Organic and Inorganic Compounds

Organic vs. Inorganic Compounds

• Inorganic substances do not contain both carbon and hydrogen; water, hydrochloric acid, and carbon dioxide are examples.
• Organic substances contain both carbon and hydrogen and are synthesized via covalent bonds.

Inorganic: Water

• Water makes up 70% of an adult’s body weight.
• Water serves as the body's lubricating fluid and a heat sink.
• It is a component of liquid mixtures, including solutions, colloids, and suspensions.
• Considered a universal solvent.

Organic: Functional Groups

• Functional groups are groups of atoms linked by strong covalent bonds that tend to function in chemical reactions as a single unit.
• Five functional groups: hydroxyl, carboxyl, amino, methyl, and phosphate.

Important Functional Groups

• Hydroxyl groups are polar and are components of all four types of organic compounds, involved in dehydration synthesis and hydrolysis reactions.
• Carboxyl groups are found within fatty acids, amino acids, and other acids.
• Amino groups are found within amino acids, the building blocks of proteins.
• Methyl groups are found within amino acids.
• Phosphate groups are found within phospholipids and nucleotides.

Carbohydrates

• Carbohydrates are molecules composed of carbon, hydrogen, and oxygen with a chemical formula of (CH2O)n.
• They are also referred to as saccharides.
• Carbohydrates come in three forms.
• Monosaccharides are monomers of carbohydrates.
• Disaccharides are made of two monomers (di = two).
• Polysaccharides are polymers and consist of hundreds to thousands of monomers.

Monosaccharides

• Monosaccharides are monomers of carbohydrates.
• Five important monosaccharides in the body: glucose, fructose, galactose, ribose, and deoxyribose.
• Glucose, fructose, and galactose are hexose sugars.
• Ribose and deoxyribose are pentose sugars.

Disaccharides

• Disaccharides are a pair of monosaccharides formed via dehydration synthesis and bonded by glycosidic bonds.
• Three important disaccharides to humans are sucrose, lactose, and maltose.
• Sucrose is commonly referred to as table sugar.
• Lactose is milk sugar.
• Maltose is malt sugar.
• In the digestive tract, disaccharides are split into their component monosaccharides via hydrolysis.

Polysaccharides

• Polysaccharides contain a few to thousands or more monosaccharides.
• Three important polysaccharides in humans: starch, glycogen, and cellulose.

Lipids

• Lipids contain few oxygen atoms that are often at the periphery of the molecule.
• Their nonpolar hydrocarbons make them hydrophobic.

Triglycerides

• Triglycerides are common dietary lipid groups also referred to as fat.
• Triglycerides are formed from the synthesis of glycerol and three fatty acid chains via dehydration synthesis.

Types of Fat Based on Shape

• Saturated fats are full of hydrogen, without double bonds.
• Unsaturated fats have one or more double bonds between carbon atoms which causes the molecules to “kink”.

Phospholipids

• Phospholipids have a bond between the glycerol component of a lipid and a phosphorus molecule.
• They have a similar structure to triglycerides.

Proteins

• Proteins are polymers made up of nitrogen-containing monomers.
• Amino acids are molecules composed of an amino group and a carboxyl group along with a variable side chain.
• 20 different amino acids contribute to human structure and function.
• All amino acids contain both an acid (carboxyl group) and a base (amino group.
• A side chain, or R-group, distinguishes the 20 amino acids from one another.

Central Dogma

• The central dogma of molecular biology illustrates the process by which DNA is transcribed into RNA, which is then translated into protein.

Peptide Bonds

• Peptide bonds link amino acids together to form peptides, polypeptides, or proteins via dehydration synthesis.
• The bonds between the amino acids are peptide bonds.

Essential and Semi-Essential Amino Acids Mnemonic

• PVT TIM HALL can be used to help remember the essential and semi-essential amino acids.
• The mnemonic stands for Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine.
• A is always ARGinine and T is never TYrosine.

Structural Organization Of Proteins

• Primary structure is the sequence of amino acids in the polypeptide chain.
• Secondary structure often forms hydrogen bonds that twist the structure making an alpha helix.
• Tertiary structure folds the shape of the protein into a three-dimensional shape.
• Quaternary structure is a shape resulting from the association of two or more polypeptide chains into one large protein.

