Bio Exam Review - 1 PDF

Unit 2 Elements of Life Recall : Living organisms require four main classes of biological macromolecules to grow, reproduce, and maintain organization: carbohydrates, proteins, lipids, and nucleic acids. - These macromolecules are made up of atoms and molecules obtained from the environment. - O...

Unit 2 Elements of Life Recall : Living organisms require four main classes of biological macromolecules to grow, reproduce, and maintain organization: carbohydrates, proteins, lipids, and nucleic acids. - These macromolecules are made up of atoms and molecules obtained from the environment. - Organisms must exchange matter with their surroundings (environment), using key elements like carbon, nitrogen, and phosphorus to construct these four essential molecules. - 25 of the 92 natural elements are known to be essential to ALL life. - Carbon, Oxygen, Hydrogen, and Nitrogen make up 96% of all living matter. Phosphorus, Sulfur, Calcium and Potassium make up most of the remaining 4% of an organism's weight. Carbon - Carbon is the backbone of all organic molecules. - It enters the biosphere through the action of plants, which use solar energy to transform atmospheric CO2 into glucose. - Glucose is passed along to animals that feed on plants, and animals that eat animals that feed on plants. - Carbon's ability to form large, complex, and diverse molecules grant it the ability to form proteins, DNA, carbohydrates and lipids. It is the element that accounts for the diversity of biological macromolecules. - This is because a C atom can form covalent bonds to as many as four other atoms, it’s well suited to form the basic skeleton, or “backbone,” of a macromolecule. Storage and Cell Formation - Carbon-based compounds, such as carbohydrates, lipids, and to some extent proteins, are the primary molecules used by organisms to store and release energy. Nitrogen Nitrogen is a key element in proteins and nucleic acids. Nitrogen is obtained primarily through the nitrogen cycle. Plants take up nitrogen in the form of nitrates or ammonium from the soil, while animals obtain nitrogen by consuming plant or animal matter. Proteins: - Nitrogen is found in the amino group (-NH₂) of amino acids, the building blocks of proteins. - Proteins are vital for nearly all cellular functions, including enzymatic activity, signal transduction, and cellular structure. Nucleic Acids: - Nitrogen is also present in the nitrogenous bases (adenine, guanine, cytosine, thymine, and uracil) that form the rungs of the DNA and RNA molecules. - These bases are essential for genetic coding, replication, and protein synthesis 7 Phosphorus Phosphorus is typically absorbed by plants from the soil in the form of phosphate ions. Animals obtain phosphorus by consuming plants or other animals. is primarily used in nucleic acids and certain types of lipids. Nucleic Acids: - Phosphorus is a component of the phosphate group in nucleotides, which form the backbone of DNA and RNA. - The sugar-phosphate backbone gives structural integrity to these molecules. Lipids - Phosphorus is also found in phospholipids, which are major components of cell membranes. - Phospholipids have a phosphate group attached to glycerol, and their amphipathic nature allows them to form bilayers, essential for compartmentalizing cellular structures. Chemistry of Life: Biological Macromolecules The architecture of biological molecules exhibit unique emergent properties arising from the orderly arrangement of their atoms. - recall major theme living systems are organized in a hierarchy of structural levels that interact - Carbohydrates, proteins, and nucleic acids are chain like molecules called polymers (from the greek polys, many, and meris, part) - recall root words - A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds. - The repeating units that serve as the building blocks are smaller molecules called monomers. Some of the molecules that serve as monomers also have other functions of their own. Carbohydrates are polymers of… Monosaccharides (eg. glucose fructose) Lipids are polymers of… Fatty acids and Glycerol (eg.glycerol and fatty acids) Proteins are polymers of… Amino acids (eg. glycine, alanine) Nucleic acids are polymers of… Nucleotides (eg. adenine, cytosine) Polymerisation (Dehydration synthesis) Polymers can be formed from monomeric subunits by condensation reactions (dehydration synthesis) A hydroxyl group (-OH) on one monomer is combined with a hydrogen atom (-H) on another monomer The two monomers become covalently bonded and a water molecule is produced as a by-product In