Carbohydrates (polymers of sugars) serve as the fuel and building material for cells Monosaccharides, single sugars, are the most simplest form - Glucose (C6 H12 O6) most common - Has a carbonyl group (C=O) and multiple hydroxyl groups (-OH) - Major cellular fuel - Fructose - Galactose Disaccharides are monomers that were incorporated from sugars not used - Formed when a dehydration reaction joins two monosaccharides ○ This is known as the covalent bond— a glycosidic linkage - Lactose - Sucrose - Plants transport carbohydrates from leaves to roots in the form of sucrose Monosaccharide Disaccharide Glucose + Galactose = Lactose (Milk) Glucose + Fructose = Sucrose (Plants) Polysaccharides consist of many sugar building blocks (polymers of sugars) 1. Storage- storing sugar for cells - Starch - Consists entirely of glucose monomers - Stored energy in plants When we need glucose as fuel, we break down the starch through hydrolysis into glucose monomers. - Glycogen - In animals, consisting of glucose monomers - Humans and other vertebrates store this in the liver and muscle cells 2. Structural- building material - Cellulose - Major component of the tough cell wall of plants - Made up of glucose, but the glycosidic linkages differ - Our bodies cannot break down cellulose the same way other animals can because we are not able to hydrolyze B Linkages in cellulose, therefore, it passes through us as insoluble fiber. Difference between elements, compounds, and molecules Elements Compounds Molecules - Substance that - Substance of two or - Group atoms formed cannot be broken more elements in a together to form the down fixed ratio smallest identifiable - Periodic Table - NaCl 1:1 unit in a pure - Emergent properties substance can emerge - Depend on chemical bonding between atoms - Hydrogen Molecules Acid and Base Difference Acid Base - A substance that donates and - A substance that reduces the H+ increases H+ concentration in a concentration in a solution by solution accepting hydrogen ions - Acidic Condition - Ex: Sodium hydroxide (NaOH) - Ex: Hydrochloric Acid (HCl) - This base reduces H+ concentration indirectly by pH Scale: 7 is basic dissociating to form hydroxide ion Acidic Solutions Basic Solutions - Solutions with higher concentration - Solutions with higher concentration of H+ than OH- of OH- than H+ pH Scale: 7 is basic Dehydration V. Hydrolysis Dehydration Hydrolysis - Monomers binds through the loss of - Polymers turn into monomers  a water molecule through the addition of water to - Small → Big break down the covalent bonds - Big → Small Saturated V. Unsaturated Saturated Unsaturated - Solid at room temperature - Liquid at room temperature - Single bonds - One or more double bonds - Structured in a straight line - Structured with kinks - More hydrogen in their structure - Less hydrogen in their structure Atomic Number of an Atom (Covalent, Valence Electrons) Molecules form depending on chemical bonding between atoms ○ Atoms with incomplete valence shells either transfer or share valence electrons, which get held together by chemical bonds (attraction) Ionic Bonds Covalent Bonds - The transfer of electrons, resulting in - The sharing of a pair of valence charged atoms called ions electrons by two atoms - Cation: + charged - Anion: - charged - The attraction between these two is known as an ionic bond -  Electron shells signify the electron’s state of potential energy 1st (lowest level) → 2nd (higher level) → 3rd (highest level) - Holds no more than 2 electron - Can hold up to 8 electrons - Hydrogen and Helium - An atom with more than 2 electrons must use higher shells Valence electrons are those in the outermost shell (valence shell) ○ They determine the chemical behavior of an atom ○ Full valence shells are inert (unreactive): Helium, Neon, and Argon Single Bond: the sharing of one pair of valence electrons Double Bonds: the sharing of two pairs of valence electrons Primary V. Secondary V. Tertiary Primary Secondary Tertiary - Sequence of - Coils and folds in - Formed through amino acids in polypeptide chain due to interactions between a protein hydrogen bonds several side chains (R - A-helix (coil)and B-pleated groups) sheets (folded) - Hydrogen