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Biology 243 > Theme 1: DNA and Genetics (A,B,C) > Flashcards

Theme 1: DNA and Genetics (A,B,C) Flashcards

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1
Q

What is a gene?

A
  • The functional unit of heredity and variation
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2
Q

What’s a genome?

A
  • The entire DNA sequence of an organism
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3
Q

What is gene expression?

A
  • Involves “turning on a gene to produce RNA and therefore proteins (a coding gene)
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4
Q

What is protein expression?

A
  • The type and abundance of protiens in the cell.
  • Proteins ultimately determine the phenotype of the cell because they control every reaction in the cell
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5
Q

What are the different types of proteins?

A
  • Enzymes - catalyze the synthesis of biomolecules
  • Structural proteins - maintenance of cell shape
  • Signalling proteins - hormones and receptors
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6
Q

What is differential regulation?

A
  • Determines whether the expression of a certain gene or protein is high or not, helps contribute to variation within a species.
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7
Q

What are the types of strain that streptococcus pneumoniae contain?

A
  • Smooth strain (s-strain) - bacterium is surrounded by a polysaccharide (a sugar) capsule. The capsule protects s-strain from the immune system, thereby allowing infection (it’s virulent)
  • Rough strain (r-strain) - lacks polysaccharide capsule, cannot evade the immune system, therefore, non-virulent.
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8
Q

What did Griffith’s experiment involving mice help discover?

A
  • After treating mice with heat-killed virulent bacteria and alive but non-virulent bacteria, he discovered that there is some sort of transforming principle (soon to be discovered as DNA) that allowed the non-virulent form of the bacteria to be transformed into the virulent form, and therefore kill the mice regardless of the s-train being heat-killed.
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9
Q

What did the Avery, Macleod, and McCarthy experiments help discover? What were the experiments?

A
  • They were able to determine that DNA is the transforming principle found in cells, not RNA or protein.
  • They eliminated each type of molecule in the S cells and observed whether transformation of R cells into the S virulent form still occurs
  • The DNA molecule was absent when the transformation did not occur.
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10
Q

What are the two life cycles of a virus (bactriophage)?

A
  • The lytic cycle - massive reproduction of virus resulting in host cell lysis (the virulent cycle, the virus is released from the host cell). The viral DNA replicates separately from bacterial chromosome
  • Lysogenic cycle - replication of viral genome (the latent stage). The viral DNA is integrated into the bacterial chromosome
  • Lysogeny can switch to lytic cycle if viral DNA is excised from bacterial chromosome
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11
Q

What did the Hershey and Chase experiment help discover? What was the experiment?

A
  • Wanted to see whether the bacteriophage injects DNA or protein into E. coli.
  • They labelled bacteriophage DNA and proteins with radioactive isotopes and allowed infection of E. coli to occur. They separated attached bacteriophages and E. coli with a belnder
  • They discovered there were no proteins found in the E.coli cells, but they were found in the detached bacteriophage, which are not heritable
  • There was DNA in the E.coli cells, none was found in detached bacteriophages
  • The final experiment that determined DNA was the hereditary molecule
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12
Q

What three components make up a nucleic acid?

A
  • Consist of equal parts:
    1) Pentose sugar (ribose or deoxyribose)
    2) Nitrogenous base (adenine, guanine, cytosine, uracil, thymine)
    3) Phosphate group
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13
Q

How exactly do ribose and deoxyribose differ as molecules?

A
  • RNA has a hydroxy group bonded to the 2’ carbon while DNA only has a hydrogen atom (it’s missing an oxygen atom)
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14
Q

Which nitrogenous bases are purines and pyrimidines?

A
  • Purines - Adenine, guanine
  • Pyrimidine - Cytosine, thymine, uracil (RNA)
    *A purine must always be paired with a pyrimidine
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15
Q

What is a nucleoside composed of?

A
  • A molecule that includes a pentose sugar and a nitrogenous base
  • Deoxyribonucleosides - 2-deoxyribose sugar + purine/pyrimidine base
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16
Q

How do the structures of the nitrogenous bases differ from one another?

A
  • Adenine - double carbon ring with no oxygens bonded using double bonds
  • Guanine - double carbon ring with one double bonded oxygen
  • Cytosine - single carbon ring with one oxygen and a nitrogen group bonded onto separate carbons
  • Thymine - single carbon ring with a separate carbon group attached
  • Uracil - single carbon ring with two oxygens bonded to the ring
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17
Q

Which nitrogen do purines and pyrimidines use to connect to one another?

A
  • The ninth nitrogen
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18
Q

What’s a nucleotide?

A
  • A nucleoside molecule and a phosphate group
  • The phosphate group is attached to carbon-5 of the ribose and deoxyribose sugars
  • Ex. Deoxyadenosine triphosphate, deoxythymidine triphosphate
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19
Q

What is DNA?

