Biological Molecules GB1 (Student) PDF

Miriam College High School SHS - STEM | S.Y. 2024 - 2025 General Biology 1 1 Biological Molecules Video Analysis  Video Analysis (AlphaFold) Leveraging AI to Understand Life 1. In what ways has AlphaFold’s ability to predict protein structures advanced our un...

Miriam College High School SHS - STEM | S.Y. 2024 - 2025 General Biology 1 1 Biological Molecules Video Analysis  Video Analysis (AlphaFold) Leveraging AI to Understand Life 1. In what ways has AlphaFold’s ability to predict protein structures advanced our understanding of biological processes and disease mechanisms? 2. How might AlphaFold’s accurate protein structure predictions influence the development of new pharmaceuticals and treatments? 3. What are the potential limitations or challenges associated with relying on AI models like AlphaFold in scientific research, particularly in the study of protein functions?  Integrity of Creation through AI “AI technologies like AlphaFold have transformed science by helping us understand life at a molecular level and offering solutions to pressing global challenges. As stewards of God’s creation, how can we responsibly use such advancements to benefit humanity and protect the environment, while ensuring that these tools are applied ethically and sustainably?” BIOLOGICAL MACROMOLECULES Four major classes of macromolecules 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids *will be discussed in General Biology 2, next SY :) Organic molecules – all contain carbon May also contain hydrogen, oxygen, nitrogen, and some other minor elements  Macromolecules consist of individual subunits called monomers Monomers are linked together via covalent bonds into polymers Formation of a disaccharide Dehydration synthesis – two molecules of glucose are linked to form the disaccharide maltose A water molecule is formed as the two monosaccharides are linked by a covalent bond Hydrolysis – process of breaking polymers down into individual monomers – also known as a dehydration reaction + Water serves as a reactant; one monomer receives a H - and the other monomer receives an OH In the dehydration reaction shown here - disaccharide maltose is broken down to form two glucose monomers Note that this reaction is the reverse of the synthesis reaction shown previous slide What is the importance of the Miller - Urey Experiment in explaining the possible origin of life? Recreating Primordial Earth What is the importance of the Miller - Urey Experiment in explaining the possible origin of life? Recreating Primordial Earth  CHEMICAL REACTIONS INVOLVING MACROMOLECULES ARE CATALYZED BY ENZYMES Enzymes are biological molecules that catalyze or “speed up” reactions Enzymes speed up hydrolysis and dehydration reactions Dehydration reactions form new bonds/require energy Hydrolysis reactions break bonds/release energy  CHEMICAL REACTIONS INVOLVING MACROMOLECULES ARE CATALYZED BY ENZYMES Specific enzymes exists for each macromolecule class Carbohydrates – broken down by amylase, sucrase, lactase, maltase Lipids – broken down by lipases Proteins – broken down by pepsin and peptidase CARBOHYDRATES Carbohydrates found in grains, fruits, and vegetables Provide energy to body in from of glucose Represented by the general formula (CH2O)n Ratio of Carbon:Hydrogen:Oxygen is 1:2:1 Three main subtypes: Photo Credit:US 1. Monosaccharides Department of Agriculture 2. Disaccharides 3. Polysaccharides MONOSACCHARIDES Monosaccharides usually have 3-7 carbons End with the suffix –ose Contain a carbonyl group C=O Aldoses - carbonyl group (indicated in green) at the end of the carbon chain Ketoses - carbonyl group in the middle of the carbon chain Trioses – three carbons Pentoses – five carbons Hexoses – six carbons  EXAMPLES OF MONOSACCHARIDES  THREE STRUCTURAL ISOMERS OF A HEXOSE MONOSACCHARIDE Structural isomers/formula (C6H12O6) 1. Glucose – important source of energy 2. Galactose – part of lactose/milk sugar 3. Fructose - part of sucrose/fruit  MONOSACCHARIDES EXIST AS LINEAR CHAIN OR RING-SHAPED MOLECULES Assume ring structure in aqueous solutions Five- and six-carbon monosaccharides exist in equilibrium between linear and ring forms Ring forms and the side chain it closes on is locked into an α or β position Fructose and ribose also form rings they form five-membered rings as opposed to the six-membered ring of glucose  DISACCHARIDE FORMATION Disaccharides form when two monosaccharides are linked in a dehydration reaction Example of disaccharide formation Glucose + Fructose = Sucrose (disaccharide) Two monomers are joined by glycosidic bond Water is also released carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group glycosidic linkage is formed between carbon 1 in glucose and carbon 2 in fructose Results in 1,2 glycosidic linkage OTHER COMMON DISACCHARIDES Common disaccharides maltose (grain sugar) lactose (milk sugar) sucrose (table sugar) All are created via formation of covalent glycosidic linkages POLYSACCHARIDES Polysaccharides – long chain of monosaccharides joined by glycosidic linkages May be branched or