week 2 - lecture notes (3).pdf

2023-09-19 Proteins BNUR 2003 Amino Acids Peptide Bonds Structure Biomedical Chemistry and Lab Diagnostics 2-Important Biochemical Molecules and Macromolecules 2-1 Proteins 2-2 Carbohydrates + Lipids 2-3 Nucleic acids and mutations Classes Carbohydrates Denaturation Electrophoresis Macromole...

2023-09-19 Proteins BNUR 2003 Amino Acids Peptide Bonds Structure Biomedical Chemistry and Lab Diagnostics 2-Important Biochemical Molecules and Macromolecules 2-1 Proteins 2-2 Carbohydrates + Lipids 2-3 Nucleic acids and mutations Classes 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. • • 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 ____________ 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 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) • An enzyme called __________________ 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 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 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 ribosomes. • ____________ RNA (mRNA) is synthesized from one strand of DNA and contains the genetic information to direct protein synthesis. • ______________ RNA (tRNA) translates the genetic code 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. Exon 1 23 Intron 1 Exon 2 Intron 2 Exon 1 Exon 2 Exon 3 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! • DNA stores instructions for almost every protein in the body. • A _________ contains the DNA instructions for one protein • The genetic code is the chemical language of DNA instructions. It takes the form of a sequence of bases (A, C, T, G). 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 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. 3. During translation ribosomes read the mRNA code in the______________ and assemble amino acids into 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. 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 chromosomes and the arrangement of genes DNA ______________ mutations involve changes in the actual sequence of DNA base pairs ABCDEFGHI ABCDEFGHI ABCFGHI ABCFEDGHI Duplication ABCDEFGHI ABCDCDEFGHI 37 Inversion Translocation ABCDEFGHI JKLMNOPQ ABCDNOPQ JKLMEFGHI 38 Mutation – Chromosomal Mutation – DNA Sequence 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 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 Frameshift mutations involve insertions or deletions and are often catastrophic! 47 12