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Chapter 17: From Gene to Protein

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1 Chapter 17: From Gene to Protein
Gene: A segment of DNA that specifies the amino acid sequence of a polypeptide DNA does not directly control protein synthesis, instead its information is transcribed into RNA

2 Overview: The Flow of Genetic Information
The information content of DNA Is in the form of specific sequences of nucleotides along the DNA strands

3 Genes specify proteins via transcription and translation
The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins The process by which DNA directs protein synthesis is called gene expression Includes two stages, called transcription and translation The Central Dogma of Molecular Genetics: There are 3 major classes of genetic biopolymers: DNA and RNA (both nucleic acids), and protein.

4 One Gene, One Enzyme hypothesis
Synthesis of all substances in living things is dictated by enzymes Remember that enzymes are proteins whose 1' structure (sequence of linked amino acids) are coded for by DNA base triplets. Beadle and Tatum experiments (1941) Purpose: "to determine if and how genes control known biochemical reaction" Work with red bread mold Neurospora crassa to find “nutritional mutants” Used radiation to create “auxotrophs”, organisms, such as a strain of bacteria, that have lost the ability to synthesize certain substances required for its growth and metabolism as the result of mutational changes.

5 Beadle and Tatum’s experiment
X-ray  mutations  loss of enzyme  lack of an AA (ex. Arg.)  mold could only grow on arginine-supplemented media Beadle and Tatum proposed that a single gene (thru a single mutation) codes for a single specific enzyme = Nobel Prize (1958)

6 The Products of Gene Expression: A Developing Story
Beadle and Tatum developed the :"One Gene - One Enzyme"  correlation: Which states that the function of a gene is to dictate the production of a specific enzyme Later found out not necessarily true: only some proteins are enzymes.   It is also true of structural proteins, chains of polypeptides, or hormones.

7 Ribonucleic Acid Why would the cell want to have an intermediate between DNA and the proteins it encodes? The DNA can then stay pristine and protected, away from the caustic chemistry of the cytoplasm. Gene information can be amplified by having many copies of an RNA made from one copy of DNA. Regulation of gene expression can be effected by having specific controls at each element of the pathway between DNA and proteins. The more elements there are in the pathway, the more opportunities there are to control it in different circumstances.

8 24.2 Gene Expression RNA (ribonucleic acid)

9 24.2 Gene Expression Three Classes of RNA Messenger RNA (mRNA)
Takes a message from DNA to the ribosomes strand Ribosomal RNA (rRNA) Makes up ribosomes (along with proteins) globular Transfer RNA (tRNA) Transfers amino acids to ribosomes Hairpin shape

10 24.2 Gene Expression Gene Expression Requires Two Steps: Transcription
Is the synthesis of RNA under the direction of DNA Produces messenger RNA (mRNA) Translation Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA Occurs on ribosomes

11 24.2 Gene Expression Transcription Messenger RNA (mRNA)
During transcription, a segment of the DNA serves as a template for the production of an RNA molecule Messenger RNA (mRNA) RNA polymerase (enzyme) binds to a promoter (“start” sequence) DNA helix is opened so complementary base pairing can occur RNA polymerase joins new RNA nucleotides in a sequence complementary to that on the DNA, in a 5’ to 3’ direction

12 Transcription of DNA to form mRNA

13 Messenger RNA mRNA - of the 64 possible 3-base combinations:
61 code for the twenty different amino acids 3 code for "stop"; i.e. chain termination Specific nucleotide sequences call for “start” of transcription (usually  AUG = methionine) = PROMOTOR sequence “stop” of mRNA synthesis = TERMINATION sequence (UAA, UGA, UAG) Finished mRNA strands are ~500-10,000 nucleotides long

14 Cracking the Code A codon in messenger RNA
Is either translated into an amino acid or serves as a translational stop signal Figure 17.5 Second mRNA base U C A G UUU UUC UUA UUG CUU CUC CUA CUG AUU AUC AUA AUG GUU GUC GUA GUG Met or start Phe Leu lle Val UCU UCC UCA UCG CCU CCC CCA CCG ACU ACC ACA ACG GCU GCC GCA GCG Ser Pro Thr Ala UAU UAC UGU UGC Tyr Cys CAU CAC CAA CAG CGU CGC CGA CGG AAU AAC AAA AAG AGU AGC AGA AGG GAU GAC GAA GAG GGU GGC GGA GGG UGG UAA UAG Stop UGA Trp His Gln Asn Lys Asp Arg Gly First mRNA base (5 end) Third mRNA base (3 end) Glu

15 During transcription The gene determines the sequence of bases along the length of an mRNA molecule Figure 17.4 DNA molecule Gene 1 Gene 2 Gene 3 DNA strand (template) TRANSCRIPTION mRNA Protein TRANSLATION Amino acid A C G T U Trp Phe Gly Ser Codon 3 5 The Process of Transcription

16 transfer RNA Small, ~80 nucleotides long.  tRNA exists as a single-stranded molecule. However, regions of double helix can form where there is some base pair complementation (U and A , G and C), resulting in hairpin loops. The RNA molecule with its hairpin loops is said to have a secondary structure. It can bind an amino acid at one end, and mRNA (anticodon) at the other end. It acts as an adaptor to carry the amino acid elements of a protein to the appropriate place as coded for by the mRNA codon (complementary). The "Wobble Phenomenon": There are only 40 different types of t-RNA and 64 codons. This means that some of the t-RNA can pair up with several different codons. This can occur because there is some third base “flexibility”.

