SBI4UI Biochemistry Teacher Solutions PDF

# SBI4UI - Biochemistry ## Unit 1 Biochemistry ### The Carbon Chemistry of Life - Carbon atoms form the backbone of biological molecules. - Carbon atoms can link together to form large chains, branched structures, and rings. - Carbon has 4 valence electrons and can form single, double & triple co...

# SBI4UI - Biochemistry ## Unit 1 Biochemistry ### The Carbon Chemistry of Life - Carbon atoms form the backbone of biological molecules. - Carbon atoms can link together to form large chains, branched structures, and rings. - Carbon has 4 valence electrons and can form single, double & triple covalent bond. - Functional Groups have polar or ionic 'qualities' that influence how they interact with other molecules. - During a dehydration reaction, water is removed from subunits as they combine to form a larger molecule. - During a hydrolysis reaction, larger molecules react with water and break down into smaller subunits. #### Carbon has: 1. 4 valence electrons in its outermost shell, and therefore each carbon atom is capable of forming 4 covalent bonds with other non-metal atoms. 2. Carbon can assemble into an astounding variety of branched and ringed structures. 3. With combinations of single, double, and triple bonds, an almost limitless array of molecules is possible. #### Biological Macromolecules - Think back to what you ate for lunch. Did any of your lunch items have a "Nutrition Facts" label on the back of them? - If so, and if you had a look at the food's protein, carbohydrate, or fat content, you may already be familiar with several types of large biological molecules we'll discuss here. - If you're wondering what something as weird-sounding as a "large biological molecule" is doing in your food, the answer is that it's providing you with the building blocks you need to maintain your body - because your body is also made of large biological molecules! We call these huge molecules 'Macromolecules'. - Just as you can be thought of as an assortment of atoms or a walking, talking bag of water, you can also be viewed as a collection of four major types of large biological molecules: Carbohydrates (such as sugars), Lipids (such as fats), Proteins, and Nucleic Acids (such as DNA and RNA). - That's not to say that these are the only molecules in your body, but rather, that your most important large molecules can be divided into these groups. - Together, the four groups of large biological molecules make up most of the dry weight of a cell. - Water, a small molecule, makes up much of the wet weight. #### What characteristics do you notice about these biological molecules? | Biological Macromolecules | Characteristics | | ------------------------------------- | -------------------------------------------- | | **Carbohydrates** (monosaccharides) | Building blocks. Very polar. | | **Proteins** | Building blocks. Amino groups + carboxyl group | | **Nucleic Acids** | Building blocks are nucleotides. | | **Lipids** | 3 fatty acids + a glycerol. | ### Functional Groups - **Define:** A Functional Group is a group of atoms that affect the reactivity of a molecule by participating in how it reacts. (This is where it will react.) | Functional Group | Major Classes of Molecule | Example | | ---------------- | --------------------------- | -------- | | hydroxyl | alcohols | | | carbonyl | aldehydes | | | carbonyl | ketones | | | carboxyl | organic acids | | | amino | amino acids | | | phosphate | nucleotides, nucleic acids, many other cellular molecules | | | sulfhydryl | many cellular molecules | | - **Unlike the non-polar, hydrocarbon chains that make up most of the biological molecule, functional groups are usually ionic or strongly polar.** - **Functional groups that exist on large biological molecules interact with other molecules and introduce different types of bonds.** - **The non-polar hydrocarbon portion of a large biological molecule do NOT.. participate in bonding** - **Therefore, they do not help to initiate biochemical reactions. Only weak, intermolecular forces (instantaneous dipoles) exist.** - **Functional groups with 'Ionic Qualities': ** - The carboxyl group acts like an acid, releasing H+ ions to become negatively charged. - The amino group acts like a base, accepting H+ ions to become positively charged. - The phosphate group acts like an acid, releasing H+ ions to become negatively charged. ### Dehydration Synthesis and Hydrolysis Reactions - Hydrolysis and dehydration synthesis reactions are among the most important reactions in cells. - **Both the assembly and breakdown of large biological molecules depend on these reactions.