Week 2 Lecture Notes on Biomedical Chemistry PDF

2023-09-19 Learning Objectives 1. List the four categories of macromolecule found in the body. BNUR 2003 2. Understand the chemical composition of amino acids and how they are linked together to form proteins. Biomedical Chemistry and Lab Diagnostics 3. Understand the four hierarchical levels o...

2023-09-19 Learning Objectives 1. List the four categories of macromolecule found in the body. BNUR 2003 2. Understand the chemical composition of amino acids and how they are linked together to form proteins. Biomedical Chemistry and Lab Diagnostics 3. Understand the four hierarchical levels of protein structure and the forces that influence them. 2-Important Biochemical Molecules and Macromolecules 2-1 Proteins 2-2 Carbohydrates + Lipids 2-3 Nucleic acids and mutations 4. Describe what protein denaturation is and how it occurs. 5. Understand the principles of protein electrophoresis and how it is used in healthcare. Describe what an enzyme is. 6. Understand the chemical composition of various carbohydrates and how they are related. 7. Understand the chemical composition of various lipids and how their properties are related to fatty acid composition. 1 2 Biochemical Molecules and Macromolecules Proteins Amino Acids Peptide Bonds Structure • • • • All biochemical molecules are derived from simple precursors from our environment (CO2, H2O, etc.) These are converted into larger molecular weight organic subunits (monomers) Monomers are linked together to form four major types of macromolecules (proteins, carbohydrates, lipids, nucleic acids) Classes Carbohydrates Denaturation Electrophoresis Macromolecules Enzymes Lipids Macromolecules are essential to life and abundant in cells. Monosaccharides Disaccharides Polysaccharides Triglycerides Nucleic Acids 3 Phospholipids Other lipids 4 1 2023-09-19 Proteins and Amino Acids Proteins are the most abundant organic molecules in cells. They all contain ________, ________, and usually Carbon oxygen ________, nitrogen hydrogen ________, ________. sulfur 5 6 Proteins and Amino Acids Proteins and Amino Acids The subunits of proteins are amino acids. There are 20 different amino acids that make up proteins. All amino acids consist of a carbon atom attached to: • An ________ group amino • A ________ group CAVDOXYI • A ________ hydrogen atom • A ________(denoted R) side chain 7 The characteristic properties of individual amino acids (in other words, the side chains) contribute to the structure and function of proteins. Here is an example amino acid, Tyrosine: 8 2 2023-09-19 non-polar areoma Proteins and Amino Acids Q:What characteristics can different side chains give amino acids? Net Charge: Some amino acids have a net negative charge (acidic), others have a net positive charge (basic), and others are neutral. Polarity: Some amino acids are nonpolar (hydrophobic) and others are polar (hydrophilic). Sulfur: Two amino acids have sulfur in their structure. 9 10 should understand name and Proteins and Amino Acids • • Aspartate and glutamate are negatively charged Arginine, histadine, and lysine are positively charged deromatic group they belong = circle structure to Proteins and Amino Acids Proteins are formed by linking together amino acids. Although there are only 20 amino acids, there is no limit on protein length, so possibilities are endless. How are amino acids linked to form proteins? To link two amino acids, a is formed and one peptide bond molecule of water is generated. This reaction is an example of dehydration synthesis. 11 12 3 2023-09-19 Levels of Protein Structure Proteins and Amino Acids where it starts Polypeptides always consist of an N-terminus and a C-terminus. Polypeptides are identified by naming amino acids from the N-terminal. In this case the polypeptide is ala-ser-gly. 13 Protein structure can be broken down to four hierarchical levels: primary, secondary, tertiary, and quaternary structure. now it holds and it functions Primary structure refers to the amino acid _______. sequence The primary structure is 2-dimensional, but determines the 3dimensional shape of the protein. 