New FA Biochem 1
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| What does it mean for genetic code to be commaless? | Read from a fixed starting point as a continuous sequence of bases
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| What does it mean for genetic code to be non-overlapping? | Read from a fixed starting point
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| What does it mean for genetic code to be universal? | Genetic code is conserved throughout evolution
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| What are the properties of the genetic code? | 1. Unambiguous. 2. Degenerate/redundant. 3. Commaless/nonoverlapping 4. Universal
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| When is genetic code not commaless/nonoverlapping? | In some viruses
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| What are exceptions to universality of genetic code? | 1. Mitochondria 2. Archaebacteria 3. Mycoplasma 4. Some yeasts
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| Name that mutation: Same amino acid, often with a base change in 3rd position of codon | Silent mutation
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| What kind of mutation is called: silent | Same amino acid, often with a base change in 3rd position of codon
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| What mutation is masked by tRNA wobble? | Silent mutations
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| Name that mutation: Changed amino acid whose structure is dissimilar to proper amino acid | Missense mutation (not conservative)
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| Name that mutation: Changed amino acid whose structure is similar to proper amino acid | Conservative missense mutation
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| What kind of mutation is called: missense | Amino acid is changed. If the structure of the new amino acid is similar to the original, it is called conservative.
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| Name that mutation: Change resulting in early stop codon | Nonsense mutation (Mnemonic: Stop the nonsense!)
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| What kind of mutation is called: nonsense | Change resulting in early stop codon (Mnemonic: Stop the nonsense!)
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| Name that mutation: change resulting in misreading of all nucleotides downstream, usually resulting in a truncated protein | Frame shift mutation
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| What kind of mutation is called: frameshift | change resulting in misreading of all nucleotides downstream, usually resulting in a truncated protein
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| Mutations ordered by decreasing severity of damage | 1. Nonsense 2. Missense 3. Silent
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| Eukaryotic genome: single/multiple origins of replication | multiple
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| Prokaryotic genome: single/multiple origins of replication | single
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| Eukaryotic genome: Trigger for replication | Consensus sequence of AT-rich base pairs
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| Prokaryotic genome: Describe DNA replication | Continuous bidirectional DNA synthesis on leading strand and discontinuous (Okazaki fragments) on lagging strand
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| Enzyme function: DNA topoisomerases | Create a nick in the helix to relieve supercoils
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| DNA Topoisomerase I: Mechanism | cuts one strand, passes the other through it then reanneals the cut strand
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| DNA Topoisomerase II: Mechanism | cuts both strands, and passes an unbroken double strand through it then reanneals the cut strand
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| Enzyme function: Primase | Makes an RNA primer on which DNA polymerase III can initiate replication
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| DNA polymerase III: Mechanism | 1. Adds deoxynucleotides to the 3' end until it reaches primer of preceding fragment 2. 3' to 5' exonuclease activity "proofreads" each added nucleotide
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| DNA polymerase III: Which direction does it read? | 3' to 5'
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| DNA polymerase III: Which direction does it write? | 5' to 3'
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| DNA polymerase III: Which direction does it proofread? | 3' to 5'
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| Enzyme function: DNA polymerase III | Elongates the chain
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| Enzyme function: DNA polymerase I | Degrades RNA primer and fills in the gap with DNA
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| DNA polymerase I: Which direction does it read? | 3' to 5'
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| DNA polymerase I: Which direction does it write? | 5' to 3'
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| DNA polymerase I: Which direction does it proofread? | 5' to 3'
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| Enzyme function: DNA helicase | Separates the two strands of DNA into single strands allowing for replication to occur. The position of these separated strands is called the replication fork.
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| Types of DNA repair - Single stranded: | 1. Nucleotide excision repair 2. Base excision repair 3. Mismatch Repair
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| Types of DNA repair - Double stranded: | 1. Nonhomologous end joining
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| Nucleotide excision repair: Mechanism | 1. Specific endonucleases release the oligonucleotide containing damaged bases 2. DNA polymerase and ligase fill and reseal the gap, respectively
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| In what condition is nucleotide excision repair mutated? | Xeroderma pigmentosa (dry skin with melanoma and other cancers)
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| Base excision repair: Mechanism | 1. Specific glycosylases recognize and remove damaged bases 2. AP endonuclease cuts DNA at apyrimidinic site 3. Empty sugar is removed 4. Gap is refilled and resealed
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| Mismatch repair: Mechanism | 1. Unmethylated, newly synthesized string is recognized 2. Mismatched nucleotides are removed 3. Gap is refilled and resealed
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| In what condition is mismatch excision repair mutated? | Hereditary Nonpolyposis Colon Cancer
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| Nonhomologous end joining: Mechanism | Brings together two ends of DNA fragments (no requirement for homology)
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| Define operator of gene expression | Site where repressors bind
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