Introduction to the Cell and Biological Molecules PDF

Introduction to the Cell and Biological Molecules Intended learning outcomes: At the end of this session you should be able to: 1- Identify the main organelles in a mammalian cell and list their functions. (Essential cell biology: p12-25) 2- List the principal differences between a prokar...

Introduction to the Cell and Biological Molecules Intended learning outcomes: At the end of this session you should be able to: 1- Identify the main organelles in a mammalian cell and list their functions. (Essential cell biology: p12-25) 2- List the principal differences between a prokaryotic and an eukaryotic cell. (Essential cell biology: p12-25) 3- Discuss the bonds important for macromolecular structure and interaction. 4- Explain the differences between hydrophobic and hydrophilic molecules in water. (Marks Basic Medical Biochemistry: p57) 5- Explain the concept of pH, pK and buffers. (Marks Basic Medical Biochemistry: p41-50). 6- Recognise and draw the generalised structure of an amino acid. (Marks Basic Medical Biochemistry: p70-78). MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: At the end of this session you should be able to: 7- Classify amino acids according to the properties of their side chains. (Harvey Biochemistry: p1-12). 8- Explain how the charges on amino acids are affected by pH. (Marks Basic Medical Biochemistry: p70-78). 9- Show how a peptide bond is formed and list its key features. (Harvey Biochemistry: p1-12). 10- Explain how amino acid charge can influence the isoelectric point of a protein. (Harvey Biochemistry: p1-12) Essential References for Session One MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 1- Plasma Membrane Function: Controls what enters & exits the cell. Structure: Phospholipid bilayer MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 2- Nucleus Function: Controls everything in the cell Structure: Contains DNA/chromosomes Enclosed by a porous double membrane called the nuclear membrane. Functions RNA synthesis RNA processing and ribosome assembly( nucleolus) DNA synthesis and repair MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 2- Nucleus Function: Controls everything in the cell MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 3- Endoplasmic Reticulum (ER) Structure: Thin folded membranes that are connected together. HAS ribosomes Function: Export of proteins, Membrane synthesis, Lipid and steroid synthesis, Detoxification reactions (Protein synthesis) MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 4- Ribosomes Function: Links together amino acids to make proteins (that means enzymes too!) Structure: Tiny organelles made of proteins & RNA. Found on Rough ER MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 4- Ribosomes Function: Links together amino acids to make proteins (that means enzymes too!) Structure: Tiny organelles made of proteins & RNA. Found on Rough ER MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 5- Vesicle Membrane-bound containers that carry substances throughout the cell…. How they related to cytoskeleton? MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 5- Vesicle Membrane-bound containers that carry substances throughout the cell…. How they related to cytoskeleton? MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 6- Golgi Apparatus/Body/Complex Function: Checks, modifies & packages proteins Structure: Closely layered stacks of membrane enclosed discs MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 7- Lysosome Function: Breaks down food, waste & damaged cell parts all within the cell Structure: Contains enzymes; membrane bound How does the cytosol is protected from lysosomal enzymes? MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 8- Peroxisome Structure: Contains enzymes; membrane bound Function: Fatty acids and purine brake down, Detoxification of hydrogen peroxide, and synthesis of cholesterol, bile acids and myelin MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 9- Mitochondria Function: Supplies energy (ATP) to the cell; site of cellular respiration; ‘powerhouse’ of cell Structure: Bean shaped; 2 membranes; has own DNA & ribosomes MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 1- Identify the main organelles in a mammalian cell and list their functions. 11- Cytoskeleton Function: Supports & shapes the cell Structure: A network of protein filaments (microtubules, microfilaments) MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 2- List the principal differences between a prokaryotic and an eukaryotic cell. 1- Prokaryotes are the simplest type of cell. 2- Prokaryotes unicellular organisms that are found in all environments. 3- Prokaryotes are smaller in size when compared to Eukaryotes. 4- Prokaryotes do not have a nuclear membrane. Their circular shaped genetic material dispersed throughout cytoplasm. 5- Prokaryotes do not have membrane-bound organelles. 6- Ribosomes are the only organelles MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 2- List the principal differences between a prokaryotic and an eukaryotic cell. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 2- List the principal differences between a prokaryotic and an eukaryotic cell. ► Cocci = spherical (round) ► Bacillus = (rod shaped) ► Spirilla = helical (spiral) MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Macromolecules Large Molecules Macromolecules are formed when monomers are linked together to form longer chains called polymers. Condensation reaction These monomers can be linked together by a process called dehydration synthesis (also called a condensation reaction) in which a covalent bond is formed between the two monomers while a water molecule is also formed from the OH groups. