Cell Structure and Synthesis

• Genomes consist of more than just genes, containing cells' total genetic information
• A gene, a heredity unit, holds data influencing characteristics (phenotype) and is a DNA segment for protein or functional RNA production
• DNA synthesis (replication) leads to RNA Synthesis (transcription) and then Protein synthesis (translation) in ribosomes

Cell Structure and Synthesis

• Atoms form molecules, which create organelles, and then cells, increasing in size
• Eukaryotic cells have DNA and genetic material in the nucleus
• The endoplasmic reticulum and Golgi apparatus define eukaryotes
• Unique to eukaryotes are lysosomes, mitochondria, peroxisomes, the nuclear envelope, and vesicles
• Cytosol, or cytoplasm, is the space/water where everything floats
• Synthesis is the process of making something
• Membrane-enclosed organelles in eukaryotic cells have key functions
• Cytosol contains metabolic pathways, aids protein synthesis, and maintains the cytoskeleton
• Nuclei contain genomic DNA and do RNA synthesis
• The endoplasmic reticulum synthesizes lipids and proteins for organelle and plasma membrane distribution
• The endomembrane system consists of multiple membranes working together, made of organelles or functional subunits

Endoplasmic Reticulum Varieties

• Smooth ER synthesizes lipids like membrane lipids and steroids
• Rough ER makes proteins using ribosomes
• Ribosomes exist in the cytoplasm and on RER and produce proteins
• Lipids and proteins are transported through vesicles to the Golgi apparatus
• The Golgi apparatus modifies lipids and proteins received from the ER and ships those lipids and proteins elsewhere

Cellular Processes

• Endocytosis involves "eating" or the cell absorbing materials
• The plasma membrane bends and encircles food to bring it inside the cell, forming an endosome
• Exocytosis is cell defecation or secretion
• Mitochondria facilitate ATP synthesis via oxidative phosphorylation
• Chloroplasts are about the same size as Mitochondria
• Chloroplasts conduct ATP synthesis and carbon fixation by photosynthesis
• Peroxisomes break down molecules and oxidatively break down toxic molecules
• Lysosomes lyse fats/molecules and perform intracellular degradation

Cytoskeleton

• The cytoskeleton gives cell protection and strength
• It supports cell structure and shape
• It is not rigid, but mobile
• It is needed for cell reproduction, cell movement, and keeps organelles in place

Types Cytoskeletal Pieces

• Microtubules are tiny protein tubes that compose the mitotic spindle
• Actin filaments (microfilaments) enable cytokinesis of the cell
• Intermediate filaments (only in some animals) provide structure, flexibility, and nuclear lamina
• Cytoplasm completely makes proteins, creating long polymers of proteins

Organelles

• Mitochondria serve as the powerhouse of the cell, producing most of the ATP
• The nucleus houses and protects genetic material

Model Organisms and Biomolecules

• Model organisms are studied to understand their organism functions
• Examples are humans, mice (mus musculus), fruit flies (Drosophila melanogaster), plants (Arabidopsis thaliana), roundworms (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and bacteria (Escherichia coli), with varying levels of multicellularity

Biomolecules

• Sugars form polysaccharides like starch and glycogen
• Amino acids create proteins
• Enzymes end in -ase
• Nucleotides become nucleic acids
• There are 4 categories of biomolecules which include the following
• Carbohydrates (sugars) are simple or complex (-ose)
• Proteins are polymers of amino acids (-ine)
• Nucleic acids are polymers of nucleotides like DNA and RNA with monomers like ATP
• Lipids feature a polymer example is lipids, oils, fats, waxes, and steroids

Macromolecules

• Sugars create polysaccharides, glycogen, etc. while in Plants it's Starch
• Fatty acids produce fats and membrane lipids
• Amino acids form proteins
• Nucleotides produce nucleic acids
• Macromolecules assemble from monomers into polymers through dehydration (synthesis or condensation) reactions
• Bond strength varies based on intermolecular forces holding atoms together

Bonds Strength & Types

• Covalent bonds are the strongest of the bond types
• Covalent bonds are represented as lines, e.g., water is a polar covalent bond
• Noncovalent bonds are weak individually
• They require a small amount of energy
• Noncovalent bonds collectively are strong
• Non-covalent bonds consist of lots of non-covalent bonds, aka hydrogen bonds
• Covalent bonds involve shared electrons between atoms
• Molecules are hydrophilic, hydrophobic, or amphipathic based on the quantity of bonds and the molecule's structure
• Fats, waxes, and oils are hydrophobic
• Membrane lipids are amphipathic
• Most other biological molecules are hydrophilic
• Carbohydrates and nucleic acids
• There are 2 types of covalent bonds
• Nonpolar covalent bonds involve equal sharing of electrons
• Molecules with mostly nonpolar bonds are hydrophobic
• Polar covalent bonds involve unequal sharing of electrons
• The most common is water

