MOLEC BIO
Terms
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copy deck
- In what fashion are the strands of DNA bonded?
- H-bonded, Antiparallel--5' end of one chain w/ 3' end of other chain
- What common protein structure depends on antiparallel H-bonding?
- B-pleated sheet
- How many bonds are GC/AT pairs are held together by?
-
GC 3 H-bonds
AT 2 H-bonds - What is hybridization?
- Hybridization (aka annealing) is the binding of two complementary strands of DNA into a double-stranded structure
- What is denaturation?
- aka melting, the separation of DNA strands
- If attached methyl groups to all the acidic phosphate oxygens along the length of DNA double helix, would the chain have higher/lower than normal Temp to denature DNA?
- Higher than normal Temp because the lack of electrostatic repulsion b/t methyl ester backbones (that is present w/electrically repelling phosphate groups)
- What sort of bonds stabilize the double helix?
- hydrophobic interactions
- When a purine is bound to a pyrimidine, what happens to the polar nature of the individual bases? Does this result in hydro-philic or -phobic interactions between the bases?
- Polar nature disappears because charge dipoles are occupied in H-bonds, causing hydroPHOBIC interactions between the bases
- The DNA helix pattern completes a full turn in how many angstroms?
- 1 complete turn every 34 angstroms (every 10 base pairs)
- The bases of a DNA molecule are # angstroms apart from one another?
- 3.4 angstroms
- What is the width of the DNA helix?
- 20 angstroms wide
- 1 Angstrom= ___ m
- 10^ -10
- # Chromosomes in prokaryotes/eukaryotes?
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Eukaryotes/humans: 46 chromosomes
Prokaryotes: 1 circular chromosome - Size comparison of bacterial/human genome
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human genome: 10^ 9 bps
bacterial genome: 10^ 6 bps - What does DNA gyrase do?
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It uses ATP to twist the circular chromosome in prokaryotes, so as to make it more compact--breaks the DNA and twists the 2 sides of circle around each other
-creates more twists in an already twisted DNA=super coils - For denser packaging of DNA, eukaryotes use...
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histones (globular proteins) around which DNA is wrapped
-nucleosomes= bead-like groups of 8 histones around which DNA is wrapped - The area between nucleosomes is called...
- linker DNA
- What is fully packed DNA called? When does this condense into a chromosome?
- chromatin,
- Based on the chemical composition of the DNA, should histones be basic or acidic?
- basic, b/c must be attracted to acidic exterior of DNA double helix
- What is the flow equation for the structure of DNA in the nucleus?
- DEOXYRIBOSE--> add base-->NUCLEOSIDE--> add 3 phosphates-->NUCLEOTIDE-->polymerize (add nucleosides together) with loss of 2 phosphates--> OLIGONUCLEOTIDE-->continues polymerization--> polynucleotide-->two complete chains H-bond in antiparallel orientation--> ds DNA CHAIN--> coiling occurs --> ds HELIX --> wrap around histones --> NUCLEOSOMES--> complete packaging --> CHROMATIN
- # of "Letters" in DNA/ proteins?
- 4 letters in DNA, 20 letters in proteins
- What did Oswald Avery discover?
- Avery showed that DNA was the active agent in bacterial transformation, i.e., pure DNA from one type of E. Coli bacteria could transform E. Coli of another type--causing it to acquire the genetic nature of first type
- Hershey and Chase
- proved that DNA was the active chemical in the infection of E. Coli bacteria by bacteriophage T2
- Process of protein synthesis from DNA
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1) info contained in DNA is copied into a messenger
2) mRNA travels to cytoplasm where it encounters ribosome & other components of protein synthesis
3) ribosome synthesizes polypeptides according to DNA's original orders - What is a codon?
- A codon is a 3 letter word, which encodes for a particular amino acid--4letters of DNS^3 (# letters in codon) = 64 possible codons, which specify the 20 aa's (more than one codon for many of the aa's)
- How many codons specify amino acids?
- 61 codons specify amino acids; 3 codons are stop codons
- What are stop codons?
- aka nonsense codons, don't code for any amino acid
- Wobble hypothesis
- Switching the 3rd nucleotide in the majority of codons will have NO EFFECT
- Why is the genetic code said to be degenerate?
- Because it has SYNONYMS (two or more codons coding for the same amino acid)
- What is intercalating?
- When compounds that look like purines and pyrimidines (with large flat aromatic ring structures) cause mutations by inserting themselves between base pairs
- 3 Kinds of Mutations
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1) Point mutations
2) Insertion mutations
3) Deletion mutations - What is a point mutation? What are their 2 classifications?
-
Single base pair substitutions.
1) TRANSITIONS- substitution of a pyrimidine for another pyrimidine or substitution of a purine for another purine)
2) TRANSVERSIONS: substitution of a purine for a pyrimidine or vice versa) - Point mutations that cause one amino acid to replace another amino acid?
- missense mutations
- Point mutations that cause a stop codon to replace a regular codon?
- nonsense mutations
- A missense mutation that causes little change in structure and function of the gene product is called...
- a conservative mutation
- Point mutations in genes that do not encode protein or alterations in the 3rd nucleotide of some codons=
- silent mutations
- Insertion and deletion cause:
- A shift in the reading frame
- Frameshift mutations
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due to insertion or deletion, causes the whole piece of DNA to be read differently
-NOT caused by inserting or deleting a whole or multiple codons - Is DNA replication semiconservative, conservative, or dispersive? Who tested this?
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Messelson and Stahl studied DNA replication to determine which it was.
ANSWER: Semiconservative
Not conservative: ds-DNA remains as is while the entirely new ds genome created
Not dispersive: both copies of genomes=composed of scattered pieces of new/old DNA - What is the function of DNA polymerase?
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-catalyzes the elongation of the daughter strand using the parental template
-checks each new nucleotide to make sure it forms a correct base-pair before it is incorporated in the growing polymer - Polymerization occurs in which direction? What acts as the Nu- to displace pyrophosphate?
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5' TO 3' !!!
The 3' hydroxyl group acts as the Nu- - What are two things that DNA Polymerase requires?
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-a template
-a primer - The template is read...
- 3' to 5' because must end up antiparallel, and replicated strand is being constructed 5' to 3'
- What is the primer and what is its purpose?
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Primer- a small chain of RNA produced by RNA polymerase (primase)
-Purpose: begins DNA replication by creating a small RNA primer that DNA polymerase can elongate by adding deoxyribonuceotides to the existing ribonucleotide primer - What do topoisomerases do? How do the single-strand binding proteins help?
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Topoisomerases cut one or both of the strands and unwrap the helix, releasing the excess tension created by helicase
-ss binding proteins help keep the strands separated - What are replication forks?
- Areas where the parental double helix continues to unwind