Lecture 2: The Chemical Level of Organization PDF

Lecture 2: The chemical level of organization ============================================= **Please read pages 43-57 for this lecture.** **Note:** - This class presumes you have a strong grasp of basic: - Atomic and molecular structure, the properties of water, acid-base chemistry, and...

Lecture 2: The chemical level of organization ============================================= **Please read pages 43-57 for this lecture.** **Note:** - This class presumes you have a strong grasp of basic: - Atomic and molecular structure, the properties of water, acid-base chemistry, and basic chemical reaction theory - **Please read pages 28-43 of the textbook carefully if you require a review.** - Chemistry Review assignment on WileyPlus Water properties Water exhibits cohesion Molecules of water stick to one another Water moderates'temperature Water can absorb a lot of energy before the temperature increases Heat goes into water to keep daytime temp low nighttime water releases heat back into environment to Sweat is another example of water controlling temperature Water expands upon freezing Solid water or ice floats on liquid The hydrogen bonds hat join water molecules in ice force water molecules into an ordered fashion called lattice Liquid water is less ordered resulting in a greater density of water molecules Reason freshwater organisms survive the winter Water is a solvent Water is a polar molecule Therefore polar and charged substances can dissolve easily in water These water loving substance are hydrophilic Examples of hydrophobic oil lipids Buffers minimize changes in ph levels Ph of blood must be kept between 7.35-7.45 Blood is more than 90% water Hydrogen bonds are important in water molecules and life Review ------ - Everything is made of **matter,** including living things - This is important because it means that the molecules in our body are subject to the same \_\_\_\_chemical\_\_\_\_\_\_\_ and \_\_\_\_\_\_\_\_\_physical\_\_\_\_\_ laws as all matter! Diagram Description automatically generated  **Above left**: Models for atomic structure. **Above right**: chemical formulas may be represented multiple ways. What is an organic molecule? ---------------------------- - Organic molecules contain \_\_\_\_\_\_carbon\_\_\_\_\_\_\_\_ - Starts with carbon skeletons held together by **covalent bonds** - If the molecule contains *only* carbon and hydrogen, it is called a **\_\_\_\_\_\_\_hydrocarbon\_\_\_\_\_\_\_\_\_\_\_** - Other atoms or molecules attached to the carbon skeleton are called **functional groups** Table 1: Selected functional groups in organic compounds  - Why should we care about functional groups? - Different chemical **structures** lead to different chemical **\_\_\_\_\_\_\_properties\_\_\_\_\_\_\_\_** - These properties will alter the **function** of these molecules in cells - E.g. Steroid hormones are modified structures based on cholesterol - Biological molecules are complex organic compounds - Every cell contains trillions of organic molecules but these molecules are made of just a few subunits - Most are **\_\_\_\_\_\_\_\_\_polymers\_\_\_\_\_\_\_\_** of **monomers** - **Four classes of biological monomers:** 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids ### Carbohydrates - Compounds containing carbon, hydrogen, and oxygen - Constitute 2-3% of total body mass - **\_\_\_\_\_\_\_\_\_\_monosaccharides\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_** or simple sugars are *monomers* of carbohydrates Shape, polygon Description automatically generated  **Above left:** Structures of select monosaccharides. **Above right:** Dehydration synthesis links monosaccharides into more complex carbohydrates. Lactose is a disaccharide. - Monosaccharides are joined together by **dehydration synthesis** - The resulting bond is called a **\_\_\_\_\_\_\_\_\_glycosidic\_\_\_\_\_\_\_\_ linkage** - **Disaccharides** are molecules formed by joining *two* monosaccharides - **Polysaccharides** are molecules made of many (100s--1000s) monosaccharides - **\_\_\_\_\_\_\_glycogen\_\_\_\_\_\_\_\_\_\_** is a branched chain of glucose monomers - Storage polysaccharide of animals - **Starches** are linear chains of glucose monomers - Storage polysaccharide of plants - Main difference is the \_\_\_\_\_\_\_\_\_\_\_stereochemistry\_\_\_\_\_\_\_\_\_\_\_\_\_ of the glycosidic bond between the monomers - Humans do not possess the enzyme to break the bonds in cellulose Shape Description automatically generated ### 1. ### Polysaccharide 2. Glycogen 3. Energy storage for animals ### ### Lipids - Hydrophobic molecules made of carbon, hydrogen, and small proportion of oxygen - Represent 18-25% of total body mass in humans - Many types of lipids: 1. Fatty acids 2. Triglycerides (fats and oils) 3. Phospholipids 4. Steroids 5. \_\_\_\_\_\_\_\_\_\_eicosanoids\_\_\_\_\_\_\_\_\_\_\_\_ 6. Fat-soluble vitamins #### Fatty acids - Hydrocarbon chain with a \_\_\_\_\_\_\_\_carboxyl\_\_\_\_\_\_ group at one end - Can be saturated or unsaturated - **Saturated fatty acids** contain only single covalent C-C bonds - **Unsaturated fatty acids** contain one or more C-C double bond  Text Description automatically generated **Above left**: S aturated vs. unsaturated fatty acid structures. **Above right**: General triglyceride structure. #### Triglycerides - Three fatty acids bonded to a glycerol backbone by **ester bonds** - **Fats** are triglycerides that are solid at room temperature - **Oils** are triglycerides that are liquid at room temperature - *Question*: In what **cells** are triglycerides stored in the human body? They are stored In fat cells - **Saturated fats** contain mostly saturated fatty acids - **Unsaturated fats** are either monounsaturated or polyunsaturated - Monounsaturated fats include olive, canola, peanut, avocado, and most nut oils - Polyunsaturated fats include corn, safflower, sunflower, soybean, and fatty fish oils #### Phospholipids - Glycerol backbone covalently linked to two fatty acids and a phosphate group - Polar phosphate "head" = hydrophilic - Fatty acid "tails" = hydrophobic - Molecules with hydrophilic and hydrophobic parts = \_\_\_\_\_\_\_\_\_amphipathic\_\_\_\_\_\_\_\_\_\_  Diagram, schematic Description automatically generated **Above left**: Phospholipids are amphipathic molecules and the main component of biological membranes. **Above right**: Steroids are lipids made from four fused carbon rings and different functional groups. #### Steroids - Steroids are formed by four fused carbon rings - Cholesterol is the starting molecule from which the body builds other steroids - Important fluidity buffer for biological membranes - Sterols are steroids with at least one \_\_\_\_\_\_\_\_hydroxyl\_\_\_\_\_\_\_ group - The hydroxyl functional group makes sterols slightly amphipathic #### Other lipids - **\_\_\_\_\_\_\_\_\_\_\_eicosanoids\_\_\_\_\_\_\_\_\_** are 20-carbon carbon compounds - Includes prostaglandins and leukotrienes = immune signaling molecules - Fat-soluble vitamins are an essential part of the human diet - Includes vitamins D, E, and K - *Question*: What is the **monomer** of lipids? No monomer of lipids ### Proteins - Large molecules made of carbon, hydrogen, oxygen, and nitrogen - Represent 12-18% of the total body mass of humans - Determine the structure of body tissues - Monomers are called **\_\_\_\_\_\_\_\_\_\_\_\_amino acids \_\_\_\_\_\_\_\_\_\_\_\_** (20 naturally-occurring) - Central carbon atom bonded to three functional groups: 1. Amino group 2. Carboxyl group 3. \_\_\_\_\_\_\_\_reactivity\_\_\_\_\_\_\_\_\_ or R group: confers unique chemical properties  - Amino acids undergo dehydration synthesis to form a covalent bond known