Lecture_2-6.pdf

Cell Biology Lecture 2: Macromolecules August 2024 Textbook sections: 3.1, 3.2, 3.3, 3.4, 3.5  Last class... We saw electronegativity, which is defined as an atom's ability to attract electrons They are essential in the formation of Hydrogen bonds In this course the fo...

Cell Biology Lecture 2: Macromolecules August 2024 Textbook sections: 3.1, 3.2, 3.3, 3.4, 3.5  Last class... We saw electronegativity, which is defined as an atom's ability to attract electrons They are essential in the formation of Hydrogen bonds In this course the following elements are considered electronegative: O, N, P, S In this course if any of these is bound to a H atom, there is a likelihood of H-bonds being formed. C is not considered electronegative in the context of biology, so when I binds to H we get a non-polar bond. Last class... We learned that macromolecules are large biologically relevant molecules that typically function in the form of polymers Today we will examine all four types of macromolecules Proteins Proteins are an abundant group of molecules that are made of amino acids. Proteins fulfill seven functions in the cell. When we examine the functioning of a cell or an organism, we are witnessing the result of protein and protein action Proteins are often considered the functional unti of the cell.  Protein function 1. Enzymes/digestion o Some enzymes participate in enzyme catalysis o In this case proteins facilitate and speed up specific chemical reactions o In many cases enzymes are used for the breakdown or digestion of larger molecules o Example: Luciferase is an enzyme that allows for the conversion of D-luciferin to oxyluciferin. This reaction allows fireflies to glow.  Protein function 2. Transport o Some proteins are used to transport molecules throughout the body or the cell. Similarly, some proteins can ac as gates or channels that allow for molecules to enter or exit the cell. o Example 1: Hemoglobin in a protein found in red blood cells that allows for the transport of oxygen throughout the body o Example 2: The lac permease is a protein that allows lactosen (a sugar) to enter the cell by carrying it through the membrane Protein function 3. Structure o Some proteins play a role in the structure of cells and their components o Example: Keratin is the protein present in your hair and nails Protein function 4. Hormones/regulation o Some proteins are involved in the control and regulation of physiological processes. These are called hormones. They are generally quite small. o Example: Insulin is a hormone involved in blood sugar regulation. If you have high blood sugar, insulin will allow cells to import glucose (sugar) from the blood. Protein function 5. Defense o Some proteins play a role in the defense of the organism that produces them. They can protect the organism against disease and predators. Venoms and toxins are included in this category. o Example: Immunoglobulins also known as antibodies, are proteins used to fight disease.  Protein function 6. Contractile/motion o Contractile proteins allow for the movement of structures. Do not confuse this with the transport function of proteins. Transport proteins move things, while contractile proteins allow things to move. o Example: Actin and myosin are the proteins involved in muscle contraction  Protein function 7. Storage o Some proteins are involved in the storage of small molecules within cells. o Example: Casein is a milk protein that stores Calcium. Protein structure There are 20 amino acids used to make proteins Humans can synthesize 11/20 of them, the other 9 are known as essential amino acids All are made of an amino group, an carboxylic acid group, and a varying functional group (R) The variation found in the R group defines the chemistry of the amino acids, and the order of the amino acids will define the nature/structure/function of the protein  Amino acids Nonpolar: have R groups that contain CH2 or CH3 Polar uncharged: contain R groups where oxygen or another electronegative element is present Charged: possess R groups that contain acids or bases that can ionize Aromatic: amino acids that have an aromatic ring present Some, such as cysteine, have special character (more later) The character of the amino acid is largely determined by the R group  Amino acids Note: only cysteine is considered special function Protein structure The function of a protein is largely determined by its structure Scientists have organized protein structure into four distinct levels: primary, secondary, tertiary and quaternary The primary structure of a protein is the sequence of amino acids found within it Protein structure When proteins are formed, there is always a free amino and carboxylic acid group at either end of the chain. Two amino acids joined together are called a dipeptide. These are called the N and C terminals N-terminal C-terminal respectively Protein structure For convenience, we number the amino acids in a polypeptide (several amino acids) chain. Amino acid #1 is ALWAYS the one located at the N-terminus of the polypeptide chain. This is because, during synthesis, amino acids are always added to the C terminal (we’ll learn more about this later this semester).  