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DNA Protein Synthesis Review: Topic 7.1 – 7.4

Explore the structure of DNA, nucleosomes, gene composition, DNA replication in prokaryotes, role of enzymes, and more. Learn about the importance of nucleosomes and the process of DNA supercoiling. Understand the difference between introns and exons in DNA. This review covers key concepts in genetics and molecular biology.

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DNA Protein Synthesis Review: Topic 7.1 – 7.4

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  1. DNA Protein Synthesis Review: Topic 7.1 – 7.4

  2. 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines 5 PO4 nucleotide PO4 • The carbon atoms in deoxyribose are numbered, with the nitrogenous bases attach to ___ and the phosphate group is attached to ___. • Nucleotides are joined by a covalent ______________ bond between the C5 phosphate group and the C3 hydroxyl group • Hence one nucleotide strand runs ________ base CH2 5 O 4 1 C N base 3 2 O P –O O 5 CH2 O O base CH2 5 1 4 O ribose 4 1 2 3 3 OH 2 OH 3

  3. 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines • Adenine (A) and thymine (T) share ___ hydrogen bonds • Guanine (G) and cytosine (C) share ___ hydrogen bonds • In order for the bases to associate (i.e. face each other), one strand must run ____________to the other (this antiparallel strand runs _______)  • Double stranded DNA forms a double helix, with 10 nucleotides per turn and the structure containing both major and minor grooves

  4. 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines

  5. 7.1.2  Outline the structure of nucleosomes • The DNA double helix contains major and minor grooves • on its outer diameter, which expose chemical groups that • can form hydrogen bonds • The DNA of eukaryotes associates with proteins called • _____________. • DNA is wound around an octamer of histones (146 bases • and 1.65 turns of the helix per octamer) • The octamer and DNA combination is secured to a H1 • histone, forming a nucleosome 

  6. 7.1.2  Outline the structure of nucleosomes

  7. 7.1.3  State that nucleosomes help to supercoil DNA and help to regulate transcription • Nucleosomes serve two main functions: • They protect DNA from damage • They allow long lengths of DNA to be packaged (supercoiled) • for mobility during mitosis / meiosis • When supercoiled, DNA is not accessible for transcription • Cells will have some segments of DNA permanently • supercoiled (heterochromatin) and these segments will differ • between different cell types

  8. 7.1.4  Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA

  9. intron = noncoding (in between) sequence exon = coding (expressed) sequence 7.1.5  State that eukaryotic genes contain introns and exons • Intron:  A non-coding sequence of DNA within a gene • (intervening sequence) that is cut out by enzymes • when RNA is made into mature mRNA • Exon: The part of the gene which codes for a protein • (expressing sequence) • Eukaryotic DNA contains introns but prokaryotic DNA • does not eukaryotic DNA

  10. 7.2.1  State that DNA replication occurs in a 5' - 3' direction • DNA replication is ________________, meaning that a new • strand is synthesized from an original template strand • DNA replication occurs in a 5' - 3' direction, in that new • nucleotides are added to the ________________such that • the strand grows from the 3' end • This means that the DNA polymerase enzyme responsible • for adding new nucleotides moves along the original • template strand in a ________direction

  11. 7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates • DNA replication is semi-conservative and occurs during the • ________of interphase • _________ unwinds and separates the double stranded DNA • by breaking the hydrogen bonds between base pairs • ________________ synthesizes a short RNA primer on each • template strand to provide an attachment and initiation point • for DNA polymerase III

  12. 7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates • ___________________ adds deoxynucleoside triphosphates  • (dNTPs) to the 3' end of the polynucleotide chain, synthesizing • in a 5' - 3' direction • The dNTPs pair up opposite their complementary base partner • (A-T, G-C) • As the dNTPs join with the DNA chain, two phosphates are • broken off, releasing the energy needed to form a • phosphodiester bond energy energy TTP ATP GTP CTP

  13. 7.2.2  Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates • Synthesis is continuous on the strand moving towards the • replication fork (_______________)  • Synthesis is discontinuous on the strand moving away from the • replication fork (_______________) leading to the formation • of ____________________ • ______________removes the RNA primers and replaces them • with DNA • ____________ joins the Okazaki fragments together to create a • continuous strand