14 Levels of Protein Structure Secondary structure refers to localized folding of the polypeptide backbone due to hydrogen bonds between the carboxyl group of one peptide bond and the amino group of another peptide bond. Two types of secondary structure: (1) ___________ eliX (2) ________________ B-pleated Sheet a Levels of Protein Structure α-helix • Hydrogen bonds form between amino acids that are 4 amino acids away on the same polypeptide chain. • Side chains point out of the helix. - • Form a “toilet paper roll” type structure. hydrogen bonds repetitive 15 16 4 2023-09-19 Levels of Protein Structure Levels of Protein Structure ß-pleated sheet • Several polypeptides are arranged such that they lie parallel to each other in the shape of a sheet. • Hydrogen bonds form between carboxyl and amino groups on different polypeptides. Tertiary structure refers to the overall 3-dimensional folding of the polypeptide chain. Different from secondary structure in several ways • Not repetitive • Involves the _______ ________ of amino acids chains side Tertiary structure is stabilized mostly by three noncovalent forces: (1) Hydrophobic interactions side chains interact non-polar (2) Ionic bonds (3) Hydrogen bonds i repetitive 17 18 Levels of Protein Structure Levels of Protein Structure now bound creating 19 together "n" snape Quaternary structure refers to the interaction of two or more polypeptides to form a larger protein that operates as a single functional unit (an oligomer). • Subunits may not be active. • Multiple subunits may allow increased activity. 20 5 2023-09-19 Levels of Protein Structure Levels of Protein Structure Hemoglobin is an oligomer consisting of four polypeptide chains. 21 22 Levels of Protein Structure We will study two major classes of proteins – globular and fibrous. Globular proteins are often water _______ with ionic SOLUDIE groups on the outside of the molecule and hydrophobic pockets tucked on the inside of the molecule. • Transportation molecules • Enzymes • Antibodies 23 Levels of Protein Structure Hydrophilic exterior (R groups of charged and hydrophilic amino acids point outwards) Fibrous proteins are water _______ and usually function in a inSOlUDIE structural capacity. Common fibrous proteins in humans include collagen and keratin. Hydrophobic pocket (R groups of hydrophobic amino acids point inwards, away from water.) 24 6 2023-09-19 Denaturation of Proteins Denaturation of Proteins The normal three-dimensional structure of a protein is called the native state. Loss of the native state usually renders proteins non-functional. This loss is called denaturation. Note that no break in the primary structure of a protein is involved in denaturation. The structure of proteins can be disrupted by four types of force: 1. Agents that disrupt hydrogen bonds • • • _________ heat Shear forces Chemicals (e.g., urea, guanidinium chloride) 2. Agents that disrupt hydrophobic interactions Why is denaturation good? • _________ _________ (acetone, alcohol) SOIVentS organic 3. Agents that disrupt electrostatic interactions • changes in _________ PH Why is denaturation bad? 4. Agents that disrupt disulfide bridges raditation treatment • _________ mercury 25 26 Protein Electrophoresis Protein Electrophoresis Proteins may be either positively or negatively charged depending on the number of positively or negatively charged amino acids. We can take advantage of this property to identify proteins using protein electrophoresis. Electrophoresis uses an electric field to separate proteins. One early use of protein electrophoresis was the rapid identification of individuals with sickle cell anemia. Sickle cell anemia involves a mutation at the 6th amino acid in one of the protein subunits of __________. nemoglobin get HbA Negatively charged 