Biology Recaps PDF

Week 1- Unit 1: Biochemistry ============================ **[Organic Chem]** Carbon has 4 valence electrons, allowing it to bond with multiple atoms at a time - forming double and triple bonds and long chains +-----------------------+-----------------------+-----------------------+ | Hydroxyl...

Week 1- Unit 1: Biochemistry ============================ **[Organic Chem]** Carbon has 4 valence electrons, allowing it to bond with multiple atoms at a time - forming double and triple bonds and long chains +-----------------------+-----------------------+-----------------------+ | Hydroxyl | Carbonyl | Carboxyl | | | | | | Hydroxyl Group |  | Carboxyl Group - | | Definition - | | Definition and Quiz | | Chemistry Term | | \| Biology Dictionary | +=======================+=======================+=======================+ | Phosphate Group | Sulfhydryl | Amino | | | | | |  | | ge4.png) | | | +-----------------------+-----------------------+-----------------------+ | Alcohol | Ether | Aldehydes | | | | | | Alcohol Functional |  | | | Examples - Lesson \| | | | | Study.com | | | +-----------------------+-----------------------+-----------------------+ | Ketones | Carboxylic Acid | Esters | | | | | |  | | Lesson \| | | | | Study.com](media/imag | | | | e12.png) | +-----------------------+-----------------------+-----------------------+ | Amine | Amide | Amino Acid | | | | | | Amine - Wikipedia |  | | +-----------------------+-----------------------+-----------------------+ **[Carbohydrates]** Macromolecules: biologically important molecules that have large chains of units called monomers, that join to become polymers Carbohydrates: used for energy, storage and structure, contain a hydroxyl and an aldehyde/ketone, (C, H & O 1:2:1) Monosaccharides: monomer of polysaccharides i.e fructose, glucose - Glucose: Energy for cells during photosynthesis and respiration. Good for storing energy and important during synthesis reactions  Disaccharides: Glycosidic links formed between 2 monosaccharide (carbon-1 & carbon 4-6). Formed via condensation and broken-down during hydrolysis Disaccharide Examples - What Is a Disaccharide? Polysaccharides: Long chains of α1-4 or α1-6 glycosidic linked sugars. Can be branched or not. (More branches = more solubility)  - Storage Polysaccharides 1. Amylose: long chain of α1-4 chains in plant starch 2. Amylopectin: long chain of α1-4 chains w/ 1-6 branched links 3. Glycogen: found in animals & is highly more branched than Amylopectin, stored in the liver and muscle cells - Structural Polysaccharides 1. Cellulose: most abundant in cell walls and have β glucose w/ long chains of β1-4 links 2. Chitin: modded glucose in exoskeletons and fungi cell walls, composed of glucosamine Dehydration Synthesis: Combines carbohydrate monomers into polymers. 1 Hydrogen on an Alcohol reacts with Hydroxyl on the other carbon to make excess water. Hydrolysis: Chemical process/reaction used to break polymers apart into smaller molecules by adding water Week 2 ====== **[Proteins + Amino Acids]** Proteins: important macromolecules that have numerous functions (i.e building blocks of cellular growth, component of anti-bodies, building enzymes & bodily fluids, hormones, structures & movement, cellular transport) and contain C, H & O and sometimes sulfur or phosphate - Peptide bond: long polymer chains are joined by a peptide bond between a Carbon & Nitrogen Amino Acids: monomers of protein, there's 20 amino acids, 8 of which humans can't produce. Consist of a central carbon (α carbon), bounded to a carboxyl group, an amino group, a hydrogen & a side chain. - Side chains can be non-polar, polar, hydrophobic, hydrophilic, charged +ve, charged -ve, basic and acidic. These characteristics affect how amino acids interact w/one another A black background with red arrows pointing to a black surface Description automatically generated Polypeptide: a peptide bond between 2 amino acids will have 2 functional groups. In longer polypeptides, there's repeated chains. - Formation -- via condensation (dehydration s.); between the amino group of one acid & the carboxyl group on the other -- the ribosome is responsible for the linkage Protein Condensation: As multiple acids link up, they will interact, changing the polypeptide from a chain to other contortions 1. Primary: the sequence of amino acids, unique to a specific protein. Consists of covalent bonds between groups 2. Secondary: Interactions w/amino acids which form hydrogen bonds. Depending on the acid & side chains, coils (helix) or pleated sheets (β sheets) form 3. Tertiary: fewer regular formations caused by side chain interactions. Include hydrophobic/phallic, H-bonds, ionic/covalent bonds & disulfide bridges. 