Nucleotides

• A nucleotide is an organic compound composed of three subunits: one or more phosphate groups, a pentose sugar (ribose or deoxyribose), and a nitrogen-containing base (adenine, cytosine, guanine, thymine, or uracil).
• Nucleotides can be assembled into nucleic acids: deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
• They can also form the energy compound adenosine triphosphate.

Adenosine Triphosphate

• Adenosine Triphosphate (ATP) comprises a ribose sugar, an adenine base, and three phosphate groups.
• It is a high-energy compound because the two covalent bonds linking its three phosphates store a significant amount of potential energy.

The Cell

• The cell is the basic unit of life, of which all organisms are made up.
• It is a highly dynamic entity based on the principle of biogenesis.

Cell Membrane

• The cell membrane is a pliable structure composed primarily of back-to-back phospholipids (a "bilayer").
• Phosphate groups are negatively charged and "water loving," thus attracted to water.
• The lipid tails are uncharged and "water fearing," thus repelling water.

Phospholipid Bilayer

• Hydrophobic tails associate with one another which forms the interior of the membrane.
• The polar heads contact the fluid inside and outside of the cell.

Structure & Composition of the Cell Membrane

• Glycoproteins are proteins with carbohydrate attached.
• Glycolipids are lipids with carbohydrate attached.
• Other components include peripheral membrane proteins, integral membrane proteins, cholesterol, and channel proteins.

Cytoplasm

• Cytosol is the jelly-like substance within the cell and provides the fluid medium necessary for its biochemical reactions.
• Organelles are each a different type of membrane-enclosed body in the cell performing a unique function.

Endoplasmic Reticulum

• Endoplasmic Reticulum is a system of channels continuous with the nuclear membrane.
• It is composed of the same lipid bilayer material and provides passages throughout much of the cell.
• It functions in transporting, synthesizing, and storing materials.
• There are two types: Rough ER and Smooth ER.

Ribosomes

• Ribosomes are the site of protein synthesis.
• They are composed of two ribosomal RNA subunits that wrap around mRNA to start the process of translation, followed by protein synthesis.

Golgi Apparatus

• A “post-office” organelle sorts, modifies, and ships off the products coming from the rough ER.
• It has a stacked flattened disc appearance.
• Products are sorted through the apparatus and released from the opposite side after being repackaged into new vesicles.

Lysosomes

• Lysosomes are vesicular organelles that form by breaking off from the Golgi apparatus.
• It conducts intracellular digestion of damaged cellular structures, food particles, and bacteria.
• Lysosomes may also be called suicide bags for cells.

Peroxisomes

• Peroxisomes are membrane-bound cellular organelles containing mostly enzymes.
• These differ from lysosomes: formed by self-replication or budding off from SER and contain oxidase and catalase enzymes.
• Functions include oxidizing poisonous substances and degrading free radicals that may damage cells.

Cytoskeleton

• Cytoskeletons are fibrillar proteins synthesized by ribosomes in the cytoplasm which enable intracellular scaffolding.
• Examples include filaments and microtubules.

Mitochondria

• Mitochondria are membranous, bean-shaped organelles that are the “energy transformer" of the cell.
• This organelle is the powerhouse of the cell, has its own genetic code, and maternal DNA transmission.

Nucleus

• The nucleus is the control center of the cell, containing large quantities of DNA (genes).
• DNA seen on microscopy is darkly staining chromatin material.
• Genes are duplicated during mitosis.
• During mitosis, chromatin organizes into highly structured chromosomes.
• Almost all nucleated cells in the body contain the same set of chromosomes and DNA.

Organization of the Nucleus and Its DNA

• The nucleus is surrounded by a membrane called the nuclear envelope.
• Proteins called pore complexes the lining of the nuclear pores regulate the passage of materials into and out of the nucleus.
• Inside the nuclear envelope is a gel-like nucleoplasm with solutes that include the building blocks of nucleic acids.
• The nucleolus is a region of the nucleus that is responsible for manufacturing the RNA necessary for constructing ribosomes.
• Genetic instructions used to build and maintain an organism are arranged in an orderly manner in strands of DNA.
• Within the nucleus are threads of chromatin composed of DNA and associated proteins.