** - **Both reactions rely on enzymes.** - **During dehydration synthesis, H₂O is Released as subunits form larger molecules.** - **During hydrolysis, H₂O is Inserted to split the large biological molecules into subunits.** ### . CARBOHYDRATES - Carbohydrates are the most abundant organic molecules on Earth. - Carbohydrates consist of carbon, hydrogen, and oxygen. - The simplest type of carbohydrate is called a monosaccharide (Single sugar unit), which is the "building block" for more complex carbohydrates. - When 2 monosaccharides join by a dehydration synthesis reaction, they form a disaccharide. - When thousands or even millions of monosaccharides link together, they form a polysaccharide, which can also be called a 'complex carbohydrate'. #### Monosaccharides | Monosaccharides | Characteristics | | ---------------- | --------------- | | **Sugars** | Highly soluble in H20. They are very polar. | | **Structure** | Chain, alpha-ring, beta-ring | | **Function** | Energy Source | | **Examples** | Glucose, galactose, and fructose | #### Disaccharides | Disaccharides | Characteristics | | --------------------- | ------------------------------------------------------------------------------------- | | **Structure** | Consist of 2 monosaccharides that are joined together by a dehydration synthesis easily digested reaction. | | **Bonds** | Alpha (α) or Beta (β) depending on the orientation of the -OH group bonded to 1-carbon. | | **Examples** | Sucrose, lactose, maltose | #### Polysaccharides - Hundreds to thousands of monosaccharides can link together to form a complex carbohydrate. - Some complex carbohydrates are important for energy sources in cells, while others are essential for structural support. - A polysaccharide is a macromolecule, which is a very large molecule assembled by the covalent linkage of smaller subunit molecules. - The dehydration synthesis reactions that assemble polysaccharides are examples of polymerization. - Polymerization is the process in which identical or variable subunits, called monomers, link together in a long chain to form a larger molecule. | Polysaccharides | Characteristics | | ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **Structure** | Very long chain or branching chains with α or β-linkage. | | **Function** | Energy source, structural support, cell-to-cell communication | | **Examples** | Starch, glycogen, cellulose, chitin. | ### Dehydration Synthesis and Hydrolysis Reactions of Carbohydrates - Hydrolysis and dehydration synthesis reactions are among the most important reactions in cells. - **Both the assembly and breakdown of large biological molecules depend on these reactions.** - **Both reactions rely on enzymes.** - **During dehydration synthesis, H₂O is produced as subunits join to form larger molecules.** - **During hydrolysis, H₂O is used to split the large biological molecules into subunits.** #### Dehydration Synthesis Reaction for Carbohydrates: - Carbohydrate storage occurs in the body during times that the body experiences a surplus of carbohydrate intake. - Carbohydrates are stored as long polymers. #### Hydrolysis Reaction for Carbohydrates: - Occurs during digestion. - Salivary Amylase in the saliva breaks down more complex sugars in their monomeric form. - Further breakdown occurs via carbohydrase throughout the digestive process. - Single carbohydrates are converted into ATP by the mitochondrion to drive all biochemical processes in the cell. ### LIPIDS - Lipids are a general term for 3 varieties of non-polar biological molecules. - Being non-polar, lipids do NOT dissolve in water. - Some lipids are stored by cells, to be used as a back-up energy source to carbohydrates. - Their insolubility in water contributes to their ability to form cellular and nuclear membranes. - Other lipids, such as cholesterols serve as hormones that regulate cellular activities and take part in the integral role that cell membranes play in keeping life literally in-tact. - Triglycerides primarily function as an alternative energy source to carbohydrates. #### Triglycerides: - One gram of this 'fat’ stores more than twice as much energy as one gram of carbohydrates. - For this reason, lipids are excellent energy storage molecules and are thus not used up first in cellular metabolism. The body prefers to metabolize carbohydrates first. - Dehydration Synthesis of a glycerol + 3 fatty acids to form a triglyceride: is catalyzed. The reverse reaction is