C785 BIOCHEMISTRY – NOTES 2022

When two DNA (deoxyribonucleic acid) sequences are complementary, they pair up and run in opposite directions, e.g., coding (non-template) and non-coding (template) are complementary. When the strands pair up, 5’ pairs with 3’ in DNA, just like A pairs with T and G pairs with C. Remember that if you pair letters, you MUST also pair numbers. Don’t forget about the numbers!  DNA is housed in a special compartment inside the cell called the nucleus. The nucleus exercises strict control over what can and cannot access the DNA.  RNA is a less stable, more temporary nucleic acid that is easily made and degraded by the cell. When information in a particular section of DNA is needed, the cell makes an RNA copy of that DNA section and that carries the information out of the nucleus to the rest of the cell. This process is known as transcription.  Proteins are the workhorses of the cell - they do just about everything that needs to be done. From providing structure to releasing energy to making nucleic acids, our cells can’t live without protein. DNA, RNA, and protein are all central to the survival of the cell.  The understanding that DNA is used to make RNA and RNA is used to make protein is known as the central dogma of molecular biology.  RNA IS SINGLE STRANDED  DNA IS DOUBLE STRANDED  THYMINE (DNA ONLY)  URACIL (RNA ONLY) ______________________________________________ Nucleotides - KEY CONCEPTS  Nucleic acids are polymers of nucleotides.  A nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups.  DNA contains adenine, guanine, cytosine, and thymine deoxyribonucleotides, whereas RNA contains adenine, guanine, cytosine, and uracil ribonucleotides.  DNA is double-stranded and forms a double helix structure that allows for information storage.  Prior to dividing , a cell copies all of its DNA using DNA replication to ensure all new cells have the DNA they need.  DNA Replication involves the formation of a replication fork, addition of RNA primers to create a “handle” for DNA polymerase, synthesis of the new DNA strand by DNA polymerase, and sealing the DNA backbone by DNA ligase.  RNA is single-stranded and is grouped into three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All three types of RNA play an important role in the central dogma.  DNA contains two polynucleotide strands whose bases pair in a predictable way through hydrogen bonding. Adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G). The A and T are linked by TWO hydrogen bonds, while C and G are linked by THREE hydrogen bonds, as shown below. Additionally, the two strands are antiparallel, which means they have opposite 5' and 3' orientations, similar to a two-way street in which traffic is oriented in opposite directions.  Both template DNA (shown in blue) and an RNA primer (shown in red) are needed for DNA polymerase to make a new DNA strand (shown in purple).  DNA stores the information needed by the cell, and RNA transforms that information into proteins via transcription and translation. With an understanding of nucleic acid structure, as well as how DNA replication enables the stored information in DNA to be passed to future generations, we now turn our attention to the different roles of RNA in the central dogma - transcription and translation. 1 This study source was downloaded by from CourseH on :08:53 GMT -06:00  Splicing is the process of removing introns and connecting the exons of a gene. It is an important part of mRNA processing prior to the exit of mRNA from the nucleus for translation.. 5’ cap addition and poly(A) tail addition are also part of mRNA processing that occur at the beginning and end of transcription, respectively. Promoters are DNA sequences near the start of a gene that are recognized by transcription factors, which recruit RNA polymerase to that gene for expression. This is an important aspect of transcription, but is not part of mRNA processing.  Which of the following is the correct order for the steps in the Polymerase chain reaction(PCR) process? Answer: Denaturation, annealing, elongation  Which of the following is NOT a required “ingredient” in a PCR reaction? RNA Primers are not required. However, DNA polymerase, DNA nucleotides, and DNA primers are required in a PCR reaction.  Which of the following changes can NOT be detected using PCR? Epigenetic changes can NOT be detectable via PCR b/c they don’t affect the DNA sequence. Transcription and Translation: A Closer Look KEY CONCEPTS  Genes are segments of DNA sequence that code for a particular product, usually a protein. Mutated genes can lead to changes in the protein and cause disease.  Transcription is the process by which the DNA sequence of a gene is copied into mRNA by RNA polymerase, and it is the first step of gene expression.  Gene expression is at least partially controlled by promoters and transcription factors that recruit RNA polymerase to a gene.  The mRNA transcripts are processed prior to translation.  Translation is the process of protein synthesis by the ribosome using the sequence information in mRNA.  During translation, the ribosome matches the codon sequence of the mRNA with the anticodon of the corresponding tRNA to ensure the correct amino acid is added to the protein. Amino acids are added to the growing protein with peptide bonds. The last chapter discussed DNA and RNA - the nucleic acids that store and transmit information in a cell. Much of the information stored in DNA is organized into discrete units of heredity known as genes. A gene is a defined segment of DNA that encodes the sequence instructions for a particular product, usually a protein. This chapter will explore how genes are transcribed into mRNA and translated into protein. NOTE: DNA AND RNA TRANSCRIPTION PROCESS: NONCODING STRAND (TEMPLATE) – IS COMPLEMENTARY; AND ANTIPARALEL (MEANING ONE GOES 5 TO 3 & OTHER GOES 3 TO 5), PLUS THEY FORM REGULAR BASE PAIRS. NOTE: CODING STRAND (NONTEMPLATE) IS NOT USED TO TRANSCRIPT. SO IT WILL BE NEARLY IDENTICAL TO THE MRNA STRAND…. EXCEPT FOR THE USE OF “T” IN DNA AND “U” IN RNA.