Central Dogma

• The central dogma of molecular biology dictates the flow of genetic information from DNA to RNA to protein.

DNA Replication

• Cells must reproduce themselves by dividing to produce two new daughter cells.
• Very few cell types in the body do not divide; nerve cells, skeletal muscle fibers, and cardiac muscle cells are examples.

DNA Molecule

• DNA is made of two strands that "complement" each other in the form of a double-stranded molecule looking like a long, twisted ladder.
• The four DNA bases include adenine (A), thymine (T), cytosine (C), and guanine (G).

Cell Growth and Division

• Somatic cells are a general term for a body cell, and all human cells, except for the cells that produce eggs and sperm.
• Somatic Cells contain two copies of each of their chromosomes.
• Humans are diploid organisms, meaning they have 23 homologous pairs of chromosomes in each of the somatic cells.

The Cell Cycle

• The cell cycle consists of two general phases, Interphase and Mitosis/cytokinesis.
• Interphase is the period of the cell cycle during which the cell is not dividing.
• Mitosis/cytokinesis is the division of genetic material, during which the cell nucleus breaks down and two new, fully functional, nuclei are formed.
• Cytokinesis divides the cytoplasm into two distinctive cells.

The Cell Cycle Phases

• The two major phases of the cell cycle include mitosis (cell division), and interphase, when the cell grows and performs all of its normal functions.
• Interphase has three phases: G1 phase, S phase, and G2 phase.

Interphase

• A cell grows and carries out all normal metabolic functions and processes in a period called G1.
• G1 phase (gap 1 phase) is the first gap or growth phase in the cell cycle.
• The S phase (synthesis phase) is the period during which a cell replicates its DNA.
• The G2 phase is a second gap phase, during which the cell continues to grow and makes the necessary preparations for mitosis.
• G0 phase is a resting phase of the cell cycle.

The Structure of Chromosomes

• Each cell contains two copies of each chromosome.
• Each copy of the chromosome is referred to as a sister chromatid.
• The centromere is the structure that attaches one sister chromatid to another.

Mitosis and Cytokinesis

• The Mitotic phase of the cell typically lasts between 1 and 2 hours.
• Here it completes mitosis, distributing the contents of the nucleus that are identically pulled apart and distributed between its two halves.
• Four major stage of Mitosis: Prophase, Metaphase, Anaphase, and Telophase
• Cytokinesis then divides the cytoplasm and cell body into two new cells.

Prophase

• The first stage of mitosis where loosely packed chromatin coils and condenses into visible chromosomes with an identical partner attached, forming the familiar X-shape of sister chromatids.
• The nucleolus disappears and the nuclear envelope also disintegrates.
• Centrioles serve as origin points from which microtubules extend.
• Each cell contains two centrosomes side-by-side, which begin to move apart during prophase.
• Near the end of prophase there is an invasion of the nuclear area by microtubules from the mitotic spindle.
• Prometaphase indicates the transition between prophase and metaphase.

Metaphase

• The second stage of mitosis where sister chromatids, with their attached microtubules, line up along a linear plane the metaphase plate.
• The metaphase forms in the middle of the cell, or the equatorial plane located between the centrosomes.
• Microtubules are poised to pull apart sister chromatids and bring one from each pair to the side of cell.

Anaphase

• Third stage of mitosis, which occurs of over a few minutes, when the pairs of sister chromatids are separated from one another, forming individual chromosomes once again.
• Chromosomes are pulled to opposite ends of the cell by their kinetochores, as the microtubules shorten.
• Each end of the cell receives one partner from each pair of sister chromatids, ensuring the two new daughter cells contain identical genetic material.

Telophase

• Final Stage of Mitosis
• Two new daughter nuclei form on the either ends of the dividing cell.
• Nucleoli also reappear within the new nuclei and the mitotic spindle which splits apart allowing each new cell to receive its own complement of DNA, organelles, membranes, and centrioles.
• The cell already begins to split in half as cytokinesis as the final stage.

Cleavage Furrow

• The cleavage furrow is made up of microfilaments during Cytokinesis
• Causes the two cells separate which finally separate.