1. 8.2 Structure of DNA DNA Protein Synthesis Review: Topic 7.1 – 7.4

2. 8.2 Structure of DNA 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 C 5 phosphate group and the C 3 hydroxyl group Hence one nucleotide strand runs ________ 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines OH CH 2 O 4 5 3 2 1 PO 4 N base ribose nucleotide OH O 3 PO 4 base CH 2 O base O P O C O –O–O CH 2 1 2 4 5 1 2 3 3 4 5 5

3. 8.2 Structure of DNA 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 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines

4. 8.2 Structure of DNA 7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding between purines and pyrimidines

5. 8.2 Structure of DNA 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 7.1.2 Outline the structure of nucleosomes

6. 8.2 Structure of DNA 7.1.2 Outline the structure of nucleosomes

7. 8.2 Structure of DNA 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. 8.2 Structure of DNA 7.1.4 Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA

9. 8.2 Structure of DNA 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 exon = coding (expressed) sequence intron = noncoding (in between) sequence

10. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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 ATPGTP TTP CTP energy

13. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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 ____________ strand is 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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 eukaryotic DNA exon = coding (expressed) sequence intron = noncoding (inbetween) sequence primary mRNA transcript mature mRNA transcript pre-mRNA spliced mRNA ~10,000 bases ~1,000 bases

21. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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 5' 3' U U A C A G APE

24. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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

27. 8.2 Structure of DNA 7.4.5 Draw and label a diagram showing the structure of a peptide bond between two amino acids

28. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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. 8.2 Structure of DNA 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=1fiJupfbSpg&feature=related http://www.youtube.com/watch?v=41_Ne5mS2ls&feature=related http://www.youtube.com/watch?v=TfYf_rPWUdY&feature=relatedhttp://www.youtube.com/watch?v=TfYf_rPWUdY&feature=related (translation) http://www.youtube.com/watch?v=SMtWvDbfHLo&feature=relmfuhttp://www.youtube.com/watch?v=SMtWvDbfHLo&feature=relmfu (transcription) http://www.youtube.com/watch?v=gbSIBhFwQ4s&feature=relmfuhttp://www.youtube.com/watch?v=gbSIBhFwQ4s&feature=relmfu (How DNA is packaged) http://www.youtube.com/watch?v=I9ArIJWYZHI&feature=relmfuhttp://www.youtube.com/watch?v=I9ArIJWYZHI&feature=relmfu (DNA replication) http://www.youtube.com/watch?v=Kzgnl5-8WAk&feature=relatedhttp://www.youtube.com/watch?v=Kzgnl5-8WAk&feature=related (replication, transcription, translation)