bonds, ionic bonds, hydrophobic interactions, Van Der Waals interactions pH Ten Folds Each pH unit represents a tenfold (10x) difference in H+ and OH- concentrations Ex: pH 3 is 10x more acidic than pH 4 pH 9 is 100x more basic than pH 7 pH 4 has 10,000 times more H+ than pH 8 pH 8 has 10,000 times more OH- than pH 4 What can cross the cell membrane? - The cell membrane is selectively permeable meaning it can only allow certain things to go in and out What Can Pass What Cannot Pass - Non polar molecules - Polar molecules - Hydrophobic molecules - Hydrophilic molecules (hydrocarbons) - Ions (sugars) Endergonic V. Exergonic Reactions Final- initial= delta G Endergonic Exergonic - Absorbs free energy - Releases free energy - Nonspontaneous - Spontaneous - Negative number - Positive Number Competitive V. Non-competitive Inhibitors (reversible) Competitive Non-competitive Inhibitors Competitive Inhibitors bind to the Non Competitive inhibitors bind to another part of an active site of an enzyme, competing enzyme, causing the enzyme to change shape, making with the substrate the active site less effective for the other substrate How can inhibition be overcome?---> Through non-competitive inhibition How do enzymes speed up chemical reactions?---> By lowering the activation energy Transport Proteins Allow passage of hydrophilic substances across the membrane Channel Proteins Carrier Proteins - Hydrophilic channel that ions or - Bind to molecules and change certain molecules can use as a shape to let molecules or ions pass tunnel through 1. Aquaporins- facilitate the - Specific for the substance it moves passage of water through so it only allows certain substances channel proteins to cross 1. Sodium-potassium pump- facilitate the passage of sodium inside the cell, and potassium out 2. Glucose transporters All organelles in Eukaryotic Cells Domains of Protists, Fungi, Animals, and Plants consist of eukaryotic cells Nucleus- cell’s genes found here; surrounded by the nuclear envelope Cytoplasm- the region between the nucleus and plasma membrane - Cytosol is the liquid that holds all the organelles Plasma membrane- the selective barrier, allowing sufficient passage of oxygen, nutrients, and waste to the cells - Double layer of phospholipids Endoplasmic Reticulum- connected directly to the nuclear envelope; there are two types- Rough and Smooth ER Golgi Apparatus: FEDEX center (Shipping and receiving center); transport vesicles leave the ER and to to the Golgi to have their protein modified Ribosomes- carry out protein synthesis in the cytosol (free ribosomes) or on the outside of the ER/Nuclear envelope (bound ribosomes) Mitochondria- generates most of the cell’s chemical energy Lysosomes- digestive enzymes surrounded by the membranes; digest macromolecules; composed of a lot of fats, proteins, polysacchs, etc.  The Cytoskeleton Microfilaments→ Intermediate Filaments → Microtubules Smallest—---> Biggest Microfilaments Intermediate filaments Microtubules - The thinnest components - Fibers with diameters in - Thickest components - Thin solid rods a middle range - Hollow rods made from - Twisted double tubulin chain of G-actin - Tubulin subunits (polymers) grows/shrinks from - AKA actin filaments tubulin dimers - Functions: - Functions: - Functions: - Structure: help - Support cell - Shape the cell resist tension shape - Guide movements - Suport: form a - Fix organelles in of organelles cortex inside the place - Separate plasma membrane chromosomes to help support - Keratin makes up the during cell cell’s shape nuclear lamina, which division - Cellular Motility: in shapes the nucleus muscle cells, Centrosomes V. Centrioles microfilaments work with another Animal cells: protein called Centrosomes are where myosin to cause microtubules grow out from and it muscle contraction is near the nucleus - Centrioles are inside the centrosomes - Before animal cells divide, centrioles replicate - Help organize microtubule assembly Sam Burnes - HGPS, progeria syndrome - Caused by a mutation in the gene that affects the cell’s structure; In kids and causes them to age rapidly - Rare, no cure, and short life expectancy Water Solutions Tonicity- the ability of a solution