17 Transfer RNA: Amino Acid Carrier

18 rRNA Ribosomal RNA is the most abundant type of RNA in cells
Ribosomes: comprised of subunits 2/3 RNA, 1/3 protein Two populations of ribosomes are evident in cells, Free and bound Free ribosomes in the cytosol initiate the synthesis of all proteins

19 The ribosome has three binding sites for tRNA
The P site The A site The E site P site (Peptidyl-tRNA binding site) E site (Exit site) mRNA binding site A site (Aminoacyl- tRNA binding site) Large subunit Small Schematic model showing binding sites. A ribosome has an mRNA binding site and three tRNA binding sites, known as the A, P, and E sites. This schematic ribosome will appear in later diagrams. (b) E P A Figure 17.16b

20 Translation (Building a polypeptide) requires Three Steps:
Initiation (requires energy) Elongation (requires energy) Termination Animation: How Translation Works. Amino end Growing polypeptide Next amino acid to be added to polypeptide chain tRNA mRNA Codons 3 5 Schematic model with mRNA and tRNA. A tRNA fits into a binding site when its anticodon base-pairs with an mRNA codon. The P site holds the tRNA attached to the growing polypeptide. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. Discharged tRNA leaves via the E site. (c)

21 Proteins: A review of structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H3N+ COO– a. primary structure C O C C N H N H C R O O C C C R C C C N O H H C H R CH N N C b (beta) sheet = pleated sheet O C N C C CH R C R O O C O H N H C C R N CH R O H N H N H C R R R O O C O C C C N R CH C O C N H C N H H H R CH R N N C H O C C N O C O R O C H N H CH O C N CH R C N R CH (alpha) helix b. secondary structure c. tertiary structure

22 Concept 17.4: Translation is the RNA-directed synthesis of a polypeptide: a closer look
Narrated animation: Protein Synthesis (with quiz) Interactive practice: Transcribe & Translate a Gene

23 Polyribosomes Several ribosomes may move along the same mRNA
Multiple copies of a polypeptide may be made The entire complex is called a polyribosome Figure 17.20a, b Growing polypeptides Completed polypeptide Incoming ribosomal subunits Start of mRNA (5 end) End of (3 end) Polyribosome An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes. (a) Ribosomes This micrograph shows a large polyribosome in a prokaryotic cell (TEM). 0.1 µm (b)

24 Overview of Gene Expression
Simple Gene Expression animation Detailed Protein Synthesis animation

25 Summary of Gene Expression

26 Regulation of gene expression
Genes are activated in some cells, but not others Genes can be active some of the time, but not others The mechanics of the “on/off” switch for genes was first identified in bacteria. 1965 Nobel Prize in Medicine François Jacob, Jacques Monod and André Lwoff. This operon enables the metabolism of lactose in Escherichia coli Animation of the lac operon

27 Regulation of Gene Expression in Eukaryotes
Animation: 4 levels: 1. Transcriptional control (nucleus): e.g. chromatin density and transcription factors 2. Posttranscriptional control (nucleus) e.g. mRNA processing 3. Translational control (cytoplasm) e.g. differential ability of mRNA to bind ribosomes 4. Posttranslational control (cytoplasm) e.g. changes to the protein to make it functional

28 Regulation of gene expression
Transcriptional control (nucleus): e.g. chromatin density and transcription factors Euchromatin: Loosely packed form of DNA; genes are transcibed Heterochromatin: tightly packed form of DNA; genes are “silenced” A transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes.

29 Transcription factors in Prokaryotes
Induction Animation: The lac operon induction Repression Animation: The trp operon Transcription factors in Eukaryotes, animation/quiz

30 Posttranscriptional control (nucleus) Processing of mRNA
After Transcription Primary “Pre-”mRNA must be modified into mature mRNA Introns are intragene segments (often, junk) Exons are the portion of a gene that is expressed Intron sequences are removed, and a poly-A tail is added Ribozyme splices exon segments together Eukaryotic mRNA modification: RNA splicing animation

31 mRNA Processing pre-RNA must be modified before translation

32 The Functional and Evolutionary Importance of Introns
The presence of introns Allows for alternative RNA splicing Additional animations of RNA processing: Processing of Gene Information: Prokaryotes –vs- Eukaryotes: How Spliceosomes Process RNA:

33 Transposons “jumping genes”
Sections of DNA that can move to new locations and disrupt gene sequences Animation See Barbara McClintock Chromosome 11 flyover

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