as a **\_\_\_\_\_\_\_peptide\_\_\_\_\_\_\_ bond** - Occurs in a **stepwise** fashion: one amino acid is added to the growing chain at a time - Few amino acids form a **peptide** - Many (10--2000) amino acids join to form a **\_\_\_\_\_\_\_\_\_\_polypeptide\_\_\_\_\_\_\_\_\_\_\_\_\_\_** - What is the difference between a peptide and a protein? - Small proteins can be a single polypeptide chain - Large proteins can be many polypeptide chains folded in complex arrangements - Protein structure determines function - The **primary structure** of proteins is the amino acid \_\_\_\_\_\_\_sequence\_\_\_\_\_\_\_\_ - Determined by **gene** sequence - The **secondary structure** of proteins are the repeated folds of proteins - May be **α-helices** or **β-sheets** - Stabilized by \_\_\_\_\_\_\_\_hydrogen\_\_\_\_\_\_\_ bonds - **Tertiary structure** of proteins is the three-dimensional shape - Determined by primary and secondary structure plus bonds and atomic forces that connect peptide chains - **\_\_\_\_\_\_\_\_disulfide\_\_\_\_\_\_\_\_ bridges** are covalent S---S bonds between sulfhydryl groups - Hydrogen and ionic bonds also support tertiary structure - **Hydrophobic interactions** are an important driver of protein folding - **Quaternary structure** is the arrangement of polypeptide chains relative to one another in multi-peptide proteins - Not all proteins have quarternary structure because not all proteins are polypeptides - Fibrous proteins form long parallel bundles and are water-insoluble - E.g. keratin (hair), actin (muscle thin filaments) - \_\_\_\_\_\_\_globular\_\_\_\_\_\_\_\_ proteins are round or "blob-like" and are water-soluble - E.g. antibodies, most enzymes - When proteins lose their structure, they are said to be \_\_\_\_\_\_\_denatured\_\_\_\_\_\_\_\_ and are biologically inactive  Diagram Description automatically generated **Above left**: Protein structure is the result of multiple levels of organization. **Above right:** Protein structure is required for protein function. Denatured proteins are biologically inactive. #### Enzymes - **Enzymes** are biological catalysts: \_\_\_\_\_\_\_\_accelerate\_\_\_\_\_\_\_\_ the rate of chemical reactions without being consumed by the reaction - Enzymes may have other components: - Nonprotein molecules that assist enzyme catalysis are called **cofactors** - Cofactors that are organic molecules are called **\_\_\_\_\_coenzymes\_\_\_\_\_\_\_\_\_\_\_** - *Question*: Would chemical reactions proceed in the human body without enzymes? - *No they would be too slow or not even happen without enzymes* How do enzymes work? 1. Substrates bind the active site, forming the **substrate-enzyme complex.** 2. The chemical reaction is performed: bonds are made/broken and atoms are rearranged. 3. The reaction products are released, freeing the enzyme to act on more substrate.  Chart Description automatically generated **Above left**: Enzymes bind substrates at the active site and rearrange matter before releasing the products for another round of substrate-binding. **Above right**: Enzymes increase the rate of chemical reactions by lowering the activation energy for the reaction. - Characteristics of enzymes. Enzymes are: 1. Highly specific: - Reactants in enzyme-catalyzed reactions are called **\_\_\_\_\_\_\_substrates\_\_\_\_\_\_\_\_** - Chemical reactions are performed on the enzyme at the **active site** - Substrates fit the active sites of enzymes through a "lock and key" mechanism 2. Efficient - Because they lower activation energy, enzymes **increase the rate** of chemical reactions - *What is activation energy? The amount of energy required to break a bond* 3. Regulated - Cells control the **synthesis** and **activity** of enzymes - **\_\_\_\_\_\_\_proenzymes\_\_\_\_\_\_\_\_\_\_\_** are inactive forms of enzymes that must be processed under the right conditions