4. Quaternary: uncommon, 2+ polypeptide chains that come together to form a functional protein i.e hemoglobin  Denaturing: change in a protein's shape & conformation - Temperature: affects H-bonding, causing a polypeptide to unfold - pH: affects charges on carboxyl & amino groups; affecting the solubility & shape of protein - different proteins function at different pHs - Salinity (salt con.): affect charged amino & carboxyl groups **[Nucleic Acids]** Nucleic Acids: large biological molecules, named for the molecules DNA found in the nucleus. Functions include storing genetic info (DNA), transmitting genetic info (mRNA), processing genetic info (ribozymes), protein synthesis, metabolism. Nucleotides: monomer of nucleic acid, consists of a nitrogen base, a pentose sugar & a phosphate group Nitrogen Bases - Purines: nitrogen containing ring-shaped molecules consisting of 2 rings (adenine & guanine) - Pyrimidines: rin - g shaped molecules containing nitrogen consisting of 1 ring (thymine, cytosine & uracil) Pentose Sugar: consists of 5 carbons, ribose & deoxyribose are sugars present in nucleotides. The hydroxyl of carbon-1 binds to the nitrogenous base. Phosphate group: attaches to the 5' carbon on the pentose sugar What are Nucleotides? - Creative Proteomics Creating polynucleotides Formed by covalent bonds between nucleotides, the phosphate group of 1 nucleotide bonds to the 3' sugar of the next nucleotide (liked by a phosphodiester linkage) - Nitrogenous bases stick out from the backbone, forming the rungs of the ladder. Nucleotide sequences are variable, inherited and specific. DNA: deoxyribose nucleic acid - Used to store genetic information, the info is turned into proteins - Formed by 2 polypeptide chains, the nitrogenous base forms H-bonds w/each other. The sugar is deoxyribose. G-C making 3 H-bonds, and A-T bind to make 2 H-bonds. - Since bases don't stick out, the 2 chains go in opposite directions to fit forming a double helix RNA: ribonucleic acid Ribose is the sugar & uracil is the base in RNA. It's single stranded (2x for viruses) - mRNA (messenger): carries coding sequence from DNA to ribosome for protein synthesis - tRNA (transfer): carries amino acids to ribosomes during protein synthesis - rRNA (ribosomal): found in ribosome; helps the catalytic sites for translation RNA is less stable than DNA due to ribose sugar **[Lipids]** Lipids: a diverse group of organic compounds including fats, oils, hormones & certain compounds of membranes. They're group together due to the fact they don't dissolve in water (hydrophobic). Functions include hormones, storing energy, cell membranes, insulation & surround nerve cells. Examples include, triglycerides, phospholipids, steroids, waxes Fatty Acids: long hydrocarbon chains found in certain lipids. Different fatty acids have different \# of carbons & double bonds. - FA's wo/ 2x bonds: saturated - Saturated acids are linear in structure, often come from animal sources & are solid at room temperature - FA's w/ 2x bonds: unsaturated (mono or poly) - Unsaturated acids are bent in structure and often come from plant sources & liquid at room temp - Cis: the hydrogen atoms on the 2x bond are on the same side - Trans: the hydrogen atoms are on different sides - Trans FA's are rare in natural sources, are linear & come from industrial processing of hydrogenating oils or we can't produce Triglycerides: used for energy storage, found in the blood & stored in adipose cells that make body fat. Released by hormones to give energy between meals - Hypertriglyceridemia: more calories are consumed than burned & there's too much triglyceride in the blood Glycerol: an ester molecule w/ 2 FA's + an alcohol Phospholipids: 2 FAs connected to a glycerol + a phosphate group + a variable head. Both phosphate & glycerol are hydrophilic (polar). The FAs are uncharged, non-polar & hydrophobic. Micelles: Amphipathic molecules formed in water w/ hydrophilic heads out & hydrophobic tails inward. - Bilayer: 2 layers of phospholipids where the hydrophilic head point to the extra/intra cellular fluid & the hydrophobic tail points outward away from water. Steroids: organic compounds consisting of 4 cycloalkane rings joined together. 17 carbons connected to 4 fused rings, includes hormones & cholesterol. - Cholesterol: component of phospholipid bilayers, strengthening the bilayer & it's a hormone precursor 3 classes of Steroids 1. Mineralocorticoids: promote reabsorption in the kidneys, increasing arterial pressure & fluid volume 2. Glucocorticoids: stimulate gluconeogenesis, decrease glucose usage by cells, mobilize FAs in adipose tissue, increase in plasma & used for energy 3. Androgen & Estrogen: sex hormones Waxes: long chains of FAs + an alcohol chain. Dehydration synthesis creates ester bonds & forms waterproof coats on plant & animals Week 3 ====== **[Enzymes]** Enzymes: proteins that act as catalysts during chemical reaction to reduce the activation energy used up. They provide an alternate pathway for the reaction without being changed in the reaction - (Anything with "-ase" at the end of it is an enzyme) Substrate: the substance an enzyme acts on Active Site: region on an enzyme where the substrate attaches Induced Fit: the active site changes shape to fit the substrate in place, changing the active site due to hydrogen and ionic bonds  Factors - Temperature \> higher temp = more active enzymes (until denaturing) - pH \> different enzymes work in different pH - Ion Concentration \> affects charged groups on protein - Certain enzymes require molecules to function right -- coenzymes - Molecules that are inorganic are called co-factors - Substrate \> more substrate = faster reaction until enzymes are saturated Inhibitors - Competitive: chemicals that resemble substrate and compete with the normal substrate - Non-Competitive: they bind to another part of the enzyme (allosteric site) that change the conformation/shape of the enzyme -- affecting the active site **[Redox Reactions -- cellular processes]** Redox Reactions: transfer of electrons Acid-Base Reaction: transfer of protons Decomposition/Synthesis: transfer of atoms (OIL RIG) Oxidation: process of loosing an electron from an atom - Reducing Agent: reactant that gives up the electron Reduction: process of gaining an electron from an atom - Oxidizing Agent: element that is reduced (gains electron) Oxidation Numbers: used to track +ve/-ve character of atoms and reflects its ability to accept or donate an electron Trends Group 1 \> +1 Group 15 \> -3 Group 2 \> +2 Group 16 \> -2 Group 13 \> +3 Group 17 \> -1 Rulings 1\. Oxidation \#s for a free element is 0 2\. Oxidation \# for a monatomic ion is the charge on the ion 3\. Oxidation \# of Hydrogen is +1 4\. Oxidation \# of Oxygen is -2; (-1 for Peroxide) 5\. For polyatomic ions, the sum of the Oxidation \#s in the ion = the \# of charge in the ion 6\. Elements in Group 1-2 & Aluminum are indicated on the table Oxidation-Reduction (Redox) Reactions - Chemistry Steps Week 4 ====== **[Acids & bases]** Water Dissociation: pure water only contains H2O molecules that occasionally react w/each other Hydronium (H3O): gives rise to acidic solution - Sour taste, turn blue litmus paper red, electrical conductivity Acids: substances that increase H3O's concentration when dissolved in water & that at least 1 ionizable H-atom in their chemical structure Hydroxide (OH): has properties of a base solution - Bitter taste, turns red litmus paper blue, electrical conductivity, slippery Bases: substances that increase OH's concentration in a solution - Ionic: formed by disassociating in water to produce OH directly - Other: formed by combing w/ H+ from water directly Strong + Weak Acids + Bases - Both can be classified as strong or weak due to the degree of ionization upon dissolving in water. Strong will dissolve completely and weaks will dissolve partially - Weak Acids and Bases tend to be reversible; when the opposing reactions occur at equal rates, the reaction is in equilibrium Neutralization: a reaction occurs when an acid is mixed w/ a base to produce salt and water pH: the acidity of a solution can be expressed in terms of H3O concentration (7 is neutral) Blood pH: when H+ ions enter the bloodstream the carbonic acid ions react w/ H+, producing bicarbonate. If a base enters the blood stream, taking away the H+ ions (protons), carbonic acid ionizes to replace the missing H+ ions. - Carbonic acid is the most important buffer in human extracellular fluid -- produces CO2 when reacting w/H20 Buffers: resist significant change in pH. Living systems usually consist of a conjugate acid-base pairing in equilibrium - Bronsted-Lowery Acids: substances that transfer protons (H+ ions) to another substance; proton donors - Bronsted Lowery Bases: substances that can accept protons from another substance; proton acceptors  **[Membranes]** Lipids and proteins are the key ingredients in membranes -- phospholipids & proteins are amphipathic & arranged as a bilayer - Not all membranes are identical-their function differs due to chemical composition and structure i.e fluid mosaic model Fluid: membranes are held together by hydrophobic interactions -- membranes in motion w/ fast drifting lipids & slower drifting proteins. - May be influenced by presence of unsaturated FA chains & cholesterol Mosaic: combination of proteins, making the membrane unique & can be fluid or anchored (strengthen the membrane). Proteins may penetrate the bilayer fully (integral) or reside on the membrane (peripheral). - Integrals typically have hydrophobic regions, spanning the bilayer, result of non-polar amino acids arranged in helices Protein functions include, transports, enzyme activity, signal transduction, intercellular joining, cell-cell recognition & attachment to cytoskeleton and extracellular matrix - Carbohydrates are found on the external face of the membrane that attach to lipids/proteins (glycol-) & enable cells to distinguish one another **[Passive Transport]** 1. Diffusion: molecules/ions dissolved