a hydrolysis reaction where 3 water molecules are required; ... H atoms to the glycerol and hydroxyl groups (-OH) to the fatty acids. #### Types of Fatty Acids: | Fatty Acids | Characteristics | | -------------------------- | ----------------------------------------------------------------------------------------------------------------------- | | **Saturated** | Fatty acids fit tightly packed, allowing for a solid consistency at room temperature. | | **Unsaturated** | Bent at the double bonds, reducing the number of Van der Waals (instantaneous Dipole) attractions along the length of the fatty acid chain, causing these fats to be liquid at room temperature. | | **When digested, saturated fats are less likely to be acted on by** | lipases, enzymes that break down lipids for cellular metabolism. | | **Unsaturated fats are more likely to be acted on by lipases and** | will be broken down and utilized by the body, instead of being stored. | ### PHOSPHOLIPIDS - Cells could not exist without the phosphate-containing lipids called phospholipids. - Phospholipids make up the lipid bilayer of cellular membranes. - An important structural feature of every cell. ### STEROIDS - Steroids are a group of lipids with structures that are based on a framework of fused carbon rings. - The most abundant steroids, the sterols, have a single hydroxyl (-OH) group at one end of the ring framework and a complex, non-polar hydrocarbon chain at the other end. - Although sterols are almost completely hydrophobic, the single hydroxyl group gives one end a slightly polar, hydrophilic character. - As a result, sterols have dual solubility properties and, like phospholipids, tend to assume positions in cells to satisfy these properties. - This dual solubility property deems these fats to be 'amphipathic'. - Cholesterol, a sterol, is an important component of the plasma membrane that surrounds animal cells. - Similar sterols, called phytosterols, occur in plant membranes. ### 3. PROTEINS - Proteins are the most complex biological macromolecules occurring in all cells. - Proteins also occur in great variety; thousands of different kinds ranging in size from relatively small peptides to huge polymers. - Moreover, proteins exhibit enormous diversity of biological function and are the molecular instruments through which genetic information is expressed. #### Amino Acid Structure - Relatively simple monomeric subunits provide the key to the structure of the thousands of different proteins. - All proteins, whether from the most ancient lines of bacteria or from the most complex forms of life, are constructed from the same ubiquitous set of 20. amino acids. - Covalently linked in a characteristic linear sequence. - Each of these amino acids has a functional group with distinctive chemical properties. - This group of 20 precursor molecules may be regarded as the alphabet by which the language of protein structure is written. - The difference between proteins is in the permutation/combination of amino acids. - Amino group: NH₂ (OR NH3+) - Carboxyl group: COOH (OR COO-) . - R-Group: Variable side chain (* Gives the a.a its characteristics ) - α - Carbon: The central Carbon. #### The 20 Common Amino Acids: - Every amino acid has the same basic structure, apart from proline. - Below each amino acid is its name, followed by its three-letter abbreviation and its letter symbol. | Amino Acids | Characteristics | | --------------------------------- | ---------------------- | | **NON-POLAR** | | | Glycine Gly/G | | | Alanine Ala/A | | | Valine Val/V | | | Cysteine Cys/C | | | Proline Pro/P | | | Leucine Leu/L | | | Isoleucine Ile/I | | | Methionine Met/M | | | Tryptophan Trp/W | | | Phenylalanine Phe/F | | | **+ CHARGE** | | | Lysine Lys/K | | | Arginine Arg/R | | | Histidine His/H | | | **POLAR** | | | Serine Ser/S | | | Threonine Thr/T | | | Tyrosine Tyr/Y | | | Asparagine Asn/N | | | Glutamine Gln/Q | | | **- CHARGE** | | | Aspartic Acid Asp/D | | | Glutamic Acid Glu/E | | ### Protein Structure - Proteins have up to 4 levels of structure, with each level imparting different characteristics and degrees of complexity to the overall protein. - Protein function is dictated by structure, and protein structures are hierarchical in nature. #### PRIMARY STRUCTURE (1): - This is the Amino Acid Sequence. - The sequence of amino acids is determined by our DNA which dictates how proteins are built. - With 20 types of amino acids there are thousands of different combinations to assemble them in. - The possible combination of primary structure