to cause a cell to lose or gain water Think of Outside the Hypertonic (A) Hypotonic (B) Isotonic Cell! Solute concentration Solute concentration Solute concentration is greater outside is less outside the is the same inside the cell cell and out (normal) Hyper= More Hypo= Less Plants Cells lose water and Cells are turgid Cells become membrane pulls (firm); Healthy Cell flaccid (limp) bc of away from the cell no net movement; wall; They undergo Plant may wilt plasmolysis → Cell death Animals Cells lose water; May Cells gain water; Will Normal; no net shrivel and die lyse (burst and swell) water movement; Stable How do cilia and flagella bend/move? Through Dyeneins, which produce the bending movements. Cytoplasm V. Cytosol Cytoplasm: region between the nucleus and the plasma membrane Cytosol: holds the organelles that are within the cytoplasm Any substance that loves or hates water Hydrophobic substances (NONPOLAR) - these are the two fatty acid tails that face towards the cell membrane and do not like water Hydrophilic substance (POLAR)- the hydrophilic heads formed from the fatty acid tails that love water Where in the nucleus makes special type of RNA for proteins (mRNA) - In the nucleolus Why is ice less dense than water? - In ice, hydrogen bonds pull molecules farther away than that in water, making them less dense and resulting in ice being able to float on water. Compounds matching to their number of Atoms Water (H₂O) Atoms: 3 (2 Hydrogen + 1 Oxygen) Carbon Dioxide (CO₂) Atoms: 3 (1 Carbon + 2 Oxygen) Glucose (C₆H₁₂O₆) Atoms: 24 (6 Carbon + 12 Hydrogen + 6 Oxygen) Sodium Chloride (NaCl) Atoms: 2 (1 Sodium + 1 Chlorine) Ammonia (NH₃) Atoms: 4 (1 Nitrogen + 3 Hydrogen) Components that make up the Extracellular Matrix Animal cells are covered by the extracellular matrix (ECM) 1. Made up of: Glycoproteins a. Collagen, proteoglycans, and fibronectin  2. Fibronectin interacts directly with the plasma membrane by binding to integrins, which are receptor proteins in the plasma membrane Active transport Transport that moves solutes against their concentration gradient, making them go from areas of low solute concentration to areas of high solute concentration ○ Low → High Requires the use of ATP Example: ○ 1. Sodium-potassium pump: Pump Na+ out of the cell and Pump K+ into the cell; We want more potassium, than sodium, much like our bodies Storage-Polysaccharides 1. Plants: Plants use starch as their primary storage polysaccharide, consisting entirely of glucose (major cellular fuel) monomers. a. When plants need energy, they can break down starch into glucose molecules for use in cellular respiration— this is done through hydrolysis 2. Animals: Animals use glycogen similarly, consisting of glycogen units a. Stored mainly in the liver and muscle tissues— when we need energy, we break down glycogen into glucose and sent off into the bloodstream for energy i. Glycogen→ Glucose→ Energy Different levels of Organization 1. Molecules: The chemical building blocks of life, such as proteins, nucleic acids (DNA and RNA), lipids, and carbohydrates. 2. Cells: The basic unit of life. Cells can be unicellular (single-celled organisms like bacteria) or multicellular (organisms composed of many cells, like plants and animals). 3. Tissues: Groups of similar cells that perform a specific function. For example, muscle tissue and nervous tissue. 4. Organs: Structures composed of different types of tissues that work together to perform specific functions. For instance, the heart, lungs, and liver. 5. Organ Systems: Groups of organs that work together to carry out complex functions. Examples include the circulatory system and the digestive system. 6. Organisms: Individual living entities that can function independently, such as animals, plants, and fungi. 7. Populations: Groups of individuals of the same species that live in a specific area and interact with one another. 8. Communities: Different populations of species that live and interact in a particular area.  9. Ecosystems: Communities of living organisms interacting with their physical environment, including non-living components like air, water, and soil. 10. Biomes: Large geographical areas characterized by specific climates and ecosystems, such as deserts, forests, and tundras. 