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Four Lipids major types of Macromolecules Diverse groups of molecules in nonpolymorphic form Carbohydrates Sugars Nucleotides Nucleic Acids Amino Acids Proteins MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Proteins Proteins consist of one or more polymers called polypeptides, which are made by linking amino acids together with peptide linkages. Peptide linkages are formed through condensation reactions. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Carbohydrates Carbohydrates are always composed of carbon, hydrogen and oxygen molecules Monosaccharides typically have five or six carbon atoms. Monosaccharides can, such as the ribose and deoxyribose of RNA and DNA, can serve very important functions in cells. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Nucleic Acid Two types of nucleic acids: DNA RNA DNA and RNA are polymers composed of subunits called nucleotides and a nitrogenous base. Five nitrogenous bases found in nucleotides: the purines adenine (A) and guanine (G) the pyrimidines MGD cytosine (C) and thymine (T) (DNA only) Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Lipids Lipids constitute a very diverse group of molecules that all share the property of being hydrophobic. Fatty acids, which make up fats and oils, can be saturated or unsaturated, depending on the absence or presence of double bonded carbon atoms. Lipids are joined together by ester linkages. Triglyceride is composed of 3 fatty acid and 1 glycerol molecule Fatty acids attach to Glycerol by covalent ester bond Long hydrocarbon chain of each fatty acid makes MGD the triglyceride molecule nonpolar and Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Chemical bonds -Forces that hold atoms and molecules together A- Intramolecular bonds 1-Covalent bond electron(s) sharing between two non metallic atoms. electron(s) either shared evenly between the atoms or not (this create ionic character). MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Chemical bonds 2- Ionic bond A bond formed between two atoms where there is a complete transfer of an electron resulting in the formation of two ions (one positive and one negative). e.g. NaCl MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Chemical bonds B- Intermolecular bonds 1-Hydrogen bonds A weak electrostatic interaction between a hydrogen atom bound to an electronegative atom (N, O) and another electronegative atom. Because they are polarized, two H2O molecules can form a linkage known as Hydrogen bond. This type of bonds have only about 1/20 the strength of covalent MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 3- Discuss the bonds important for macromolecular structure and interaction. Chemical bonds 2-Van der Waals Forces A weak interaction between any two atoms in close proximity. 3-Hydrophobic Interactions Force that bring two non-polar molecules together when they exist in polar environment. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 4- Explain the differences between hydrophobic and hydrophilic molecules in water. Properties of water are important biologically : Water is polar molecule. Water is highly cohesive (hydrogen bonds between water molecules). Water is the principal fluid medium of the cell. Many cellular chemicals are dissolved in the water. Water Helps in regulation of temperature since it is able to absorb large amounts of heat. Helps in regulation of intracellular pH since it is amphoteric solvent. Used for transport – delivers nutrients and removes waste from cells MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 4- Explain the differences between hydrophobic and hydrophilic molecules in water. Water is a dipolar molecule in which the oxygen atom carries a partial negative charge and the hydrogen atoms carry partial positive charges. For molecules to be soluble in water, they must contain charged or polar groups that can associate with the partial positive and negative charges of water. Thus, the solubility of organic molecules in water is determined by both the proportion of polar to nonpolar groups attached to the carbon–hydrogen skeleton and to their relative positions in the molecule. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 4- Explain the differences between hydrophobic and hydrophilic molecules in water. HYDROPHILIC MOLECULES Substances that dissolve readily in water are termed hydrophilic. They include ions and polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar molecule and carry it into solution. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 4- Explain the differences between hydrophobic and hydrophilic molecules in water. Polar groups or molecules are called hydrophilic (water loving), and nonpolar groups or molecules are hydrophobic (water fearing). The water molecules interacting with a polar or ionic compound form a hydration shell around the compound, which includes hydrogen bonds and/or ionic interactions between water and the compound. Compounds that have large nonpolar regions are relatively water-insoluble. They tend to cluster together in an aqueous environment and form weak associations through van der Waals interactions and hydrophobic interactions. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 4- Explain the differences between hydrophobic and hydrophilic molecules in water. HYDROPHOBIC MOLECULES Substances that contain a preponderance of nonpolar bonds are usually insoluble in water and are termed hydrophobic. Water molecules are not attracted to such hydrophobic molecules and so have little tendency to surround them and bring them into solution. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. pH The pH scale is a convenient way of expressing the concentration of H+ in solution. The term pH is defined by the expression: pH = -log [H+] The “p” symbol denotes “negative logarithm of”. A low pH represents a high concentration of H+ and hence an acidic solution. A high pH represents a low concentration of H+ (and a high concentration of OH-) and hence a basic solution. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. Weak acid and Buffers Strong acids and bases completely dissociate in solution. For example, if you place HCl in water the compound dissociates into H+ and Cl- ions so that there are no molecules of HCl remaining. Of more interest in biological systems are weak acids and bases; these are compounds that are not completely dissociated when dissolved in water. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. Weak acid and Buffers Consider ethanoic (acetic) acid, CH3COOH, a group that is often present in many biological systems and molecules. Acids are defined as molecules that can donate protons and when this molecule is placed in water it dissociates to release a H+ and the ethanoate (acetate) anion, CH3COO-. This is a reversible reaction and can be represented by: MGD Session 1 MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. Weak acid and Buffers The tendency of an acid to lose a proton is defined by the acid dissociation constant, Ka. This can be defined by: Ka = [H+] [A-]/[HA] Ka values are usually converted to pKa values just like pH: pKa = -log Ka The stronger the tendency of an acid to dissociate the lower the pKa value Virtually all biological processes are pH dependent. The pH of a solution will affect the charge on biological molecules and it is essential that biological molecules are kept in their optimal ionic state in order to function correctly. Therefore, keeping pH relatively constant is very important and multicellular organisms achieve this by using buffers. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. Weak acid and Buffers Buffers are mixtures of a weak acid and its conjugate base and they work by resisting changes in pH when a small amount of acid or alkali is added to them. In titration curve for ethanoic acid in the middle of the curve there is a relatively flat region where the addition of acid or alkali only results in a small change in pH. This is known as the region of buffering. In this region the concentration of ethanoate ion and ethanoic acid is similar. In general, buffers are only effective in a pH range of pKa +/- 1 MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. Weak acid and Buffers MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. A. The Bicarbonate Buffer System The major source of metabolic acid in the body is the gas CO2, produced principally from fuel oxidation in the tricarboxylic acid (TCA) cycle. CO2 dissolves in water and reacts with water to produce carbonic acid, H2CO3, a reaction that is accelerated by the enzyme carbonic anhydrase. Carbonic acid is a weak acid that partially dissociates into H and bicarbonate anion, HCO3. B. Bicarbonate and Hemoglobin in Red Blood Cells The bicarbonate buffer system and hemoglobin in red blood cells cooperate in buffering the blood and transporting CO2 to the lungs. Most of the CO2 produced from tissue metabolism in the TCA cycle diffuses into the interstitial fluid and the blood plasma and then into red blood cells (Fig. 4.9, circle 1). Although no carbonic anhydrase can be found in blood plasma or interstitial fluid, the red blood cells contain high amounts of this enzyme, and CO2 is rapidly converted to carbonic acid (H2CO3) within these cells. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 5- Explain the concept of pH, pK and buffers. C. Intracellular pH Phosphate anions and proteins are the major buffers involved in maintaining a constant pH of ICFs. The inorganic phosphate anion H2PO4 dissociates to generate H and the conjugate base, HPO4 with a pKa of 7.2.. Thus, phosphate anions play a major role as an intracellular buffer in the red blood cell and in other types of cells. Organic phosphate anions such as glucose 6-phosphate and ATP also act as buffers. ICF contains a high content of proteins that contain histidine and other amino acids that can accept protons in a fashion similar to hemoglobin. D. Urinary Hydrogen, Ammonium, and Phosphate Ions The nonvolatile acid that is produced from body metabolism cannot be excreted as expired CO2 and is excreted in the urine. Most of the nonvolatile acid hydrogen ion is excreted as undissociated acid that generally buffers the urinary pH between 5.5 and 7.0. A pH of 5.0 is the minimum urinary pH. The acid secretion includes inorganic acids such as phosphate and ammonium ions, as well as uric acid, dicarboxylic acids, and TCA such as citric acid (see Table 4.2). One of the major sources of nonvolatile acid in the body is sulfuric acid (H2SO4). Urinary excretion of H2PO4 helps to remove acid. To maintain metabolic homeostasis, we must excrete the same amount of phosphate in the urine that we ingest with food. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 6- Recognise and draw the generalised structure of an amino acid. Amino acids 1. Structure Amino acids are the building blocks for the formation of proteins. Early studies found that there are 20 different amino acids that are commonly found in proteins. They all have a similar structure: a carboxyl group (-COO-) and an amino group (-NH3+) are covalently bound to a central carbon atom (the α carbon). In addition, the side chain or R group, which differs between amino acids, is also bonded to the α carbon. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 6- Recognise and draw the generalised structure of an amino acid. Amino acids 1. Structure All of the amino acids, except for glycine contain an α carbon bound to 4 different groups. Therefore, the α carbon is a chiral centre and the amino acids exhibit stereoisomerism. condition in which two ormore isomers have identical molecularstructures but with differing MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 7- Classify amino acids according to the properties of their side chains. 2. Classification Amino acids are most commonly classified by the chemical nature of their R group. The most common way to do this is to classify them according to their tendency to interact with water at pH 7.0 i.e. their polarity. Amino acids can also be classified in other ways; for example, amino acids containing a benzene ring are described as aromatic whilst those that lack rings are aliphatic. The side chains of some amino acids are charged at pH 7.0 and can be classified according to whether they are positively or negatively charged. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 7- Classify amino acids according to the properties of their side chains. 2. Classification MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 7- Classify amino acids according to the properties of their side chains. 2. Classification MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 7- Classify amino acids according to the properties of their side chains. 2. Classification MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 7- Classify amino acids according to the properties of their side chains. 2. Classification MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 7- Classify amino acids according to the properties of their side chains. 2. Classification MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 8- Explain how the charges on amino acids are affected by pH. Acid – Base Properties The amino and carboxyl groups, as well as some of the R groups are able to ionize (gain or lose a proton). Amino acids that lack an ionisable R group exist as a dipolar or zwitterions when dissolved in water at pH7.0. The relative amount of the zwitterion, the fully protonated or fully deprotonated forms are dependent upon pH. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 8- Explain how the charges on amino acids are affected by pH. Acid – Base Properties The amino and carboxyl groups, as well as some of the R groups are able to ionize (gain or lose a proton). Amino acids that lack an ionisable R group exist as a dipolar or zwitterions when dissolved in water at pH7.0. The relative amount of the zwitterion, the fully protonated or fully deprotonated forms are dependent upon pH. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 9- Show how a peptide bond is formed and list its key features. 4. The Peptide Bond Proteins are linear polypeptides that are formed by linking amino acids. Amino acids are covalently bonded to one another via a peptide bond which forms between the carboxyl group of one amino acid and the amino group of a second. MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 9- Show how a peptide bond is formed and list its key features. 4. The Peptide Bond Key Feature of the Peptide Bond: - All the atoms of the bond are in the same plane - No rotation about the peptide binds due to double bond characteristics - Carbonyl oxygen and Amide hydrogen are in the trans orientation MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 10-Explain how amino acid charge can influence the isoelectric point of a protein. Amino acids form internal salts called zwitterions In the pure solid state and in aqueous solution near neutral pH, amino acids exist almost completely as zwitterions MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 10-Explain how amino acid charge can influence the isoelectric point of a protein. Properties of Amino Acids… ► In zwitterions of amino acids with uncharged side chain, the +ve and –ve Charges cancel one another ► Amino acids in which the +ve and –ve charges are balanced is at its isoelectric point ► The pH at which this balancing occurs is isoelectric pH ► An amino acids is least soluble at its isoelectric pH MGD Session 1  Introduction to the Cell and Biological Molecules Intended learning outcomes: 10-Explain how amino acid charge can influence the isoelectric point of a protein. The isoelectric point (IP) is the pH at which the amino acid has an overall zero charge The isoelectric points (IP) of amino acids range from 2.8 to 10.8 Glycine, with an IP of 6.0 exist as a positively charged species at a pH below 6.0 MGD Session 1