is limitless = diversity! #### SECONDARY STRUCTURE (2): - The primary structure is further arranged into regular units. - The secondary structure occurs when hydrogen bonds form between the amino group of one amino acid and the carboxyl group of another amino acid downstream of the polypeptide chain. - These hydrogen bonds are usually formed to keep non-polar parts away from water. - There are two main types: - Alpha Helices - Beta-pleated Sheets #### TERTIARY STRUCTURE (3): - This is the result from the interactions between the side chains (R groups) of the amino acids embedded in α-elices and β-sheets. - The secondary structures Alpha-Helices + Beta-Pleated + and also the side chains interacting with the aqueous environments around the protein. #### QUARTERNARY STRUCTURE (4°): - Some proteins stop at the tertiary structure, but others go further. - Quaternary proteins join other tertiary structogether to form a larger more complex functional unit. - Hemoglobin is an example of a 4° structure. - It is composed of four tertrary polypeptides, each consisting of more than 140 amino acids. #### Additionally Regarding Proteins: - Many proteins require a non-protein component to function. - This is common in many cases throughout the body. Without these additions the proteins do not perform their functions. These addition are called: Prosthetic Heme Groups. - Denaturation: Extreme conditions (such as temperature and pH) can unfold a protein. - This results in a loss of both structure and function of the protein. - This involves the disruption and possible destruction of both the 2° and 3° structures. - Denaturation reactions are strong enough to break peptide bonds! - Therefore the primary structure (sequence of amino acids) remains the same. - Disassembly of the primary structure occurs via digestion and requires the use of a class of enzymes called PROTeases. ### Enzymes - An enzyme is a biological catalyst with a specific three-dimensional shape which is necessary for its function. - The active site of an enzyme is specific to a particular substrate(s) - Enzyme activity is affected by [Enzyme] and Substrate concentration, temperature, and pH. - The cellular activity of living organisms controlled with enzymes. - An enzyme is a special type of biological molecule (protein) that speeds up... a chemical reaction without being consumed or changing the product of the reaction. - Each enzyme has a specific three-dimensional shape. - This shape determines which reaction it catalyzes. - For a chemical reaction to move forward, it must overcome an energy barrier, and this is where enzymes are important. - Enzymes bind to a specific reactant (or reactants), called a Substrate, in doing so, they decrease the energy barrier so that the reacti proceeds at a faster rate than it would without the enzymes. #### Enzymes and Substrates - Each type of enzyme catalyzes the reaction of only one type of molecule or one group of closely related molecules. - Enzyme specificity explains why a typical cell needs about 4000 different enzymes to function. - Enzymes are much larger than the substrate. - The substrate interacts with only a very small region of the enzyme, called the active site. - The Induced-Fit Model is a model of enzyme activity that describes how an enzyme changes shape to better accommodate a substrate. - Just prior to substrate binding, the enzyme changes its shape so that the active site becomes more precise in its ability to bind its substrate. - An enzyme-substrate complex is formed and then the enzyme converts the substrate(s) into one or more products. - This model is more than a simple 'lock & key' analogy. - Many enzymes require a cofactor (often metals like copper, iron or zinc), a non-protein group that binds to an enzyme and is essential for catalytic activity. Organic cofactors, called coenzymes play similar roles. ### NUCLEIC ACIDS - Nucleic Acids are the assembly instructions for all proteins in living organisms. - Two types of nucleic acids exist: DNA and RNA - Nucleic acids are polymers of monomeric units called nucleosides. - A nucleoside consists of three parts linked together by covalent bonds: - a nitrogenous base formed from rings of carbon and nitrogen atoms, - a 5-carbon ring-shaped sugar, and - three phosphate groups. - Each nitrogenous base links covalently to a 5-carbon sugar, either deoxyribose (in DNA) or ribose (in RNA). #### DNA and RNA: Nucleotide Polymers - DNA (Deoxyribonucleic acid) stores the information that is responsible for inherited traits in all