other words, covalent bonds are created between monomers by removing a water molecule Dehydration synthesis reaction The types of bonds that get created are: Glycosidic linkages - the covalent bonds formed when monosaccharides are joined together to form polysaccharides Phosphodiester bonds - the covalent bonds formed when nucleotides are connected to form polynucleotide chains (DNA or RNA) Peptide bonds - covalent bonds formed when amino acids are linked to for polypeptide chains of proteins Ester linkages - the covalent bonds formed when connecting fatty acid chains to form triglycerides and phospholipids Digestion (Hydrolysis) Polymers can be broken down into their monomeric subunits by hydrolysis reactions A water molecule is split to provide the -H and -OH groups required to break the covalent bond between twomonomers In other words, covalent bonds are broken between monomers by adding a water molecule In living organisms, hydrolysis is a key reaction in the digestion of food, as well as metabolic reactions, cellular functions and cellular recycling. Chemistry of Life: Carbohydrates Biological macromolecules such as nucleic acids, proteins, carbohydrates, and lipids are composed of monomers connected by specific types of bonds. The structure and function of these polymers depend heavily on how their monomers are assembled. Complex carbohydrates comprise sugar monomers whose structures determine the properties and functions of the molecules. - They are made of C, H and O (‘carbo’ – contains carbon ; ‘hydrate’ – contains H and O) - Carbohydrates are composed of recurring monomers called monosaccharides (‘mono’ – single ; 'saccharide’ – sugar) Monosaccharides Structure Monosaccharides form ring structures as it is a more energetically favorable configuration A hydroxyl group (-OH) links to a carbonyl group (=O) to form a cyclic structure connected by an oxygen atom Types of Monosaccharides Most monosaccharides have either 5 carbons (pentose sugars) or 6 carbons (hexose sugars) The name describes the number of carbons – not the shape (e.g. fructose is a hexose sugar but forms a pentagon) 1. An example of a pentose sugar is ribose – which is a core component of RNA nucleotides and is also found in coenzymes (such as ATP) - DNA nucleotides have a modified form of this pentose sugar in which an oxygen atom is removed (deoxyribose) 2. An example of a hexose sugar is glucose – which is primarily used as a source of energy (it is digested via cell respiration to produce ATP) - Glucose can exist as one of two isomers (⍺-D glucose or ß-D glucose) depending on the orientation of the 1’-OH group Function of Monosaccharides The primary role of most monosaccharides is to function as a source of stored chemical energy for the cell - Energy stored within the covalent bonds can be released through oxidation to form ATP (through the process of cellular respiration) - Oxidation of monosaccharides means that the monosaccharide loses electrons, typically through the addition of oxygen or the removal of hydrogen atoms. Form fits function - Monosaccharides are small, polar molecules which makes them hydrophilic (water-soluble), and so can dissolve in water which makes them easy to transport between cells - The cyclic structures of monosaccharides make them more stable energetically favorable than straight chains - Because most monosaccharides they are both soluble and stable, they are easy to transport within aqueous solutions (eg. blood or cytosol) - Some monosaccharides can be partially digested for a low energy yield (anaerobic) or completely digested for a higher yield (aerobic) Glucose is the most common monosaccharide to be used as an energy source because it holds all four properties listed above Polysaccharides Monosaccharides can be linked together by hydrolysis synthesis reactions to form polysaccharides - The bond that is created is called a glycosidic linkage and water is released as a by-product - The polymer formed depends on the monomers involved and their bonding arrangements (the types of sugars involved, glucose, ribose, etc) - Polysaccharides can also be complexed with other molecules (e.g. glycoprotein, glycolipid) Types of Polysaccharides - Three key polysaccharides can be produced from glucose alone – cellulose, starch and glycogen - The type of polymer formed depends on the isomer of glucose involved and the bonding arrangement between the subunits 1. Cellulose - Polymers of β-glucose will form the polysaccharide cellulose - The β-glucose monomers form alternating arrangements (every second monomer is inverted), making linear chains - Because the polysaccharides are linear, they can be grouped into bundles and cross-linked with multiple hydrogen bonds - These cross-linked bundles function to increase the structural integrity and mechanical stability of the polymer - Cellulose has a key structural role in eukaryotic plant cells – it functions as the primary component of the plant cell wall 2. Starch (Plants) and Glycogen (Humans) - Polymers of ⍺-glucose are used in short-term energy storage - In both glycogen and starch, the ⍺-glucose monomers are connected via 1’ – 4’ glycosidic linkages to form helical structures - Starch can exist as linear strands (amylose) or be branched (amylopectin) due to the presence of additional 1’ – 6’ linkages - Glycogen is a more highly branched molecule than amylopectin as it possesses more frequent 1’ – 6’ linkages - Branching causes the polysaccharides to adopt a more compact structure, but their large molecular size renders them insoluble in water - This means that glycogen and starch are efficient storage molecules but not suitable for transport within aqueous solutions (like the blood or sap) - However the carbohydrates can be readily digested to release monomers or dimers for transport to other tissues Chemistry of Life: Lipids Lipids are a class of non-polar organic molecules that serve a variety of functions within cells. Unlike other classes of organic molecules, they are not composed of recurring monomers – although they may possess discrete subunits. Lipids are commonly composed of hydrocarbons arranged into either chains (fatty acids) or fused rings (steroids). Hydrophobic Properties Hydrocarbons are nonpolar (they lack charged regions) and will not dissolve in polar substances like water - Hence lipids are considered to be hydrophobic molecules (they are water-repelling) The hydrophobic properties of lipids have many important biological roles - Waxes are used to prevent water loss from leaves while birds coat their feathers with oil to render them waterproof - Phospholipids provide a structural framework for cells by forming spontaneous membranes in aqueous solutions - Lipids in foods help the body to absorb certain fat-soluble micronutrients, including vitamins A and D The hydrophobic properties of lipids make them difficult to transport around the body Types of Lipids Lipids can be categorized into three groups based on their chemical composition and physical properties: 1. Triglycerides  ​ Structure: Composed of one glycerol molecule bonded to three fatty acids. ​ Function: Main form of fat storage in the body; used for energy. ​ Example: Fats and oils (like butter, olive oil). 2. Phospholipids ​ Structure: Consists of one glycerol molecule, two fatty acids, and a phosphate group. ​ Function: Major component of cell membranes; forms a bilayer structure in cell membranes. ​ Example: Phosphatidylcholine. 3. Steroids ​ Structure: Made of four fused carbo=n rings with various functional groups attached. ​ Function: Involved in signaling and structure (e.g., cholesterol is part of the cell membrane and precursor for hormones). ​ Example: Cholesterol, estrogen, testosterone. Ester linkages Simple and compound lipids contain fatty acids within their structure, which are covalently attached to an alcohol (such as glycerol) via an ester bond. This linkage involves dehydration synthesis (water released). Fatty acids Lipids will possess different properties according to the type of fatty acid they possess. - Fatty acids are primarily classified according to the presence or absence of double bonds between the carbon atoms in the chain. Fats versus Oils Living organisms store their lipids as either fats or oils depending on the type of fatty acid involved (saturated or cis-unsaturated) - These fatty acids differ in the shape of their hydrocarbon chains (straight or bent) Fats (Saturated) - have straight chains that can be more tightly packed, making them more efficient for energy storage - this tight packaging increases the number of intermolecular forces between the fatty acid chains, resulting in a higher melting point - This means it takes higher temperatures to keep them liquid and they will typically exist as fats (solid at a room temperature of 25ºC) Oils (Unsaturated) - (cis) fatty acids have kinked chains that cause them to be more loosely packed - This means there are fewer intermolecular forces and less energy is required to separate the fatty acids, resulting in a lower melting point - Consequently, they will remain liquid at cooler temperatures and so usually exist as oils (liquid at a room temperature of 