to be active - **E.g. Prothrombin** is the inactive form of thrombin blood clotting ### Nucleic acids - Made of carbon, hydrogen, oxygen, nitrogen, and phosphorus - Can be either **deoxyribonucleic acid (DNA)** or **ribonucleic acid** **(RNA)** - **Genes** are made of DNA - **Genes are a section of the dna that makes a specific protein** - DNA is \_\_\_\_\_\_\_transcribed\_\_\_\_\_\_\_\_ to RNA - RNA is \_\_\_\_\_\_\_\_\_translated\_\_\_\_\_\_\_by ribosomes to proteins - Monomers are called **\_\_\_\_\_\_\_nucleotides\_\_\_\_\_\_\_\_\_\_**, which are made of a: - **Nitrogenous \_\_\_\_base\_\_\_\_** - **Pentose sugar** - **Phosphate group**  - DNA contains A, G, C, and T - RNA contains A, G, C, and U - A and G are purines = double-ring bases - T and C are pyrimidines = single-ring bases - *How do the bases pair?* *One purine pairs with one pyrimidine* - In DNA, the pentose sugar = **deoxyribose** - In RNA, the pentose sugar = **ribose.** - The phosphate groups + pentose sugars = **\_\_\_\_\_\_\_backbone\_\_\_\_\_\_\_\_** of the molecule - Due to the properties of nucleotides, DNA forms a **double helix** - Proposed in 1953 by James Watson and Francis Crick - Bases form the "rungs" Diagram Description automatically generated  **Above left:** DNA forms a double helix because of the chemical properties of the nucleotides. **Above right:** RNA has many roles in the cell, including encoding messages from genes to ribosomes (mRNA), catalyzing chemical reactions as part of ribosomes (rRNA), and bringing amino acids to ribosomes during translation (tRNA). - DNA is the genetic material of all living things - DNA \_\_\_\_\_\_\_\_replication\_\_\_\_\_\_\_\_: makes a new copy of the double helix using one strand as a template - A change in the nucleotide sequence of DNA is called a **mutation** - **RNA** is single-stranded - There are **three** major types of RNA: 1. Messenger RNA (mRNA) 2. Ribosomal RNA (rRNA) 3. Transfer RNA (tRNA) - Adenosine triphosphate is a biologically-important nucleotide - **Adenosine triphosphate** or **ATP** is the \_\_\_\_energy\_\_\_\_\_\_\_ currency of cells - Consists of three phosphate groups bound to adenosine (adenine + ribose) - ATP is produced by **exergonic** cellular reactions - ATP is consumed by **endergonic** cellular reactions to do cellular work Diagram Description automatically generated - The loss of the terminal \_\_\_\_\_\_\_\_phosphate\_\_\_\_\_\_\_\_ by **hydrolysis** releases a large amount of energy - But ATP can be regenerated! - The synthesis of ATP is catalyzed by **ATP \_\_\_\_\_synthase\_\_\_\_\_\_** during aerobic cellular respiration (more later) Text Description automatically generated Summary ------- - Biological molecules are diverse organic molecules - There are four classes: carbohydrates, lipids, proteins, and nucleic acids - All are polymers of monomers **except** lipids - The structure of biological molecules has a strong relationship with their function *Suggested study aid:* Compare and contrast the structures of DNA and RNA by completing the table below: Feature DNA RNA ----------------------------- --------------------------------------------------------- -------------------------------------------------- Nitrogenous bases atcg aucg Pentose sugar deoxyribose ribose Single- or double-stranded? double single Mechanism of replication? Semi-conservative (uses an existing strand as template) In cells, RNA is transcribed from a DNA template Biological function(s) Codes for mrna Codes for protein Stability Types *Suggested study aid*: Complete the table below to review biological molecules **Biological molecule** **Elements** **Name of Monomers** **Name of Polymers** **Biological functions** ------------------------- -------------- ---------------------- ---------------------- -------------------------- Carbohydrate cho Lipid Protein chon Nucleic Acid