living things. - RNA (Ribonucleic acid) is typically a transcript of your DNA, which plays a major role in creating all proteins your cells require for cellular and thus life functions. - DNA and RNA consist of chains of nucleotides, with one nucleotide linked to the next by a single bridging phosphate group between the 5’-carbon of one sugar and the 3’-carbon of the next sugar in line. - This type of linkage is called a phosphodiester bond. - The arrangement of the alternating sugar and phosphate groups forms the backbone of a nucleic acid chain. - The nitrogenous bases of the nucleotides project from this backbone. - In a DNA chain, each nucleotide contains a deoxyribose, a phosphate, and one of the four bases A, T, G, or C. - In an RNA chain, each nucleotide contains ribose, a phosphate, and one of the four bases A, U, G, or C. - DNA is a double-stranded molecule in which the two strands of DNA run antiparallel to each other. - This means that they are oriented in the opposite directions. - The end with the phosphate group is referred to as the 5’ end, and the opposite end of the same strand, with the deoxyribose sugar, is referred to as the 3’ end. - Bases on opposite strands of DNA hydrogen bond to one another to form a double-stranded DNA molecule. - As base pairs form between two strands of DNA, the molecule is twisted into a double helix. #### The Molecular Basis of Inheritance - DNA is an information molecule. - DNA stores information for making other large molecules, called proteins. - These instructions are stored inside each of your cells, distributed among long structures called chromosomes. - These chromosomes are made up of thousands of shorter segments of DNA, called genes. - Each gene stores the directions for making one functional protein. - One gene. One protein. #### The Chemical Structure of DNA - **Deoxyribose Sugar Numbering Rule** - Start numbering carbon atoms to the right of the oxygen atom in the ring. - **Nucleotide Building Block** - **Glycosidic Bond** - **Phosphodiester Bond** - **Hydrogen Bond** #### The Double Helix - Double stranded helix as determined from Rosalind Franklin's (1920-1958) X-ray diffraction pattern. - DNA is a polymer of Nucleic Acids. - Each nucleotide (part of the DNA polymer) consists of a: - 5 carbon (deoxyribose) SUGAR - a nitrogenous BASE attached at their 1' carbon - a Phosphate group attached to their 5' carbon. - DNA is a 2 stranded molecule that run in opposing directions. - This is Known as Anti Parallel - The ... end of one strand of DNA aligns with the ..3.. end of the other strand. - The prime end of the molecule is dictated by the distal carbon number of the ribose sugar. - Phosphodiester bonds between the phosphate and deoxyribose sugar hold the backbone strand together. - Glycosidic bonds hold the nitrogenous bases to the deoxyribose sugar. - Hydrogen bonds between complementary base pairs hold the 2 strands together. - The 2 strands are held together by... bonding positions for hydrogen (A) to (T) and (G) to (C).. - Adenine and Guanine are double ring structures or Purines. - Thymine and Cytosine are single ring structures or Pyrimidines. ### The Structure of the Plasma Membrane: The Fluid Mosaic Model - The plasma membrane, according to the 'fluid mosaic model', is composed mainly of proteins and lipids. #### Each PHOSPHOLIPID consists of two major parts: 1. A polar head that gives it a hydrophilic property - Attracting to water 2. A pair of non-polar tails that give it a hydrophobic property and - Repulsion by water. #### In plasma membranes, phospholipids arrange themselves into two layers or 'BILAYERS'. 1. The hydrophilic heads of the outer layer face the extracellular fluids. 2. The hydrophilic heads of the inner layer face the cytosol #### The tails acts as a barrier which separates the external + internal cell environment #### Cholesterol: 1. Increases membrane fluidity and flexibility. 2. Makes the membrane less permeable to water-soluble substances, such as ions. 3. Aligns according to polarity of the phospholipids they sit within. (-OH aligns with the polar heads of the phospholipids). #### There are different types of membrane proteins that render the membrane asymmetrical: 1. **Integral Membrane Proteins:** Span the entire membrane and serve a specific function such as transport or enzymatic activity or triggering signals. 2. **Peripheral Membrane Proteins:** Do not span the entire membrane and serve functions such as attachment and recognition. 3. **Glycoproteins.