27 most proteins speed can be are negative , But must determine the level of negativity HbS Neutral 28 determined by size : charge on cell 7 2023-09-19 Amino Acids Peptide Bonds Structure BNUR 2003 Classes Biomedical Chemistry and Lab Diagnostics Denaturation Electrophoresis 2-Important Biochemical Molecules and Macromolecules 2-1 Proteins 2-2 Carbohydrates + Lipids 2-3 Nucleic acids and mutations Enzymes Monosaccharides Disaccharides Polysaccharides 1 2 Carbohydrates • Carbohydrates (CHO) make up only 1-2 % of our body weight but provide most our chemical energy! • They are water soluble and are composed of _________, carbon _________ and _________ in a ratio of 1:2:1. hydrogen oxygen Carbohydrates Five- (pentose) and six-carbon (hexose) sugars are the most common. D-glucose is also called dextrose (blood sugar). prime • 3 carbon Carbonyl Group CHO can be simple sugars (monosaccharides and disaccharides) or more complex molecules called polysaccharides. Hydroxyl group 4 1 2023-09-19 Carbohydrates Carbohydrates The most common form of glucose in our bodies is cyclical in structure. Monosaccharides can be linked to form larger structures. Two monosaccharides are joined by a ____________ link to form a glycosidic disaccharide. This reaction is another example of dehydration synthesis. Dehydration synthesis Hydrolysis Glucose C6H12O6 Fructose C6H12O6 Subtract Ha0 creating a disacoride : monosacride Water Sucrose C12H22O11 Glycosidic link + monosacride through getting rid of a water Disaccharides can be broken down into monosaccharides through hydrolysis. common 5 6 Carbohydrates Carbohydrates Polysaccharides consist of tens or hundreds of monosaccharides joined together through dehydration synthesis reactions involving either: • 1,4 glycosidic links or • 1,6 glycosidic links Amylopectin and glycogen are polysaccharides with both 1,4 and 1,6 linkages. Amylopectin & Glycogen: Branched chains = 1,4 and 1,6 linkages Amylose and cellulose both have 1,4 glycosidic links. branching patterns carbonyl grOUP 7 8 2 2023-09-19 Lipids Unlike carbohydrates, lipids do not share a common base. Instead lipids are substances that can be extracted from tissues using organic solvents. Lipids are insoluble in water. hydrophobic Lipids include: Monosaccharides • • • • Disaccharides Polysaccharides Triglycerides ___________ triglycerides Phospholipids Steroids Fat-soluble vitamins Phospholipids Other lipids 9 Lipids 10 Lipids Glycerol backbone Triglycerides are the most common lipid. They contribute to body form and serve as an energy reserve. Triglycerides are composed of: • A glycerol backbone • Three fatty acids There are many different types of fatty acids, and the specific fatty acids that form a triglyceride determine its structure and function. 11 Carboxyl group Fatty acid (palmitic acid, Saturated) C15H31COOH Hydrocarbon chain 12 3 2023-09-19 Lipids Lipids Ester attaching linkage to chain Glycerol Oleic acid (unsaturated) (C17H33COOH) Palmitic acid (saturated) (C15H31COOH) + H2 O + ~ instable ~ making this melting point like a creating a bend Stearic acid (saturated) (C17H35COOH) + Fatty acids are: • Usually composed of an even number of carbon atoms (16 and 18 are most common) • Mostly saturated (only single C-C bonds) zipper" saturated with hydrogens melting point unsaturated H2O back Characteristics of fatty acids: • Longer carbon chains = higher melting points length matters • All else being equal, higher degree of unsaturation = lower melting points H2O cis configuration Molecule of fat (triglyceride) 13 14 Lipids Lipids Fatty acid melting point comparison Phospholipids consist of a glycerol backbone (like triglycerides) in carbons are linked to fatty acids and the third carbon is a phosphate group. Fatty Acid Structural Formula Isomer M.P. which two Common Name (ºC) ___________________________________________________________________________________ bonded to Butyric CH3(CH2)2-COOH -7.9 Caproic CH3(CH2)4-COOH -3.4 