  14. 7.2.3  State that DNA replication is initiated at many points in eukaryotic chromosomes • Because eukaryotic genomes are (typically) much larger than • prokaryotic genomes, DNA replication is initiated at many • points simultaneously in order to limit the time required for • DNA replication to occur • The specific sites at which DNA unwinding and initiation of • replication occurs are called origins of replication and form • replication bubbles • As replication bubbles expand in both directions, they • eventually fuse together, and generate two separate semi- • conservative double strands of DNA

  15. 7.3.1  State that transcription is carried out in a 5' - 3' direction • Transcription is carried out in a _______direction (of the new • RNA strand)

  16. 7.3.2  Distinguish between the sense and antisense strands of DNA • DNA consists of two polynucleotide strands, only one of which • is transcribed into RNA • The ____________ strandis transcribed into RNA • - sequence will be complementary to the RNA sequence • and will be the "DNA version" of the tRNA anticodon • sequence  • The _________ strand is not transcribed into RNA • - Its sequence will be the "DNA version" of the RNA • sequence (identical except for T instead of U)

  17. 7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator • A gene is a sequence of DNA which is transcribed into RNA • and contain three main parts: • __________:  Responsible for the initiation of transcription (in • prokaryotes, a number of genes may be regulated by a single • promoter - this is an operon) • _______________: The sequence of DNA that is actually • transcribed (may contain introns in eukaryotes) • __________: Sequence that serves to terminate transcription • (mechanism of termination differs between prokaryotes and • eukaryotes)

  18. 7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator • Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence and involves a number of steps: • RNA polymerase binds to the promoter and causes the • unwinding and separation of the DNA strands • Nucleoside triphosphates (NTPs) bind to their • complementary bases on the antisense strand (uracil pairs • with adenine, cytosine pairs with guanine) • RNA polymerase covalently binds the NTPs together in a • reaction that involves the release of two phosphates to gain • the required energy

  19. 7.3.3  Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator • ________________ synthesizes an RNA strand in a 5' - 3' • direction until it reaches the terminator • At the terminator, RNA polymerase and the newly formed • RNA strand both detach from the antisense template, and the • DNA rewinds • Many RNA polymerase enzymes can transcribe a DNA • sequence sequentially, producing a large number of • transcripts • Post-transcriptional modification is necessary in eukaryotes

  20. intron = noncoding (inbetween) sequence exon = coding (expressed) sequence 7.3.4  State that eukaryotic RNA needs the removal of introns to form mature mRNA • Euakaryotic genes may contain non-coding sequences • called _________ that need to be removed before mature • mRNA is formed • The process by which introns are removed is called • ____________ • The removal of exons (alternative splicing) can generate • different mRNA transcripts (and different polypeptides) • from a single gene ~10,000 bases eukaryotic DNA pre-mRNA primary mRNA transcript ~1,000 bases mature mRNA transcript spliced mRNA

  21. 7.4.1  Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA using ATP for energy • Each different tRNA molecule has a unique shape and • chemical composition that is recognized by a specific tRNA- • activating enzyme • The enzyme (____________________________) • first binds the amino acid to a molecule • of ATP (to form an  amino acid-AMP • complex linked by a high energy bond)

  22. 7.4.1  Explain that each tRNA molecule is recognised by a tRNA-activating enzyme that binds a specific amino acid to the tRNA using ATP for energy • The amino acid is then transferred to • the _______ of the appropriate tRNA, • attaching to a terminal CCA sequence • on the acceptor stem and releasing the • AMP molecule • The tRNA molecule with an amino acid • attached is thus said to be ‘________' and • is now capable of participating in • translation • The energy in the bond linking the • tRNA molecule to the amino acid • will be used in translation to form a • _____________ between adjacent amino acids

  23. 7.4.2  Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites • Ribosomes are made of protein (for stability) and _________ • ____________ (for catalytic activity) • They consist of two subunits: • - The small subunit contains an mRNA binding site • The large subunit contains three tRNA binding sites - an • aminacyl (A) site, a peptidyl (P) site and an exit (E) site Met C A U 5' G U A 3' E P A

