Nucleic acids and protein synthesis

THE FUNCTIONS OF DNA Nucleic acids and protein synthesis The full name of DNA is deoxyribonucleic acid. Every nucleotide has the same sugar molecule and phosphate group, but each nucleotide contains one of four nitrogen bases. DNA has three roles/purposes/functions: 1. Storing information genes are segments of DNA that carry messages to make proteins. 2. Copying information so that when cells divide, all cells get a complete copy of the genetic material. 3. Transmitting information DNA is passed from parents to offspring. Nucleotides are the building blocks of DNA. Each nucleotide contains a phosphate group, a five carbon sugar, and a nitrogen base. The five carbon sugar is called deoxyribose. Covalent bonds hold the sugar of one nucleotide to the phosphate group of another nucleotide to form chains. CHARGAFF S RULE The four nitrogen bases that make up DNA are adenine, thymine, guanine, and cytosine. Adenine and Guanine are called purines. Purines have 2 rings of carbon and nitrogen atoms. Thymine and Cytosine are called pyrimidines. Pyrimidines have a single ring of carbon and nitrogen atoms. 1949-Erwin Chargaff showed that in DNA, the number of adenines equal the number of thymines, AND the number of cytosines equal the number of guanines. However, the amount of each nucleotide was not the same among different organisms. Base-pairing / Chargaff s rule: Adenine will always pair with Thymine; A and T are complimentary. Cytosine will always pair with Guanine; C and G are complimentary. THE DNA MOLECULE IS A Rosalind Franklin and Maurice Wilkins used X ray diffraction to take first picture of DNA. Determined a two dimensional picture of DNA s structure. James Watson and Francis Crick 3-D shape of DNA being 2 strands of nucleotides that form a spiral staircase or double helix. THE DNA MOLECULE IS A DNA is a twisted ladder with alternating patterns of phosphates and sugars making the sides of the ladder. Each rung is a purine/ pyrimidine pair held together by hydrogen bonds. 1

THE DNA MOLECULE IS A n The base pair rules tell us what the rungs can be, A and T or G and C. n Each strand of the double helix is complementary to each other; the sequence of 1 strand determines the sequence of the other. n The two strands of DNA in the double-helix are antiparallel they run in opposite directions. n DNA is double stranded base pairing allows for easy copying; one strand serves as a template for a new strand. n DNA replication the process of making a new DNA strand. n Occurs before cells divide. n Ensures that when cells divide, each cell produced has an entire copy of the organism s DNA. n DNA double helix is unzipped by an enzyme called a helicase. Helicase breaks hydrogen bonds linking the nitrogen bases. n Occurs at the replication forks of the double helix. n At the replication fork; an enzyme called DNA polymerase moves along the strands, reading the nitrogen base of each nucleotide, and adding the complementary nucleotide to the new strand. n Remember that A and T are complimentary; C and G are also complimentary. n Telomeres tips of chromosomes where DNA is hard to replicate. n Telomerase enzyme that adds repeated DNA sequences to the ends of the chromosomes to prevent loss of the telomere DNA during DNA replication. n The double-stranded DNA helix has a strand that runs 5-3 and one that runs 3 to 5. n DNA polymerase can only add new nucleotides to the 3 end of DNA! n This creates leading and lagging strands during DNA replication. n DNA ligase must use primers to copy DNA on the lagging strand. n Okazaki fragments n Watch minutes 2:49-8:20 in this video for more details: n http://www.youtube.com/watch?v=fbmo_rmxxlw n Replication in prokaryotes single circular chromosome; replication begins and proceeds from ONE location on the chromosome. Replication in eukaryotes many linear chromosomes; replication begins and proceeds from hundreds of locations on each chromosome. Gene segment of DNA that codes for a protein. n Cells transfer the information found within the genes on DNA into a set of working instructions for use in building proteins. n This working set of instructions of the gene is called ribonucleic acid or. n is a nucleic acid made of chains of nucleotides, just like DNA. n is a single strand of nucleotides; DNA is double stranded. n The sugar in is a 5 Carbon sugar called ribose; DNA s sugar is deoxyribose. n does not contain Thymine, but has replaced Thymine with the base Uracil. 2