11. Biosphere: The highest level of organization, encompassing all ecosystems on Earth, where life exists. Structure of Water/Polarity - Water consists of two hydrogen molecules and one oxygen molecule Hydrogen Bonding: - Hydrogen atom covalently bonded to one electronegative atom, bonds w/ another electronegative atom Polarity: - These bonds are generally weak as they are at the end of their “poles” so there is a slightly, or partial, negative oxygen atom attracting to a slightly positive hydrogen atoms What bonds can form?: Hydrogen bonds Why can more bonds be created?: Polarity (allows water molecules to form hydrogen bonds w/ each other) What forces allow water to go up against gravity? - Cohesion and Adhesion: help to transport water against gravity in plants - Evaporation: Water from the leaves also play an important role in water transport Formation of Bonds with Cabron - The electron configuration of carbon gives it covalent compatibility with many different elements Descriptions of DNA Structure: Double Helix: DNA consists of two long strands that coil around each other, forming a double helix shape. Nucleotide Composition: Each strand is made up of nucleotides, which include a phosphate group, a sugar (deoxyribose), and one of four nitrogenous bases (adenine, thymine, cytosine, or guanine). Base Pairing: Complementary Base Pairing: The nitrogenous bases pair specifically (adenine with thymine, and cytosine with guanine) through hydrogen bonds, which stabilize the double helix structure. DNA: A-T; C-G RNA: A-U; C-G Antiparallel In DNA double helix, two backbones run in opposite 5’-3’ directions from each other Alpha Helix Strands held together by H-bonds between paired bases, giving DNA its helical structure Polymers made up of Monomers Polysaccharides: Monomer: Glucose Example Polymer: Starch, Glycogen, Cellulose Proteins: Monomer: Amino Acids Example Polymer: Polypeptides, Proteins Nucleic Acids: Monomer: Nucleotides Example Polymer: DNA, RNA Two Classes of Nitrogenous Base and their Pairings 1. Purines (pure silver– Ag): Purines are involved with Adenine (A) and Guanine (G)--> Ag (Silver) a. Double-ring structures 2. Pyrimidines: involved with Cytosine, Thymine/Uracil a. Single-ring structures Bonds in DNA 1. Covalent Bonds (phosphodiester bonds) form the DNA backbone. 2. Hydrogen Bonds between base pairs stabilize the double helix. 3. Van der Waals Forces contribute to the overall stability of the DNA structure. Endocytosis 1. Phagocytosis (cell “eating”) a. Cells engulf a particle in a vacuole; Vacuole fuses with a lysosome to then digest the particle 2. Pinocytosis (cell “drinking”) a. Cells take in small amounts of liquid and dissolved substances 3. Receptor-mediated endocytosis a. Cells take in specific molecules that fit into its receptors on its surface; They do this through the binding of ligands, which are molecules that bind to a specific receptor site of another molecule. They all require energy in the form of ATP— changing the shape, creating vesicles, and having specific molecules bind to specific receptors The Different Bonds Ionic Bond Polar Covalent Bond Nonpolar Covalent Bond - Transfer of an - One atom is more electronegative - Atoms share the electron - Atoms do not share he electron equally electron equally - Cation - This is known as electronegativity - Have the same - Anion where one atom has a slightly electronegativity - Ion more negative charge than a - Opposites positive one or vise versa attract - Ex: NaCl - Ex: H20: oxygen attracts electrons - Ex: O2; Two atoms of stronger than hydrogen does the same element Isotopes Two atoms of the same element (same number or protons [atomic number] ) but differ in number or neutrons ○ So different mass numbers! Hydrocarbons Different Linkages Glycosidic Ester Phosphodiester Disulfide Bridges The covalent bonds In fat: where three Joins together Strong that forms a fatty acids are adjacent covalent disaccharide joined to glycerol nucleotides by bonds that through to create a this covalent reinforce the dehydration triacylglycerol, or a bond protein’s synthesis of two triglyceride structure