  24. 7.4.2  Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites • Ribosomes can be either found freely in the cytosol or bound • to the rough ER (in eukaryotes) • Ribosomes differ in size in eukaryotes and prokaryotes • (eukaryotes = 80S ; prokaryotes = 70S) • E

  25. 7.4.3  State that translation consists of initiation, elongation, translocation and termination • Translation occurs in four main steps: • Initiation:  Involves the assembly of an active ribosomal • complex • Elongation: New amino acids are brought to the ribosome • according to the codon sequence • Translocation:  Amino acids are translocated to a growing • polypeptide chain • Termination: At certain "stop" codons, translation is ended • and the polypeptide is released • E

  26. 7.4.4  State that translation occurs in a 5' - 3' direction • The start codon (_____) is located at the 5' end of the mRNA • sequence and the ribosome moves along it in the 3' direction • Hence translation occurs in a ________ direction release factor Leu Val Ser Met Met Ala Leu Met Met Leu Leu Trp tRNA C A G C G A C C C A A G A G C U A C C A U A U U A U G A A 5' 5' A A 5' C U U 5' A A G G A G U U G U C U U U G C A C U 3' G G U A A U A A C C mRNA 3' 3' 3' U G G U A A 3' E P A

  27. 7.4.5  Draw and label a diagram showing the structure of a peptide bond between two amino acids

  28. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons • Pre-Initiation: • Specific tRNA-activating enzymes catalyze the attachment • of amino acids to tRNA molecules, using ATP for energy • Initiation: • The small ribosomal subunit binds to the 5' end of mRNA • and moves along it until it reaches the start codon (AUG) • Next, the appropriate tRNA molecule binds to the codon • via its anticodon (according to complementary base pairing) • Finally, the large ribosomal subunit aligns • itself to the tRNA molecule at its P-site • and forms a complex with the small • ribosomal subunit

  29. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons • Elongation: • A second tRNA molecule pairs with the next codon in • the ribosomal A-site • The amino acid in the P-site is covalently attached via a • peptide bond to the amino acid in the A-site

  30. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons • Translocation: • The ribosome moves along one codon position, the • deacylated tRNA moves into the E-site and is released, • while the tRNA bearing the dipeptide moves into the P- site • Another tRNA molecules attaches to the next codon in the • newly emptied A-site and the process is repeated • The ribosome moves along the mRNA sequence in a 5' - 3' • direction, synthesizing a polypeptide chain • Multiple ribosomes can translate a single mRNA sequence • simultaneously (forming polysomes)

  31. 7.4.6  Explain the process of translation, including ribosomes, polysomes, start codons and stop codons • Termination: • Elongation and translocation continue until the ribosome • reaches a stop codon • These codons do not code for any amino acids and instead • signal for translation to stop • The polypeptide is released and the ribosome disassembles • back into subunits • The polypeptide may undergo post-translational modification • prior to becoming a functional protein

  32. 7.4.7  State that free ribosomes synthesis proteins for use primarily within the cell, and that bound ribosomes synthesis proteins primarily for secretion or for lysosomes • Ribosomes floating freely in the cytosol produce proteins for • use within the cell • Ribosomes attached to the rough ER are primarily involved in • producing proteins to be exported from the cell or used in the • lysosome • These proteins contain a signal recognition peptide on their • nascent polypeptide chains which direct the associated • ribosome to the rough ER

  33. 7.4.7  State that free ribosomes synthesis proteins for use primarily within the cell, and that bound ribosomes synthesis proteins primarily for secretion or for lysosomes http://www.youtube.com/watch?v=gbSIBhFwQ4s&feature=relmfu (How DNA is packaged) http://www.youtube.com/watch?v=SMtWvDbfHLo&feature=relmfu (transcription) http://www.youtube.com/watch?v=TfYf_rPWUdY&feature=related (translation) http://www.youtube.com/watch?v=I9ArIJWYZHI&feature=relmfu (DNA replication) http://www.youtube.com/watch?v=Kzgnl5-8WAk&feature=related (replication, transcription, translation) http://www.youtube.com/watch?v=1fiJupfbSpg&feature=related http://www.youtube.com/watch?v=41_Ne5mS2ls&feature=related

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