A
  • A polymer of deoxyribonucleotides
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20
Q

How do nucleotide monomers polymerize?

A
  • They join together using phosphodiester bonds
  • Covalent bonds form between phosphate and the C-3’ and C-5’ of 2 pentose sugars
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21
Q

What is the overall charge of a DNA molecule?

A
  • It is negative
  • This is done by the 5’ end containing a negative phosphate group and the 3’ end containing a neutral hydroxy group.
  • Also helps add polarity
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22
Q

What is Chargaff’s rule?

A
  • %A = %T ; %C = %G
  • Also %purines = %pyrimidines
  • A, C, G, and T are not present in equal amounts
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23
Q

What did x-ray diffraction studies reveal about the 3D structure of DNA?

A
  • DNA molecules were cylindrical and about 2nm in diameter
  • 0.34 periodicity suggested that bases were stacked like pennies on top of one another
  • X-shape pattern indicates helical structure
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24
Q

How does base pairing work in a DNA double helix?

A
  • Base pairing is complimentary and so the base pair sequence on one strand can be used to specify the sequence of the other strand
  • Base pairs are stacked flat, lying perpendicular to the axis and contribute to the stability of the double helix
  • Hydrogen bonding between bases keeps two strands intact
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25
Q

How many hydrogen bonds are found between each purine-pyrimidine pair?

A
  • G-C: 3 bonds
  • A-T: 2 bonds
26
Q

How does nucleic acid hybridization occur?

A
  • It’s the annealing (joining) of single strands of DNA or RNA
  • A highly-specific process, as the two strands must be complimentary in sequence, also temperatre-driven and concentration-dependent
27
Q

What was Watson and Crick’s model of DNA replication?

A
  • Complementary base pairing allows parental strands to act as templates for DNA replication of new strands
  • Parental strands can unwind by breaking the hydrogen bond between bases
  • Semiconservative replication, where the double helix will contain a parental strand and a new daughter strand
28
Q

How is DNA organized in prokaryotes?

A
  • Typically organized into one, predominantly circular chromosome while there are also small, independent circular DNA called plasmids in the cytoplasm
29
Q

How is DNA organized in eurkaryotes?

A
  • Their chromosomes are linear and enclosed in a nucleus.
30
Q

What’s chromatin?

A
  • A given region of DNA with its associated proteins on a chromosome
31
Q

What are the three major components of eukaryotic chromosomes?

A
  • Origins of replication - DNA sequences along chromosome which initiate DNA replication
  • Centromere - DNA sequences required for correct segregation of chromosomes by directing formation of the kinetochore (a large protein complex) in which the mitotic spindle attaches
  • Telomeres - DNA sequences located at the ends of the chromosome that prevent degredation and allow proper replication of the chromosomal ends (bacteria do not have telomeres)
32
Q

What’s the ploidy of eukaryotic cells?

A
  • Majority of eukaryotic cells are diploid (two copies of each chromosome)
  • Eukaryotes who are polyploid are often very large protists as they need to produce more RNA/proteins to sustain their size
33
Q

Why is the chromosomal structure beneficial for DNA?

A
  • Helps protect DNA from damage (naked DNA is very unstable)
  • Chromosomes can be easily separated and transmitted to each daughter cell during cell division.
34
Q

What are histones?

A
  • They’re positively charged proteins that DNA wind around
  • Positively charged since DNA is negatively charged.
  • Prokaryotes do not have histones, only eurkaryotic cells do. They still have proteins, just not histones.
35
Q

What’s a nucleosome?

A
  • A type of large histone that is composed of 8 histones (4 different types) where large portions of DNA wrap up witin these nucleosomes
36
Q

Bacterial chromosomes need not be compacted as much as in eukaryotes. Why is this?

A
  • They don’t have as many base pairs as eukaryotes
  • Smaller genome
37
Q

What’s the difference between euchromatin and heterochromatin?

A
  • Euchromatin - regions with lower DNA compaction and genes are actively expressed
  • Heterochromatin - regions of high DNA compaction where gene expression is silenced. This is because they’re not yet to be transcribed
38
Q

What are the two types of heterochromatin?

A
  • Constitutive - DNA always highly compacted. Includes centromeres and sub-telomeric regions.
  • Facultative - Can switch to euchromatin depending on cell type and during development
39
Q

What does semi-conservative replication mean?

A
  • Each daughter strand remians paired with its complementary parental strand.
40
Q

How did Meselson and Stahl determine semi-conservative DNA replication?

A
  • They tracked parental and newly-synthesized DNA strands over several generations with nitrogen isotopes (incorporated due to the nitrogenous bases)
  • The original parental strands were grown in a 15N medium, where they were then transferred into a 14N medium where the daughter strands were produced
  • Once spun, the original, heavier strands would appear lower on the vial and the first replication appeared higher due to its lighter weight, while the second replication (two daughter strands) appears even higher.
41
Q

How does nucleotide synthesis occur?

