BSCI170 Chapter 1 - Principles of Life PDF

**[BSIC170 Chapter 1 (Dr. Choi)]** **[Introduction: Lecture \#1 8-27-2024]** [Principles of Life: ] - - - - [Biology is a Broad and Diverse Field of Study: ] - [Diversity of Complexity of Life: ] - - - - - [Common Aspects in Living Organisms: ] - - - - -...

**[BSIC170 Chapter 1 (Dr. Choi)]** **[Introduction: Lecture \#1 8-27-2024]** [Principles of Life: ] - - - - [Biology is a Broad and Diverse Field of Study: ] - [Diversity of Complexity of Life: ] - - - - - [Common Aspects in Living Organisms: ] - - - - - [Key Features in Living Organisms: ] - - - - - - [The Basic Structural and Functional Unit of Life: The Cell: ] - - - [Cell Theory: ] - - - [Energy Transformation in Living Organisms:] - - - - - [How did life evolve?] - - [Evolution]: - - - - - - - [Fundamental Force of Evolution - Mutation:] - - - - - - - [Genome: ] - - - - - - - [Bioinformatics:] - - - - [Chapter 1 - Principles of Life: ] - - - - - - - **[Overview of Cells & Basic Chemistry: Lecture \#2 8-29-2024]** [Prokaryotes vs. Eukaryotes:] - - - - - [Cell Analogy:] - - - - [Prokaryotic Cells: ] - - - - - - [Eukaryotic Cells:] - - - - - [Cell Structure & Function ] +-----------------------+-----------------------+-----------------------+ | [Name:] | [Description: | [Image:] | | | ] | | +=======================+=======================+=======================+ | Endomembrane System | Interconnected |  | | | modifying, and | | | | packaging protein and | | | | lipids) | | +-----------------------+-----------------------+-----------------------+ | Cell Membrane (aka | Acts as a protective | Cell membrane \| | | plasma membrane) | barrier | Definition, Function, | | | | & Structure \| | | | | Britannica | +-----------------------+-----------------------+-----------------------+ | Cytoplasm (aka | A gel-like interior |  | | | reactions and | | | | cellular processes | | | | happen here | | +-----------------------+-----------------------+-----------------------+ | Rough Endoplasmic | Makes proteins (has | Endoplasmic Reticulum | | Reticulum (ER) | ribosomes) | (Rough) | | | | | | | When the ribosome | | | | needs to be | | | | synthesized it | | | | targets the ER which | | | | happens in the | | | | cytosol | | | | | | | | Goes to the rough ER | | | | because it has a | | | | ribosome | | | | | | | | Protein is ready for | | | | transport within the | | | | cell | | +-----------------------+-----------------------+-----------------------+ | Smooth Endoplasmic | Lipid synthesis and |  | +-----------------------+-----------------------+-----------------------+ | Golgi Apparatus | Sorts and ships | Golgi Body | | | proteins to their | | | | respective | | | | destinations in the | | | | cell (analogy: post | | | | office) | | | | | | | | Gogi sends material | | | | back and forth to the | | | | ER | | | | | | | | Cis face (close to | | | | ER): receives protein | | | | and lipids for | | | | processing | | | | | | | | Trans face (close to | | | | the plasma membrane): | | | | sorts and ships | | | | proteins to their | | | | destinations | | | | | | | | Will go to various | | | | places for secretion | | | | (whether the plasma | | | | membrane or other | | | | places throughout the | | | | cell) | | +-----------------------+-----------------------+-----------------------+ | Nucleus | Houses the DNA and |  | | | | | | | Contains genetic | | | | information (DNA) | | | | | | | | DNA is stored but | | | | also replicated here | | | | | | | | Inside the nucleus, | | | | there are chromatin | | | | and chromones which | | | | are the organized DNA | | | | | | | | The nucleus is where | | | | transcription (RNA | | | | synthesis) happens | | | | | | | | The genetic | | | | information from the | | | | nucleus will be | | | | carried to the | | | | cytoplasm to be | | | | translated into a | | | | protein | | +-----------------------+-----------------------+-----------------------+ | Lysosomes | Has digestive enzymes | Lysosome | | | that work in acidic | | | | conditions | | | | | | | | Responsible for the | | | | breakdown | | | | | | | | Protection and | | | | digestion | | | | | | | | They get rid of | | | | harmful pathogens | | | | | | | | Phagocytosis: digest | | | | food for energy | | | | | | | | Breakdown bad | | | | organelles | | +-----------------------+-----------------------+-----------------------+ | Mitochondria/Chloropl | Turns chemical energy |  | | | | | | | Production of energy | | | | | | | | Animal Cell | | | | | | | | Cellular respiration | | | | | | | | Found in all | | | | eukaryotic cells | | | | | | | | Contains DNA | | | | | | | | \_\_\_\_\_\_\_\_\_\_\ | | | | _\_\_\_\_\_\_\_\_\_\_ | | | | \_\_\_\_\_ | | | | | | | | Sunlight into | | | | chemical energy | | | | through | | | | photosynthesis | | | | | | | | Two membranes: stroma | | | | and thylakoids | | | | | | | | Stroma: inner | | | | membrane | | | | | | | | Tylakids: internal | | | | membrane structure | | | | | | | | Contain DNA | | +-----------------------+-----------------------+-----------------------+ | Vacuole | Stores nutrients in | Vacuole -- | | | the cell | Definition, Structure | | | | \... | | | | | | | | \* In both plant & | | | | animal cells \* | +-----------------------+-----------------------+-----------------------+ | Ribosomes | Synthesizes proteins |  | | | | | | | Composed of ribosomal | | | | RNA (rRNA) and | | | | proteins | | | | | | | | rRNA synthesis and | | | | ribosome assembly | | | | happen in the nucleus | | | | (inside of the | | | | nucleus) | | | | | | | | Ribosomal protein | | | | needs to be | | | | transported into the | | | | nucleus | | | | | | | | Non-membrane bound | | | | structure for protein | | | | synthesis | | | | | | | | Ribosomes that re not | | | | associated with ER - | | | | synthesize proteins | | | | that function in the | | | | cytosol | | +-----------------------+-----------------------+-----------------------+ | Cell Wall | Acts as a rigid | Cell Wall Lesson for | | | barrier against | Kids: Definition & | | | things going in and | Function Video | | | out of the cell. ONLY | | | | found in plant cells. | | +-----------------------+-----------------------+-----------------------+ | Vesicles | Transports proteins |  | +-----------------------+-----------------------+-----------------------+ [Basic Chemistry:] - - - - - - - - - - - - - - - +-----------------+-----------------+-----------------+-----------------+ | Protons | = | Electrons | Protons and | | | | | Electrons are | | | | | the SAME \# | +=================+=================+=================+=================+ | Protons | = | Atomic Number | Protons and the | | | | | Atomic \# are | | | | | the SAME \# | +-----------------+-----------------+-----------------+-----------------+ | Protons | \- | Atomic Mass | Equals the | | | | | Neutrons | +-----------------+-----------------+-----------------+-----------------+ | Protons | - | Neutrons | = Atomic Mass | +-----------------+-----------------+-----------------+-----------------+ [Example:]  - - - - - - - - - - - - - - - - - - - [Atoms Bond to Form Molecules: ] - - - - - - - - - - - **[Water & Molecular Interactions: Lecture \#3 9-3-2024]** [Matter, Elements, & Atoms:] - - - - - - - [Structure of an Atom:] - - - - - [Atomic Number & Atomic Mass] - - - - - [Protons, Electrons, and Neutrons ] - - - - - - - - [Isotopes:] - - - - - - - [Ions: ] - - - [Isotopes & Ions:] - - - - - [Atomic Interactions:] - - - [Atomic Orbitals & Electrons:] - - [Shells & Orbitals of Electrons:] - - - - [Atomic Orbitals:] - - - - - - [Valence Electrons:] - - - - - [Octet Rule: ] - - - - [Noble Gas