25ºC) Specific Functions 1. Energy Storage - Triglycerides in adipose tissues are used for long-term energy storage in animals 2. Thermal Insulation - Triglycerides have low thermal conductivity, meaning they have a limited capacity toconduct heat and are effective thermal insulators 3. Structure - Phospholipids are one of the key structural components of all cell membranes that are responsible for the formation of lipid bilayers - Phospholipids consist of a polar head (hydrophilic) composed of a glycerol and a phosphate molecule and two non-polar tails (hydrophobic) composed of fatty acid chains - Because phospholipids contain both hydrophilic (water-loving) and lipophilic (fat-loving) regions, they are classed as amphipathic 4. Communication - Steroids are derived lipids composed of four fused carbon rings. - Because they are non-polar, they can pass through the phospholipid bilayer and will commonly be utilized as signaling molecules (hormones). Chemistry of Life: Proteins Proteins are organic compounds that contain nitrogen as well as carbon, hydrogen, and oxygen. Some proteins also contain sulfur and phosphorus. They are an extremely diverse class of organic compounds that fulfill a wide array of functions within a cell. Proteins function as the ‘worker’ molecules of a cell – they are encoded by nucleic acids (DNA) and are expressed in accordance with the specific genetic instructions of a particular cell. Amino Acids - monomers of proteins Proteins are composed of long chains of recurring monomers called amino acids - Each amino acid contains a central alpha carbon linked to an amine group, carboxyl group, a variable group and a hydrogen atom There are 20 standard amino acids which are universal to all living organisms - Of the 20 standard amino acids, 9 are considered to be essential amino acids. This means that the human body cannot create them at the level needed for normal growth, and so we must obtain them from food. - A shortage of one or more essential amino acids in the diet will prevent the production of specific proteins - There are 11 non-essential amino acids. These are amino acids that the body can synthesize on its own, even if they're not obtained directly from food. An amino acid consists of the following: 1. A central carbon atom. 2. A carboxyl group. 3. An amino group. 4. A hydrogen atom. 5. A variable side chain (called “R”) that is different for each amino acid. The “R” group carries distinct chemical properties that determine the way a protein folds. Peptides In order to make a protein, amino acids must be bonded together by dehydration synthesis. - The bond forms between the amino group of one amino acid and the carboxyl group of another, releasing a water molecule. - The newly formed bond is called a peptide bond. - The resulting molecule, made from 2 amino acids, is called a dipeptide. When more amino acids are added to either end of a dipeptide, a linear polypeptide chain is made. - All proteins consist of at least one of these polypeptides or amino acid chains. - The sequence of amino acids is encoded by genes and the assembly of a polypeptide chain occurs at the ribosome Protein Structure and Function The structure of a protein is determined by the order of the amino acids in a polypeptide sequence. The different variable “R” group side chains will have distinct chemical properties (e.g. charged, non-polar, etc.) which will cause a protein chain to fold into different arrangements and become a complex 3-dimensional structure. The way a protein molecule folds plays a critical role in determining its eventual function and level of biological activity Denaturation Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties Denaturation can be caused by certain conditions: - Temperature (heat may break structural bonds) - pH (alters protein charge ➡ changes solubility & shape) Functions Transport - Protein channels help move molecules across cell membranes, transport substances and materials. Hormones - the “chemical messengers” that carry signals from one cell or tissue to another to regulate functions. Enzymes - the substances needed for nearly all biological processes that accelerate chemical reactions. Movement - drive everything from the contraction of muscles to the movement of organelles within cells. Immunity - antibodies found in the body that help the immune system to identify and fight foreign objects Structure -components of cells and tissues, such as muscles, bones, and cartilage. Sensation - often the main components of sensory receptors, specialized cells that detect changes in the environment.