Protein structure In secondary structure, the peptide groups (the part that is not the R group) (aka the protein backbone) in any protein can interact in order to form hydrogen bonds The chemistry of the R groups is irrelevant in the formation of secondary structure Secondary structures tend for form regular patterns termed α- helices and β-pleated sheets Both these motifs (patterns) will lead to regions that will be cylindrical or planar in shape Not all amino acids participate in secondary structure Protein structure The tertiary structure of a protein is its final globular structure It is therefore the level of structure a protein must achieve in order to become functional Protein structure The tertiary structure results from the organization of the secondary structure motifs and all the other amino acids in the protein It results due to the interactions between the R groups of the amino acids The interactions are: hydrogen bonds (occur between teo polar uncharged amino acids), disulfide bridges (occur between two cysteine amino acids), ionic bonds (occur between two charged amino acids of opposite charge), van der Wall interactions (also known as hydrophobic interactions) and hydrophobic exclusions/interactions (occur between non-polar amino acids) Protein structure Protein structure Protein structure Some protein require several individual polypeptides to function properly The association of these individual polypeptides is known as the quaternary structure Tertiary level interactions also allow for these polypeptides to interact chemically Protein structure Protein structure The 3D structure of a protein is paramount to its function When a protein loses its structure, it generally loses its function This is known as denaturation, it can occur via heat, treatment with acid, ionizing radiation, reducing agents and other processes Denaturation occurs because these conditions destabilize the non-covalent interactions occurring at tertiary and quaternary levels of structure. Protein structure Some patterns are present in many proteins, these are termed motifs Beta barrel motif Helix turn helix motif Protein structure Larger proteins have regions called domains Each domain has a specific function within the protein itself Carbohydrates AKA sugars AKA polysaccharides Made of C, H, O in a 1:2:1 ratio. Eg: Glucose: C6H12O6 Are used as energy source or as structural components of cells and organisms A monomer of a polysaccharide is known as a monosaccharide, or simple sugar. These can have a wide range of carbon atoms 6-Carbon sugars 5-Carbon sugars 3-Carbon sugar Glyceraldehyde Carbohydrates Isomers play a key role in carbohydrate biochemistry Structural isomers Stereo isomers Carbohydrates Glucose is the most important carbohydrate in terms of energy consumption and storage Present in α or β form (isomers) Carbohydrates When multiple monosaccharides are linked together, they form poly saccharides. Disaccharides: polymers made of 2 simple sugars Starch is an important poly saccharide. It is made of long chains of α-glucose. Used as energy storage. These can be hundreds of glucose molecules long. Found in plants. Similar to glycogen in animals Carbohydrates Cellulose: Structural polysaccharide found in plants. Found in cell walls. Made of chains of hundreds of glucose molecule Structurally identical to starch, except made of β- glucose. Generally indigestible except for certain ruminants (cows).  Nucleic acids Nucleic acids contain the information necessary for the successful functioning of the cell and heredity Two types: deoxyribonucleic acid (DNA), ribonucleic acid (RNA)  Nucleic acids Nucleic acids are polymers of nucleotides Nucleotides are comprised of a phosphate group, a pentose (5-Carbon) sugar (varies with the nucleic acid), and a nitrogenous base  Nucleic acids There are 5 different nitrogenous bases found in nucleotides (more later this semester) Nucleic acids DNA carries all the necessary information for heredity and the functioning of the cell Information coded by the sequence of bases in the molecules Sugar present is deoxyribose Comprised of two chains held together by hydrogen bonds that have complementary base pairing and a double helix shape  Nucleic acids RNA is a single stranded nucleic acid Made of ribose sugar Has several functions within the cell, transfers information from DNA to the rest of the cell in the form of messenger RNA (mRNA), is part of the ribosome in the form of ribosomal RNA (rRNA), and carries amino acids to the ribosome in the form of transfer RNA (tRNA) Lipids Diverse group of molecules All are water insoluble aka hydrophobic High amount of non-polar carbon- hydrogen bonds Lipids Fat molecules are commonly called triglycerides They are made of a glycerol molecule as well as three fatty acid chains, Fatty acids vary in length and character Lipids Fatty acids can be saturated, monounsaturated or polyunsaturated  Lipids The saturation level of the fatty acid dictates the melting point of the triglyceride molecule The double bonds in unsaturated fatty acids prevent full packing of the lipids, lowering the melting point  Lipids Steroids are another class of lipid Steroids have important roles in cell growth and cell structure Testosterone can control cell growth while cholesterol is important in the structure of the cell membrane  Lipids Phospholipids are amphipathic molecules Lipids Phospholipids form bilayers or micelles in aqueous environments Homework Sign and upload lab and microscope safety sheets Lab on Wednesday Online quiz on moodle on Friday.