A
  • Nucleotides can only be added to the new strand at the 3’-OH end (therefore, DNA synthesis occurs in the 5’-3’ direction
  • Hydrolysis of pyrophosphate (P-O-P) provides energy for the formation of new phosphodiester bond.
42
Q

What are some of the properties of DNA polymerase?

A
  • Creates the new DNA strand ONLY IN THE 5’-3’ DIRECTION (can only add new bases to the 3’-OH end of existing strands
  • READS the template strand in the 3’-5’ direction
  • To start syhtesis, it requires a RNA primer with a 3’-OH end
  • Has a single active site that can synthesize four different reactions (one for each base)
43
Q

What’s a replisome?

A
  • A molecular machine composed of multiple enzymes that work together to replicate DNA
44
Q

What is helicase resonsible for?

A
  • Unwinding the double helix by breaking hydrogen bonds (starts the replication process)
45
Q

What does primase do?

A
  • Creates RNA primers for DNA polymerase so that it can start synthesizing the daughter strand
46
Q

What do the single-stranded binding proteins do?

A
  • Stabilizes the ssDNA before repilcation by preventing the two template strands from coming together again so that they can be copied.
47
Q

What does DNA topoisomerase/gyrase do?

A
  • removes super coils that form ahead of the replication fork, relieves torque of mainly circlar DNA (relaxes DNA)
48
Q

What does DNA polymerase III do?

A

-Synthesizes DNA by adding nucleotides to the new DNA strand
- One of the key enzymes

49
Q

What does DNA polymerase I do?

A
  • Removes RNA primer and fills the gaps with DNA
50
Q

What does the sliding clamp do?

A
  • Attaches DNA pol III to DNA template, makes replication more efficient
51
Q

What does DNA ligase do?

A
  • Joins the ends of DNA segments by forming phosphodiester bonds
52
Q

What is the main difference between the leading strand and the lagging strand?

A
  • The leading strand is continuously synthesized, while the lagging strand is discontinuously synthesized, creating Okazaki fragments
53
Q

What direction does DNA Pol III move in?

A
  • It moves in the 3’-5’ direction in relation to the template strand, while nucleotides are being synthesized in the 5’-3’ direction
54
Q

What are the three stages of DNA replication in bacterial chromosomes?

A

1) Initiation - Unwinding and separation of the two template strands (one origin of replication)
2) Elongation - Simultaneous synthesis of the two new DNA strands from the template strands by DNA polymerase
3) Termination - DNA replication stops when it reaches the termination site (opposite side of the origin of replication) or at the end of the chromosome

55
Q

How does eurkaryotic DNA replication differ from prokaryotic replication?

A
  • Eukaryotes have much larger genomes, as well as linear chromosomes
  • There are multiple origins in eurkaryotic DNA replication
  • There are also complications replicating the ends of linear chromosomes
56
Q

What is the Polymerase Chain reaction?

A
  • A method of creating multiple DNA replications by denaturing and reannealing (using a primer) an original template copy of DNA
  • Can be repeated for 30 cycles
57
Q

Whats the End Replication Problem?

A
  • There’s a requirement for RNA primer to initiate new DNA synthesis which makes it difficult to fully replicate the 3’ ends of DNA strands (DNA polymerase can’t fill it in)
  • If telomeres aren’t present, there will be additive loss at the ends of chromosomes
58
Q

What are telomeres?

A
  • They’re non-coding, single stranded DNA added to the 3’ end of chromosomes by telomerase (an enzyme)
  • Made up of a lot of G’s and T’s
  • Telomeres are worn away after each cell division
  • When the telomere region is gone, the cell stops dividing
  • They exist to ensure that the ends of linear chromosomes are fully replicated
59
Q

What is telomerase?

A
  • An enzyme that restores shortened telomeres
  • Not present in most eukaryotic cells
  • Only present in gametes and stem cells
60
Q

How is telomerase and cancer related?

A
  • Many cancers acquire mutations that activate the telomerase gene to negate the limitations of rapid cell division.
61
Q

How does DNA polymerase III proofread the newly synthesized strands?

A
  • DNA pol II is able to detect mistakes and uses 3’-5’ exonuclease activity to remove the most recent mismatched nucleotides
  • DNA pol II replaces correct nucleotide and resumes synthesis of the new DNA strand
62
Q

How does DNA mismatch repair (MMR) work?

A
  • Covers for errors not corrected by proofreading
  • Two DNA binding proteins MutS and MutL recognize the mismatch
  • Exo1 5’-3’ exonuclease excises the region of daughter strands surrounding the mismatch (including the mismatch itself)
  • DNA Pol III fills the gap and repairs the match
  • The nick leftover is sealed by DNA ligase

Biology 243 (8 decks)

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