unbranched May consist of multiple types of monosaccharides Molecular weight could be > 10,000 daltons Glycogen stores (black granules) in spermatazoa of flatworm POLYSACCHARIDES CAN BE DISTINGUISHED BY THEIR GLYCOSIDIC LINKAGES Starch is composed of Amylose and Amylopectin The monomers are joined in two linkage types 1. α 1-4 glycosidic bonds 2. α 1-6 glycosidic bonds Amylose = unbranched glucose monomers in α 1-4 glycosidic bonds Amylopectin = branched glucose monomers in α 1-4 and α 1-6 glycosidic bonds  CELLULOSE – A POLYSACCHARIDE FOUND IN THE CELL WALL OF PLANTS Cellulose - glucose monomers are linked in unbranched chains by β 1-4 glycosidic linkages Every glucose monomer is flipped relative to the next one resulting in a linear, fibrous structure CHITIN (credit: Louise Docker) The hard exoskeleton of arthropods is composed of the polysaccharide chitin Chitin also contains nitrogen https://commons.wikimedia.org/wiki/File:Chitin.svg  LIPIDS Lipids are a diverse group of non-polar hydrocarbons Non-polar hydrocarbons Hydrophobic lipids in the fur of aquatic mammals protect are hydrophobic them from the elements (credit: Ken Bosma) (water-fearing)  LIPIDS Functions of lipids Long-term energy stores Provide insulation from environment for plants and animals Serve as building blocks for some hormones Important component of cellular Hydrophobic lipids in the fur of membranes aquatic mammals - protect sthem from the elements (credit: Ken Bosma) Types of lipids Fats Oils Waxes Phospholipids Steroids FATS AND OILS Fats – Contain two main components 1. Glycerol 2. Fatty Acids Triacylglycerol – formed by joining three fatty acids to a glycerol backbone The glycerol molecules are attached to the fatty acids via an ester linkage Three molecules of water are released in this reaction FATS AND OILS SATURATED AND UNSATURATED FATTY ACIDS Stearic acid is a common saturated fatty acid. This means it contains no carbon-carbon double bonds in the carbon-backbone Pack tightly and exist as solids at room temperature (butter, fat in meats, etc) May be associated with cardiovascular disease – should be limited in your diet SATURATED AND UNSATURATED FATTY ACIDS Oleic acid is a common unsaturated fatty acid Contains at least one carbon-carbon double bond in carbon chain backbone Monounsaturated fat = one double bond Polyunsaturated fat = more than one double bond Most unsaturated fats are liquids at room temperature – referred to as oils WHAT’S THE DEAL WITH TRANS-FATS? Each double bond of an unsaturated fat may be in one of two positions Cis configuration – hydrogens on same side of chain Trans configuration – hydrogens on opposite side of chain Cis-acids have a kink in the chain They cannot be packed tightly Liquid at room temperature Trans-acids – no kink Can be created through processing Foods with trans fat may increase LDL cholesterol in humans (bad for heart  ESSENTIAL FATTY ACIDS Alpha-linolenic acid is an example of an omega-3 fatty acid Essential fatty acids – required but not synthesized by the body – must be part of diet Omega-3 fatty acid (found in salmon, trout, tuna) Omega 6-fatty acid These fats are heart healthy Reduce risk of heart attack, reduce triglycerides in blood, lower blood pressure WAXES Long fatty acid chains esterified to long chain alcohols Hydrophobic and prevent water from sticking to surface (credit: Roger Griffith) Found on the feathers of some aquatic birds and on the surface of leaves from certain plants PHOSPHOLIPIDS Modifiers attach to the phosphate group at the Phospholipid - molecule with two fatty position labeled R acids and a modified phosphate group attached to a glycerol backbone The phosphate may be modified by the addition of charged or polar chemical groups Two common chemical groups that attach to phosphate are choline and serine PHOSPHOLIPIDS  PHOSPHOLIPIDS ARE MAJOR CONSTITUENTS OF THE PLASMA MEMBRANE Amphipathic molecule The hydrophilic head groups of the phospholipids face the aqueous solution The hydrophobic tails are sequestered in the middle of the bilayer Phospholipids contribute to dynamic nature of plasma membrane STEROIDS Steroids have a closed ring structure Four linked carbon rings Many have a short tail Structure is different from that of other lipids  STEROIDS 1. They are hydrophobic 2. They are insoluble in water Cholesterol is the most common steroid Synthesized in liver Precursor to other hormones such as testosterone and estradiol Precursor to vitamin D Precursor to bile salts  PROTEINS Most abundant organic molecules Have a diverse range of functions Regulatory functions Structural functions Protective functions Transport Enzymes Toxins  A CLOSER LOOK AT PROTEIN FUNCTION -- ENZYMES Enzymes – catalysts in biochemical reactions Specific enzyme for specific substrate Types of enzymes Catabolic – breakdown substrates Anabolic – build more complex molecules Protein (enzyme) Catalytic – affect the rate of reaction that catalyzes conversion of Maltose to Glucose Credit: Thomas Shafee  PROTEIN TYPES AND FUNCTIONS Type Example Functions Digestive enzymes Amylase, lipase, Help in