in the cytoplasm & extracellular fluid are in constant random motion (high to low concentration) a. Molecules Size: larger = more difficulty diffusing b. Polarity: small polar molecules can cross membranes at the same rate as small non-polar molecules c. Charge: charged molecules can't diffuse across membranes 2. Osmosis: movement of water across membranes due to the impermeability of the solute & amount differing on either side a. Hypertonic: 2 solutions w/ unequal osmotic concentration, moves to solution with more solute - Animal Cells: Crenation (water leaves) - Plant Cells: Plasmolysis (water leaves) b. Hypotonic: moves to solution with less solute - Animal Cells: Lysis (bursts) - Plant Cells: Turgor Pressure (water in & fills vacuole) c. Isotonic: 2 solutions have the same osmotic concentration - Animal Cells: water in and out - Plant Cells: water in and out  3. Facilitated Diffusion a. Charter Protein: hydrophilic interior provides an aqueous channel for polar molecules to pass when open b. Carrier Protein: bind to molecules to assist (like enzymes) (low diffusion rate) **[Active Transport]** 1. Primary: cellular process that uses ATP directly to move molecules from one side of the membrane to another. 2. Secondary: uses an electromagnetic gradient as a source of energy to transport molecules across a cell membrane against the gradient **[Membrane Assisted]** 1. Endocytosis: A cell engulfs material by folding the cell membrane around it & then pinching off to form a vesicle inside the cell a. Phagocytosis: cell eating b. Pinocytosis: cell drinking c. Receptor-Method: receptors Endocytosis - Wikipedia 2. Exocytosis: allows large macromolecules to leave the cell via vesicles containing the cell's waste or extra content **[Cell Organelles]** Nucleus: a membrane bound structure containing the cell's heredity information, controls and growth reproduction - Nucleolus: site of rRNA transcription and processing ribosome activity-cells require large numbers of ribosomes to meet the needs of protein synthesis (5-10 million) Ribosomes: production of proteins; large macromolecules w/ 2/3 RNA and 1/3 protein. They read the nucleotide sequences of mRNA into protein sequences via genetic code Endoplasmic Reticulum: composed of branching tubes and flat sacs extending through the cytosol. It takes up ½ the membrane and the ER lumen space occupies 10% the cell volume. The ER membrane separates the lumen from the cytosol, mediating transfer of molecules between the two compartments - Smooth: lack of ribosomes & not as common in cells. Contain ER exit site for vesicles containing new proteins/lipids, (more evident in cells that prioritize lipid metabolism) - Rough: covered w/ribosomes, processes and produces proteins to be exported from the cell. Amino acids are folded into 3D displays, then chemicals (carbohydrates) are added, and finally transported Golgi Apparatus: flat membrane enclosed sacs (cisternae) & vesicles. The Golgi processes proteins from ER to be sorted, processed or transported to destinations. Proteins from ER enter the cis face, then go to the Golgi, and exit via trans face. Glycolipids & sphingomyelin for animal cells are processed here Vesicles: Transport vesicles play a role in molecule traffic between different membrane-enclosed compartments, transporting materials taken up at the cell's surface & are key to organization Vacuoles: membrane bound organelles that provide specialized environments for biochem & biophysical processes essential for cellular function. It occupies 90% in plant cell volume & ¼ in fungi cells. Animal cells have hydrolytic enzymes enriched w/lysosomes. For plant cells it, does a bunch of storage and structure things Mitochondria: surrounded by a double membrane system w/ inner & outer mitochondrial membrane. The inner forms foids (cistae) that extends to the interior (matrix). It's responsible for energy to break down carbs & FA's, which is converted to ATP & have their own DNA Chloroplasts: large & long organelles responsible for photosynthesis in PLANTS. Bounded by a double membrane called the chloroplast envelope, & a 3^rd^ internal membrane called the thylakoid membrane. It forms flatten disks called thylakoids & arranged in stacks (grana). Has 3 compartments a. Intermembrane space between 2 membranes of the envelope b. The stroma; lies inside the envelope but outside the thylakoid membrane c. The thylakoid lumen Cell Walls: connects cells to tissue, signals plant growth/division & controls plant organ shape -- embryogenesis and growth. Able to withstand osmotic turgor pressure of the cell -- lateral strength. - Arranged in layers of cellulose microfiber in the matric of pectin & hemicellulose. It coats the outside of the membrane. The porosity of the membrane permits soluble factors to diffuse across the cell wall & interact w/ receptors on the membrane. It's a selective filter water & ions can diffuse across.