Configuration:] - - - [Noble Gas:] - [Practice: ] - - - - - - [Chemical Bonds] - - - - - - - - [Covalent Bonds] - - - - - - - - - - - - - -  - - - - - - [Ionic Bonds:] - - - - - - [Water, H2O:] - - - - - - [Properties of Water:] - - - - - - - - [Cohesion & Adhesion:] - - - - - - [Water as Solvent:] - - - - - - - - - [What is important in the formation & the breakdown of molecules:] - - - - - - - [Moderation of Temperature:] - - - - - - - - [Water is denser as a liquid than as a solid] - - - - [Dissociation of Water] - - - - +-----------------------+-----------------------+-----------------------+ | Covalent Bonding | - - - | | +=======================+=======================+=======================+ | Ionic Bonding | - - - - - - |  | +-----------------------+-----------------------+-----------------------+ | Hydrogen Bonding | - - - | | +-----------------------+-----------------------+-----------------------+ | Van Der Waals Bonding | - - - - - - |  | | | - | | +-----------------------+-----------------------+-----------------------+ **[Functional Groups: Lecture \#4 9-5-2024]** [Cations & Anions] - - [Water forms a hydration shell around charged:]  - - - - [Salts are ionic compounds consisting of anions and cations: ] - - - [Electronegativity in the periodic table:] - - - [Dissociation of Water:] - - - - - - [Acids & Bases:] - - - - - - - [Calculating pH:] - - - - - - - - - - - - [pH Scale:] - - - - - - - - [Buffers] - - Example:  - - - -  - - [Water - The Solvent of Life] - - - - - - - [Polar vs. Non-polar molecules] - - - [Carbon & Functional Groups ] - - [Hydrocarbons ] - - - -  - - - -  - - [Functional Groups:] - - - - +-----------------------+-----------------------+-----------------------+ | [Name:] | [Function:]{.underlin | [Image:] | | | e} | | +=======================+=======================+=======================+ | Hydroxyl Group | Polar - unequal | | | | sharing (has more | | | | electronegative force | | | | compared to H) | | | | | | | | One oxygen atom and | | | | one hydrogen atom | | | | (-OH) | | | | | | | | Involved in hydrogen | | | | bonding in water | | | | | | | | Often participates in | | | | condensation | | | | reactions (a chemical | | | | reaction that | | | | combines two | | | | molecules to form a | | | | single molecule) | | | | | | | | Makes alcohols more | | | | hydrophilic | | | | (water-loving) | | +-----------------------+-----------------------+-----------------------+ | Carbonyl Group | One carbon atom |  | | (Aldehydes or | oxygen atom, written | | | Kentones) | as C=O. It looks like | | | | this: -C=O | | | | | | | | \"Carbon-oxygen | | | | double bond\" | | | | | | | | In aldehydes, it\'s | | | | at the end of a | | | | carbon chain (like in | | | | formaldehyde) | | | | | | | | Makes these compounds | | | | reactive | | | | | | | | Energy-releasing | | | | reactions | | | | | | | | Polar: unequal | | | | sharing (has more | | | | electronegative | | | | force) | | +-----------------------+-----------------------+-----------------------+ | Carboxyl Group | Combines -OH | | | | (hydroxyl) and -C=O | | | | (carbonyl) | | | | | | | | Written as --COOH | | | | | | | | It as a carbon atom | | | | double-bonded to an | | | | oxygen atom and | | | | single-bonded to a | | | | hydroxyl group (an | | | | oxygen and a | | | | hydrogen). | | | | | | | | Charged and acidic | | | | | | | | Makes these acids | | | | able to donate a | | | | hydrogen ion (H+) in | | | | water | | +-----------------------+-----------------------+-----------------------+ | Amino Group | Amino acids are |  | | | protein | | | | | | | | One nitrogen atom and | | | | two hydrogen atoms, | | | | written as --NH₂. | | | | | | | | Can act as a base | | | | because it can accept | | | | a hydrogen ion (H+) | | +-----------------------+-----------------------+-----------------------+ | Sulfhydryl Group | One sulfur atom and | | | | one hydrogen atom, | | | (Thiols) | written as --SH. | | | | | | | | A small | | | | \"sulfur-hydrogen\" | | | | tag attached to a | | | | molecule | | | | | | | | Creating bridges that | | | | help hold protein | | | | structures together | | +-----------------------+-----------------------+-----------------------+ | Phosphate Group | One phosphorus atom |  | | | oxygen atoms, written | | | | as --PO₄. | | | | | | | | DNA and ATP (a | | | | molecule that | | | | provides energy in | | | | cells), the phosphate | | | | group play a crucial | | | | role. | | | | | | | | Helps in energy | | | | transfer and storage. | | +-----------------------+-----------------------+-----------------------+ | Methyl Group | One carbon atom | | | | bonded to three | | | (Alkyl) | hydrogen atoms, | | | | written as --CH₃. | | | | | | | | Nonpolar (equally | | | | shared) | | | | | | | | This group is often | | | | found sticking off of | | | | larger molecules. | | +-----------------------+-----------------------+-----------------------+ **[Macromolecule - Carbohydrates & Lipids: Lecture \#5 9-10-2024]** [Recognize & Identify Functional Groups:] - - - - - - - -  - can lose an H+ which will turn the molecule into a -1 charge. → (Shown here) - can gain an H+ which will turn the molecule into a + 1 charge → (Shown here) [Macromolecules:] - - - - - - - - - - - - - - - [Carbohydrates: ] - - - - - - - - - - - - [Isomers of Glucose:] - [Monosaccharides: ] - - - - - - - - - - - - linear. - - - - [Monosaccharides and Disaccharides: ] - - - [Disaccharides:] - - - - - [Oligosaccharides] - - - [Polysaccharides] - - - - - - - - - - - - [Polysaccharides can be Branched or Unbranched:] - - - - [Lipids:] - - - [Types of Lipids - Fatty Acids:] - - - - - - - - - - - [Triglycerides:] - - - - - - [Synthesis of a Triglyceride:] - - - - - - [Lipid Molecules: ] - - - - [Structure of Phospholipids:] - - - - [Lipoproteins:] - - - [Other Lipid Functions:] - - - - - **[Proteins & Nucleic Acids: Lecture \#6 9-12-2024]** [Nucleic Acids:] - - - [DNA - storing information ] [RNA - express the DNA] --------------------------------------------------------- -------------------------------------------------------- Double-stranded structure Typically single-stranded Contains sugar deoxyribose Contain sugar ribose Adenine (A), guanine (G), cytosine (C), and thymine (T) Adenine (A), guanine (G), cytosine (C), and uracil (U)  - - - - - - - - - - [Pentose Sugar:] - - - - - - - - - - [DNA & RNA:] - - - - - [Nitrogenous Base: (A, C, T, U, and G)] - - - - - thymine (T), and uracil (U) - adenine (A) and guanine (G) - - - in DNA and RNA, respectively - [Phosphate Group:] - - - - - - [Nucleosides: ] - - - - - - sugar molecules (ribose or deoxyribose) - - - [Nucleic Acids Structure:] - - [Nucleic Acids Synthesis: ]   - [Complementary Base Pairing Interactions:]  - - - - [DNA Double Helix: ] - - - - [RNA Structure: ] - - - - [Different types of RNA:] - - - - - - - - - - [Information storage in Nucleic Acids:] - - - - - - - - - [Proteins (polypeptides):] - - - - [Amino Acid Monomer:] - - [Charged Amino Acids:] Hydrophilic side chains [Polar (uncharged) Amino Acids:] Form hydrogen bonds , do not ionize (gaining pos or neg charge) and become charged  [Nonpolar Amino Acids:]  ["Special case" Amino Acids:] Joining together to form proteins (carboxyl and the amino of another) [Peptide Bond Formation: ] - - - - - [Protein Structure - Four levels: ] - - - -  [Protein Structure (primary structure): ] - - - - - - - - [Protein Structure (secondary structure):] - - - - - - [Protein structure (tertiary structure): ] - [Disulfide Bond:] - - - - [Protein structure (quaternary structure):] - - [Factors that impact protein structure: ] - - - -  [Chemical Bonds:]