digestion of food by catabolizing nutrients into pepsin, trypsin monomeric units Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton Hormones Insulin, thyroxine Coordinate the activity of different body systems Defense Immunoglobulins Protect the body from foreign pathogens Contractile Actin, myosin Effect muscle contraction Storage Legme storage proteins, Provide nourishment in early development of the embryo and Egg white (albumin) the seedling AMINO ACIDS Amino acids are the monomers that make up proteins Fundamental structure Central carbon atom (α-carbon) Amino group (-NH2) Carboxyl group (-COOH) Hydrogen Side chain (R-group) AMINO ACIDS HAVE DIVERSE CHEMICAL PROPERTIES 20 common amino acids commonly found in proteins Each amino acid has a different R group (variant group) R-groups determine the chemical nature of each amino acid Nonpolar aliphatic Polar Positively charged Negatively charged Nonpolar aromatic  MORE ON AMINO ACIDS Amino acids are represented by a single upper case letter or three letters Valine = V or Val Aspartic Acid = D or Asp Essential Amino acids – the following must be supplied in diet for humans isoleucine leucine cysteine The sequence and of number amino acids determine protein shape, size and function  PEPTIDE BOND FORMATION Amino acid monomers are linked via peptide bond formation (dehydration synthesis reaction) Carboxyl group of one amino acid is linked to the amino group of the incoming amino acid A molecule of water is released as part of the reaction  WHAT’S THE DIFFERENCE BETWEEN POLYPEPTIDES AND PROTEINS? Polypeptide – a chain of amino acids joined together in peptide linkages Protein – a polypeptide or multiple polypeptides Often combined with non-peptide prosthetic groups Has a unique structure and function Many proteins are modified following translation (process of creating a new protein) PROTEIN SYNTHESIS  SHAPE OF PROTEINS IS CRUCIAL TO THEIR FUNCTION Protein shape is based upon four levels of structure 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quatenary structure  PRIMARY PROTEIN STRUCTURE Primary structure – the unique sequence of amino acids in a polypeptide Example above is bovine serum insulin – The sequence of amino acids in the A and B chain polypeptides is unique to this protein Protein function could be compromised if alterations in the order of amino acids was to be made PRIMARY PROTEIN STRUCTURE Amino acid sequence is based upon gene encoding that protein A change in the nucleotide sequence of DNA could lead to a change in amino acid This could lead to a change in protein structure and function  SICKLE CELL ANEMIA – HOW A CHANGE IN ONE AMINO ACID CAN IMPACT HUMAN HEALTH Change occurs in β-chain of hemoglobin normal hemoglobin-amino acid at position seven is glutamic acid sickle cell hemoglobin-glutamic acid is replaced by a valine THE RESULT OF A SINGLE AMINO ACID CHANGE OUT OF 600 AMINO ACIDS THAT CODE FOR HUMAN HEMOGLOBIN Sickle cells are crescent shaped, while normal cells are disc-shaped blood smear, visualized at 535x magnification using bright field microscopy (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell) SECONDARY PROTEIN STRUCTURE Secondary structure – local folding of the polypeptide 1. α-helix (alpha)– formed by hydrogen bond between oxygen in carbonyl group and an amino acid 4 positions down the chain 2. β-pleated sheet - hydrogen bonding between atoms on the backbone of the polypeptide chain GRAPHIC REPRESENTATION OF SECONDARY PROTEIN STRUCTURE α-helix and β-pleated sheet are secondary structures of proteins form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone Certain amino acids tend to form an α-helix Others amino acid favor formation of β-pleated sheet TERTIARY PROTEIN STRUCTURE Tertiary structure – the unique three dimensional structure of a polypeptide Due to chemical interactions between R-groups on amino acids Ex. 1 - R-groups with like charges are repelled from one another Ex. 2 – R-groups that are hydrophobic will cluster in interior of protein Ex. 3 – Cysteine side chains form disulfide bridges EXAMPLES OF TERTIARY STRUCTURE Tertiary structure of proteins is determined by a variety of chemical interactions hydrophobic interactions ionic bonding hydrogen bonding disulfide linkages QUATERNARY PROTEIN STRUCTURE Quaternary Structure – interactions between several polypeptides that make up a protein Weak interactions between subunits help stabilize the structure PUTTING ALL THE PIECES OF PROTEIN STRUCTURE TOGETHER The four levels of protein structure can be observed in these illustrations (credit: modification of work by National Human Genome Research Institute) DENATURATION AND PROTEIN FOLDING Protein structure and shape can Heating an egg to extreme be changed if chemical temperatures can lead to interactions are broken irreversible denaturation of egg protein (albumin in egg goes from liquid to solid) Protein structure/shape can change with altering primary structure due to: Changes in pH Changes in temperature Denaturation – Changes in Credit: freefoodphotos.com protein structure that leads to changes in function