monosaccharides CO2 and the Ocean - CO2 is the main product of fossil fuel combustion and oceans will absorb 25% of the human-generated CO2 - Ocean acidification is the process when CO2 dissolves in seawater to form carbonic acid. 7 Characteristics of Life 1. Order 2. Reproduction 3. Growth and Development 4. Energy Processing 5. Regulation 6. Response to the Environment 7. Evolutionary Adaptation Are Viruses Living or Nonliving? Why? (know 2 out of the 3) Viruses are not living - Why? 1. They cannot reproduce on their own (they must first infect a host cell that replicates their DNA for them) 2. They do not grow or develop 3. Cannot process energy on their own What is it called when DNA is not dividing? What happens? - The special name is Chromatin - What happens?: They spread out in the nucleus - Packaging: The DNA is wrapped around proteins, keeping it organized and compact in the nucleus. - Gene Expression: Chromatin allows certain genes to be "turned on," meaning the DNA can be read to make proteins. - Preparation for Division: When the cell gets ready to divide, chromatin can condense into chromosomes. What is it called when it is about to divide? What happens? - When it is about to divide it is known as chromosomes - What happens?: - Tight Packing: The DNA coils up to become visible chromosomes. - Copying: Each chromosome makes a copy of itself, resulting in two identical parts called sister chromatids. - Line Up: The chromosomes line up in the middle of the cell to ensure both new cells get the same DNA. What is it called in Maintain pH? - Buffer systems help with maintain our pH by minimizing changes in concentrations of H+ and OH- in a solution - Examples: - Bicarbonate and Phosphate Buffers: Neutralize acids and bases in blood and cells. - Protein Buffers: Help maintain pH through binding hydrogen ions. - Respiratory Control: Adjusts breathing to regulate CO₂ and pH. 2 Processes 1. Phagocytosis- engulfs the cells by “eating it” 2. Autophagy- Lysosomes use their enzymes to recycle cells own material What is Electronegativity? - Electronegativity is an electron’s attraction for the electron’s in a covalent bond - The more electronegativity, the stronger it can pull electrons toward itself Why is it considered polar? - A bond is considered polar when the atoms involved have different electronegativities, leading to unequal sharing of electrons. What macromolecule is not a polymer made up of monomers? - LIPIDS - Lipids are made up of larger structures and consist mostly of hydrocarbons; Lipids include a variety of compounds like fats, oils, steroids, and phospholipids. They are primarily formed from fatty acids and glycerol but do not have a consistent monomeric structure, which is a characteristic of a polymer. Why can’t we break down cellulose? - We cannot break down cellulose because of a difference in the glycosidic linkages; - We use enzymes that digest starch by hydrolyzing a-linkages, and we CANNOT hydrolyze b-linkages in cellulose Tay-Sachs: What is it and What Organelle is Involved? - In Tay-Sachs, lysosomes are not able to break down lipids and affecting the growth of the brain, causing the lipids and brain to get bigger - The specific organelle involved in Tay-Sachs disease is the lysosome. Lysosomes are responsible for breaking down waste material; Lysosomes cannot properly break down GM2 ganglioside due to the lack of the Hex-A enzyme. 2 Organelles that detoxify poisons 1. Lysosomes Function: Lysosomes contain enzymes that break down waste materials, cellular debris, and harmful substances. They help in degrading toxins and recycling cellular components. 2. Peroxisomes How: Peroxisomes contain peroxidases, which are specific enzymes that break down fatty acids and detoxify harmful substances. Hydrogen peroxide is a product of this, which then has to be detoxified as well by removing hydrogens, converting it into water and oxygen, thereby detoxifying it. Other mechanics Peroxisomes remove hydrogen by breaking down hydrogen peroxide. Smooth Endoplasmic Reticulum helps make substances more water-soluble, aiding in detoxification ○ -OH group gets added to make drugs more water soluble and easier to flush out the body, done in the liver.