Caprylic CH3(CH2)6-COOH 16.7 Capric CH3(CH2)8-COOH 31.6 Lauric CH3(CH2)10-COOH 44.2 Myristic CH3(CH2)12-COOH 53.9 Palmitic CH3(CH2)14-COOH 63.1 Stearic CH3(CH2)16-COOH Melt 69.6 indicates unsaturated unstable cis Palmitoleic CH3(CH2)5-CH=CH-(CH2)7-COOH 0 cis Oleic CH3(CH2)7-CH=CH-(CH2)7-COOH 15 trans Elaidic CH3(CH2)7-CH=CH-(CH2)7-COOH 46.5 Linoleic CH3(CH2)4(CH=CH-CH2)2(CH2)6-COOH all cis -5 Linolelaidic CH3(CH2)4(CH=CH-CH2)2(CH2)6-COOH all trans 28 Linolenic CH3CH2(CH=CH-CH2)3(CH2)6-COOH all cis -11 Elaidolinolenic CH3CH2(CH=CH-CH2)3(CH2)6-COOH all trans 29 Arachidonic CH3(CH2)4(CH=CHCH2)3CH=CH(CH2)3COOH all cis -49.5 = justafattysearup = ~ 15 16 4 2023-09-19 Protein Electrophoresis Enzymes Enzymes are important macromolecules needed to sustain life. They are almost always ________ proteins. glODUlar The change of just one amino acid affects the migration of the protein in the electric field! • HbA Negatively charged -neg cathode HbS We will talk much more about them in later units, but for now note that enzymes are proteins and the structure of individual enzymes is critically important to their function. Neutral +pos anode HbA HbS HbS/HbA 29 30 8 2023-09-19 Proteins Amino Acids Peptide Bonds Structure BNUR 2003 Classes Biomedical Chemistry and Lab Diagnostics 2-Important Biochemical Molecules and Macromolecules 2-1 Proteins 2-2 Carbohydrates + Lipids 2-3 Nucleic acids and mutations Carbohydrates Denaturation Electrophoresis Macromolecules Enzymes Lipids Monosaccharides Disaccharides Polysaccharides Triglycerides Nucleic Acids 1 Phospholipids Other lipids 2 Learning Objectives Proteins 1. Describe the structure of DNA, including the monomer subunits of DNA and structure of the double helix. 2. Describe the process of DNA replication. Understand why the DNA double helix is so important in our understanding of DNA replication. Carbohydrates Macro- DNA Structure molecules Lipids DNA Replication RNA Structure Protein Synthesis The Genetic Code Mutation of DNA 3. Describe the structure of RNA and how is differs from DNA. 4. Describe the processes of transcription and translation and understand how proteins are synthesized. Describe how the genetic code works. 5. Understand what a mutation is and describe the effects of various types of mutations on the human body. Nucleic Acids 3 4 1 2023-09-19 DNA Structure DNA Structure The monomer units that form DNA are phosphate , deoxyribose and the four DNA bases (adenine, guanine, thymine, cytosine). The four DNA bases are can subdivided into two types: purines (adenine & guanine) and pyrimidines (thymine & cytosine). Purines Phosphate Deoxyribose Pyrimidines We will refer to the five carbons of deoxyribose as 1’ (pronounced “one prime”), 2’, 3’, 4’ and 5’ 5 6 DNA Structure A nucleoside is formed by a bond between deoxyribose and a base . Bases are attached at the 1’ carbon of the deoxyribose. DNA Structure A nucleotide is formed by a bond between deoxyribose and a base and a bond to a phosphate group. Phosphate groups can attach at either the 3’ or 5’ carbon. deoxyadenosine 5’-Deoxyadenosine monophosphate 7 8 2 2023-09-19 DNA Structure DNA Structure Nucleotides can be linked together by form single stranded DNA. • • phosphodiester The DNA bases are shown only as C, A, T, & G. This is an arbitrary sequence. Each strand of DNA has a 5’ end and a 3’ end. 9 DNA Structure • Complementary base pairs are linked by ____________ hydrogen bonds bonds to Naturally occurring DNA is usually double stranded.The two strands of DNA form a double helix. • The backbone of the DNA strand is formed by alternating phosphate and deoxyribose units. • The bases project towards the inside of the helix and occur in complementary pairs • A with T • T with A • C with G • G with C 10 DNA Structure Notice that A and T form only two hydrogen bonds. Phosphate Sugar Adenine (A) Thymine (T) Sugar Phosphate • These hydrogen bonds are fundamental to maintaining the stability of the double helix • C and G form three H bonds Adenine nucleotide Hydrogen bonds Thymine nucleotide • A and T form two H bonds 11 12 3 2023-09-19 DNA Structure DNA Structure 5’ end 3' 3’ end 5' The two strands of DNA are antiparallel. The sugar-phosphate backbone of one strand is upside down relative to the backbone of the other strand. Sugar-phosphate backbone Sugars Phosphates 3’ end 5’ end 13 5 3 5 3 14 : : DNA Structure The double helical structure of DNA is incredibly important. Why? DNA Replication What is required for the synthesis of new DNA? • Template DNA • The four different deoxynucleotide triphosphates (collectively called d-NTP, individually called d-ATP, d-TTP, d-GTP, d-CTP) raw ingredients • An enzyme called __________________ DNA polymerase The hydrogen bonds that hold together the helix are relatively weak compared to the covalent bonds that hold together the sugar-phosphate backbone • If we heat DNA above 60 or 70 degrees C, we can form single stranded DNA • Importance?? 15 hydrogen bonds - weak 16 4 2023-09-19 DNA Replication 1 2 DNA Replication 3 The double helix of the parental DNA separates as weak hydrogen bonds between bases break in response to the action of replication enzymes. Parental strand 3′ end Enzymes catalyze the formation of sugarphosphate bonds between sequential nucleotides on each resulting daughter strand. 5′ end Parental strand 1 Hydrogen bonds form between new complementary nucleotides and each strand of the parental template to form new base pairs. Replication fork creates new strand Of DNA 2 3 Daughter strand 3′ end Parental strand 5′ end Parental strand Daughter strand forming 17 RNA Structure RNA is structurally similar to DNA but differs in the following ways: • Ribose instead of deoxyribose • Usually single stranded • Uracil instead of thymine 19 18 RNA Structure We will consider three types of RNA: • ___________ RNA (rRNA) are integral components of ribosomal ribosomes. • ____________ RNA (mRNA) is synthesized from one strand messenger of DNA and contains the genetic information to direct protein synthesis. • ______________ RNA (tRNA) translates the genetic code transfer into the correct amino acid sequence. 20 5 2023-09-19 RNA Structure Eukaryotic ribosomes contain four different rRNAs. They are named after their sedimentation coefficients. Remember that ribosomes consist of two subunits, the large ribosomal subunit and the small ribosomal subunit. RNA Structure • Messenger RNA (mRNA) is synthesized from one strand of DNA (the antisense/template strand) and contains the genetic information to direct protein synthesis. • mRNA has the same sequence as the other DNA strand (the sense/coding strand), except with uracil instead of thymine. 18S rRNA is part of the small subunit 28S, 5.8S, and 5S rRNA are part of the large subunit Sense/coding strand Antisense/template strand mRNA 21 22 RNA Structure Messenger RNA is also modified in several ways; we will talk about intron splicing. will be sliced Exon 1 Intron 1 Exon 2 > Exon 1 23 Intron 2 Exon 3 will actually be transcribed Exon 2 Exon 3 24 6 2023-09-19 Protein Synthesis RNA Structure Transfer RNAs (tRNAs) bring the correct amino acid to the ribosome during ___________. Let’s look at the general structure of a tRNA and then talk more about them in a few slides! will bind to a • DNA stores instructions for almost every protein in the body. • A _________ contains the DNA instructions for one protein gene • The genetic code is the chemical language of DNA instructions. It takes the form of a sequence of bases (A, C, T, G). specific amino acid The anticodon is 3 bp and binds to mRNA during translation 25 Protein Synthesis 26 Protein Synthesis The central dogma of molecular biology describes the flow of information in a cell. 1. During gene ____________ DNA is uncoiled and histones are activation removed so that information can be accessed. How do we get from a DNA sequence to a completely assembled protein? 