Hydrogen, Molecules, and Sugars

• Oxygen is often involved in these as well as Leads to "H" bonds
• Both kinds form when two atoms share electrons
• Both are very strong bonds
• Most molecules have a combination of bond types
• Polar covalent bonds often use oxygen because oxygen atoms are electronegative
• Electronegativity: ability of atom to pull electrons towards itself
• Water: oxygen is electronegative and hydrogen is electropositive
• Surface tension: water molecules hydrogen bonding to each other
• A single H bond is weak, while multiple H bonds are quite strong
• Hydrogen bonds are weak between a slightly positive hydrogen atom and a slightly negative atom
• H bonds provide water's special properties like surface tension, the ability to dissolve molecules, and the ability to hold heat
• Polar molecules make hydrogen bonds with other polar molecules
• Hydrophilic molecules can hydrogen bond with water
• Carbohydrates
• Hydrophobic molecules repel water
• Hydrogen bonds in proteins and DNA strands hold double helices together
• In living creatures, carbohydrates are both structural molecules and also store enery
• Cell walls are carbohydrate and protein conglomerates -- Plants have cellulose, crab shells have chitin, and bacterias contain peptidoglycan
• Sugars provide energy storage and structure
• General sugar formula is (CH2O)n, where n = 3, 4, 5, 6
• Glucose (C6H12O6), is a simple sugar and can be arranged into polymers
• Glycogen consists of individual glucose molecules branched together
• Complex sugars fall under polysaccharides

Lipids, Nucleic Acid Functions

• Lipids' functions are for long-term:
• Energy storage, insulations, structural components, and protection
• Triglycerides are fats and oils, and are found in phospholipids of the plasma membrane
• Signaling information is stored in hormones
• steroids
• Lipids derive from fatty acids (carbon and hydrogen)
• No oxygen is in fatty acid tails
• They are entirely hydrophobic
• Fatty acids attach to a polar head (hydrophilic)
• Nonpolar (C+H)(Only nonpolar covalent bonds)
• Amphipathic molecules have one area that loves water and another that hates it --- Amphibian
• Amphipathic liquids form into membranes
• They feature hydrophobic, non-polar fatty acid chairs and also polar heads
• Double covalent bond that is unsaturated fatty acids bend/kink in molecular level
• Liquid oil
• Saturated fatty acids are straight
• Solids
• Other lipids
• Have a hydrocarbon tail from a fatty acid
• Cholesterol is in all animal membranes and consists of one oxygen molecule on one side
• Amphipathic Testosterone contains two oxygen molecules
• Nucleic acids store genetic information and help make proteins
• DNA and RNA contain instructions in nucleotide sequences
• Nucleotides are monomers
• ATP synthesis and carbon fixation
• Two major polymers exist, including -- DNA: deoxyribonucleic acid -- RNA: Ribonucleic acid

Nucleotides

• Deoxy is the major difference between DNA & RNA
• RNA contains sugars across from a double helix
• Nucleotides include the following: -- Phosphate group: yellow circle -- 5 carbon sugar: blue (usually) -- Nitrogenous base -- DNA, RNA
• Complementary Base-Pairing;
• A::T has 2 H bonds and G::C has 3 H bonds
• Purines always pair with a pyrimidine
• 5 carbon sugars differentiate DNA from RNA
• In the deoxy form molecules, it takes off the oxygen
• @2 prime RNA= OH, DNA=H

Life Molecular Interaction

• Molecules must have physical interaction for life to exist
• Covalent bonds hold atoms into molecules
• Molecules with oxygen are made of have polar covalent bonds
• Polar covalent bonds lead to Hydrogen bonds
• Hydrogen impacts solubility AND interaction to other polar moleules like carbohydrates
• ATP is a special nucleotide for energy in cells -- ATP represents the energy currency of a cell -- ATP (adenosine triphosphate) is a
• High energy molecule (last 2 unstable bonds)

Proteins

• Metabolism → enzymes Structure → keratin and collagen Transport → hemoglobin and membrane proteins Defense → antibodies Regulation → protein hormones, insulin Motion → muscle proteins
• Proteins are polymers of amino acid monomers
• General formula of amino acids: Levels exist in Protein Organization:
• Primary Protein Structure features a Sequence of chain in amino acids
• Secondary Protein Structure has Local folding of the polypeptide chain into helices or sheets
• Tertiary Protein Structure presents like 3 Dimensionial folding pattern with side chain interactions
• Quaternary Protein Structure features Protein consisting of more than one amino acid chain
• ATP (adenosine triphosphate) carries, and transfers energy, also presents in most energized form vs ADP

ATP & Proteins

• Organisms consume energy to build ordered cells and bodies
• Reactions are coupled to transfer energy
• Activated carrier molecules temporarily house and transport the energy
• ATP drives chemical reactions
• Proteins collapse into a lowest-energy conformation
• Shape can be affected by changes in biochemistry, like denaturation
• Shapes is required for function of:
  • Which amino presents
  • Primary structure - linear strand - to determine function and structure
• Proteins
• Hydrophobic forces can separate atoms (nonpolar) regions
• R group influences acids
• Side chains determine proteins

Cellular genomes contain total genetic information, not just genes. Synthesis involves DNA replication, RNA transcription, and protein translation. Eukaryotic cells have DNA in the nucleus and unique organelles like lysosomes and mitochondria.