DNA compared to How many strands? Nucleotide subunit Bases DNA 2 1 Deoxyribose sugar Thymine (T) Adenine (A) Guanine (G) Cytosine (C) T A G C Nitro -gen Base Phosphate Group Deoxyribose Sugar Phosphate Group Ribose sugar Uracil (U) Adenine (A) Guanine (G) Cytosine (C) Ribose Sugar Nitro -gen Base U A G C n Three forms of are messenger (m), transfer (t), and ribosomal (r). n All 3 s are responsible for processing the information in a gene into protein. The process of transferring the information in genes to proteins is called gene expression. THREE TYPES OF n m used as a blueprint or template for a protein; carries DNA s information from the nucleus to site of translation (ribosomes in cytoplasm). n t decodes m into amino acid sequences. n r part of a ribosome s structure (the other component of ribosomes is protein). n Gene expression occurs in 2 stages. n The first, transcription is where DNA is transferred to m. n The second stage; translation, is when the information in m is used to make protein. n Transcription takes place inside the nucleus. n Transcription begins when polymerase binds to the beginning of a gene on a region of DNA. n The region of DNA to which polymerase binds is called a promoter. Promoters are sequences of DNA that act as a start signal. n The polymerase begins to unzip and separate the double helix. n The polymerase uses only one of the DNA strands as a template for m The noncoding or complimentary strand is the template for m synthesis. n Follows the same base pairing rules as replication except Uracil is used in place of Thymine. n nucleotides are added one at a time in the active site of the polymerase. n DNA reforms the double helix following the Polymerase. n Transcription occurs at about 60 nucleotides per second. n Terminator - the stop signal in the sequence of DNA Polymerase detaches here. 3

n n Coding DNA: CTC TTG ATC ATG Non-coding/complimentary DNA: GAG AAC TAG TAC n : CUC UUG AUC AUG Post transcriptional m processing n editing - m must be processed, or prepared for the next phase of gene expression, translation. n Introns non-coding gene regions that are cut out of the molecule in the nucleus. n Exons expressed sequences of the molecule; codes for a protein. n The introns are cut out and the exons are spliced together to make a final m. Post transcriptional m processing n A protective cap and tail are then added before the m leaves the nucleus through one of the pores and heads to the cytoplasm where translation will occur on ribosomes. http://207.207.4.198/pub/flash/26/transmenu_s.swf THE GENETIC CODE n Instructions on m are written as a series of three nucleotide sequences called a codon. n Each codon (set of three nucleotides) corresponds to a certain amino acid or a stop signal. n 64 possible codon combinations. n Genetic code collection of codons of m, each of which directs the incorporation of a particular amino acid during protein synthesis. Codon Table START AND STOP CODONS n Start codon or initiator codon AUG; cues the start of translation by inserting a methionine. n Thus, all proteins begin with the amino acid methionine. n Translation proceeds until a stop codon is reached. n Stop codon triggers the end of translation. n Translation when ribosomes in the cytoplasm use the sequence of codons in m to assemble amino acids into polypeptide chains. n t is a single stranded folded into a compact shape with three loops. n One loop has a three nucleotide sequence (called an anticodon) that is complementary to one of the 64 codons. n Each t carries one amino acid. n t bonds with m at the codon/ anticodon site by hydrogen bonds. n Every t carries a particular amino acid that corresponds to the particular codon. n Once the amino acid has been added to the growing polypeptide chain, the t is released. n Many amino acids link to form peptides once a peptide is folded into its proper shape it is considered a protein. 4

Central Dogma n Central dogma of molecular biology information is transferred from DNA to to protein. n This allows gene expression, or DNA,, and proteins working together to put the genetic information contained in cells into action. - Prokaryotes n Prokaryotic gene expression is regulated by DNA binding proteins. n These regulatory proteins help switch genes on and off. n Operon group of prokaryotic genes regulated together. n Promoter DNA sequence where polymerase binds to begin transcription. n Operator DNA sequence where regulatory proteins can bind to repress transcription. n Eukaryotic gene expression is also regulated by DNA binding proteins, however, eukaryotes typically regulate individual genes, not groups of them. n TATA box short sequence of DNA that marks the beginning of a gene; used to help position polymerase. n Transcription factors proteins that help regulate gene expression by binding DNA promoter/enhancer sequences and blocking or activating transcription. n Promoter/enhancer sequences of DNA with binding sites for multiple transcription factors. n Not all genes are expressed in all eukaryotic cells. n Cell specialization all cells in multicellular organisms contain all of the organism s DNA, yet they only transcribe and translate part of it. n Ex. Liver cells only transcribe and translate liver specific genes while skin cells only transcribe and translate skin specific genes. n interference (i) used to regulate gene expression in eukaryotes. n During i, micros (mis) bind to transcribed m to block it from being translated into protein. n Differentiation when gene regulation allows eukaryotic cells to become specialized in structure and function. n Occurs during embryonic development. n Homeotic genes aka master control genes specific group of genes that controls the identity of body parts in embryos. n Homeobox genes code for transcription factors that activate other genes important for development and differentiation. n In flies, these are called Hox genes. n The environment also plays a role in the regulation of prokaryotic and eukaryotic gene expression. 5