** Face the exterior of the cell and play a role in cell recognition and cell-cell interactions. #### Lipid Orientation: - Lipid molecules in all biological membranes are highly dynamic (not 'static') or "fluid", which is critical for membrane function. - The lipid molecules exist in a double layer, called a bilayer, that is less than 10nm thick. - By comparison, this page is about 100,000nm thick. - Millions of times a second, the lipid molecules may: 1. Exchange places. 2. Rotate about their axis. 3. Exchange places with other lipids. 4. Vibrate in place. 5. Attempt to switch halves of the bilayers (change sides) ### Transport Across Membranes - For a cell to survive and function, it must take nutrients, expel waste, and communicate with its environment and neighboring cells. - This exchange of substances is a complex process because the plasma membrane must be highly selective. - The cell uses specific mechanisms to transport small molecules into and out of the cell. - Some of these methods require membrane proteins. - Some of these membrane proteins must employ the use of ATP/ENERGY, to assist in the movement of molecules into and out of the cell. #### Passive Transport: 1. **Simple Diffusion:** The unassisted movement of substances across the cell membrane. - What molecules travel this way? small, uncharged, hydrophobic molecules. - How do they move? Their own kinetic energy. *(ex. O2, CO2, N2 (non-polar))* 2. **Facilitated Diffusion (Carrier Protein):** - Move with the conc. gradient [High]→ [low] - Carrier proteins bind the molecule + it changes shape to allow molecules to pass through. 3. **Facilitated Diffusion (Channel Protein):** - Move with the conc. gradient [High]→ [low] - Allows a hydrophilic pathway in the membrane for a specific molecule (polar) to pass (aqua purins) - Enables charged ions to pass. 4. **Osmosis:** (Specific Definition/Description of the Diffusion of H2O molecules. Net Movement into the cell (Hypotonic); Net Movement out of the cell (Hypertonic); No Net Movement (Isotonic)) are terms to describe the direction of water moving across the membrane as a result of solute/solvent concentrations. #### Active Membrane Transport - Active transport is when energy (ATP) is Required to allow molecules to move against the conc. gradient (CLow) to [High]). - Proteins embedded in the membrane bind to the transported substance and move them against the gradient. #### Primary and Secondary Active Transport - All primary active transport pumps move positively charged ions, such as H+, Ca2+, Na+, and K+, across membranes. - Examples: - H+ (proton pump) - Ca2+ (calcium pump) - Na+/K+ (sodium/potassium pump) - Because of the ion charges, as well as chemical reactions, an electrochemical gradient is created. - A secondary active transport pump uses the concentration gradient of an ion, established by a primary pump, as its energy source. - For example, the driving force for most secondary active transport in animal cells is the high outside/low inside Na+ gradient set up by the sodium-potassium pump. - Secondary transport is facilitated by two mechanisms, known as symport (solute moves through the membrane channel in the same direction as the driving ion) and antiport (the driving ion moves through the membrane channel in one direction, providing the energy for the active transport of another molecule in the opposite direction). #### Endocytosis and Exocytosis (Bulk Transport) - The largest molecules that can be transported across cellular membrane by passive or active transport are about the size of amino acids or a monosaccharide such as glucose. However, eukaryotic cells can export and import much larger molecules by two other mechanisms called EXOCYTOSIS and ENDOCYTOSIS. - Both processes require energy, thus both processes stop if the cell cannot make ATP...!! - **Endocytosis:** Endocytosis moves aggregate molecules into the cell for cellular functioning. - **Extracellular solutes** are trapped in a pit-like depression and brought into the cell for use. ('phagocytosis') - **Extracellular H2O** is taken in, along with any other molecules that happen to be in the solution of water. ('pinocytosis') - **Exocytosis:** All eukaryotic cells secrete materials outside the cell through exocytosis, usually to move proteins and wastes out of the cell.. - Cells in the digestive tracts secrete proteins (enzymes) and other digestive solutes. - Also, glandular cells in mammals secrete hormones which also need to be enclosed in a vesicle when transported within the cell and also within the extracellular fluid and blood.