27 2. During transcription DNA instructions are copied to mRNA in the _______________ by RNA polymerase. nucleus 3. During translation ribosomes read the mRNA code in the______________ and assemble amino acids into CYtOPIaSM polypeptides. Polypeptides are further processed in the RER and Golgi apparatus. 28 7 2023-09-19 Protein Synthesis Transcription: instructions are copied from _____ to ______ Protein Synthesis Translation: polypeptides assembled by decoding the ______ code. triplet Note that the genetic code is degenerate.What does this mean? 29 30 31 32 8 2023-09-19 33 34 Protein Synthesis The central dogma of molecular biology describes the flow of information in a cell. Video: Transcription and Translation https://www.youtube.com/watch?v=41_Ne5mS2ls 35 36 9 2023-09-19 Mutation – Chromosomal Mutation Deletion Any change in a nucleotide sequence is called a mutation. We can subdivide mutations into two broad classes: • • _______________ Mutations affect the overall structure of ChrOMOSOMAl chromosomes and the arrangement of genes DNA ______________ mutations involve changes in the sequence actual sequence of DNA base pairs Inversion ABCDEFGHI ABCDEFGHI ABCFGHI ABCFEDGHI Translocation Duplication ABCDEFGHI ABCDCDEFGHI 37 ABCDEFGHI JKLMNOPQ ABCDNOPQ JKLMEFGHI 38 Mutation – Chromosomal Mutation – DNA Sequence DUODIeM change : has been made https://www.pathwayz.org/Tree/Plain/CHROMOSOMAL+MUTATIONS#:~:text=Chromosome%20mutations%20or%20'block'%20mutations,of%20DNA%20containing%20many%20genes. 39 40 10 2023-09-19 Mutation – DNA Sequence Mutation – DNA Sequence Substitutions involve the change from one nucleotide to another (as shown on the previous slide). The severity of the substitution depends on whether an amino acid change will result.We will show the mRNA sequence instead of the DNA sequence. Substitutions involve the change from one nucleotide to another (as shown on the previous slide). The severity of the substitution depends on whether an amino acid change will result.We will show the mRNA sequence instead of the DNA sequence. Original mRNA: Original a.a.: UUU CGC AUU GAU Phe-Arg-Iso-Asp Original mRNA: Original a.a.: UUU CGC AUU GAU Phe-Arg-Iso-Asp New mRNA: UUU CGC AUC GAU New mRNA: Original a.a.: UUU CGC AUC GAU Phe-Arg-Iso-Asp 41 42 Mutation – DNA Sequence Mutation – DNA Sequence Substitutions involve the change from one nucleotide to another (as shown on the previous slide). The severity of the substitution depends on whether an amino acid change will result.We will show the mRNA sequence instead of the DNA sequence. Original mRNA: Original a.a.: UUU CGC AUU GAU Phe-Arg-Iso-Asp New mRNA: UUU CGC AUG GAU 43 silent mutations Substitutions involve the change from one nucleotide to another (as shown on the previous slide).The severity of the substitution depends on whether an amino acid change will result. We will show the mRNA sequence instead of the DNA sequence. Original mRNA: Original a.a.: New mRNA: New a.a.: UUU CGC AUU GAU Phe-Arg-Iso-Asp UUU CGC AUG GAU Phe-Arg-Met-Asp Iso and Met are both hydrophobic 44 11 2023-09-19 Mutation – DNA Sequence Mutation – DNA Sequence The severity of missense mutations depends on the nature (hydrophobic, charge, etc.) of the changed amino acid. Nonsense mutations involve a premature stop codon 45 46 Mutation – DNA Sequence distored sequence Frameshift mutations involve insertions or deletions and are often catastrophic! 47 shift everything down 12 1. Given the mRNA sequence AUGUCAGAUCCUUAA, write the doublestranded DNA sequence that would have produced this mRNA sequence. 2. Show the amino acid sequence that would be expected from this mRNA 3. You are bombarded by cosmic rays. YEARGRGH! A gene now produces this mRNA instead: NEW mRNA-AUGUCAAUCGCUCUAA OLD mRNA- AUGUCAGAUCCUUAA What mutations have occurred? 4. Show the amino acid sequence that would be expected from this new mRNA. What kind of mutation has happened? What kind of effect would you expect it to have on protein folding?