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Chemistry of Living Systems > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

Define: Chargaf’s Rule

A

DNA of all organisms should have a 1:1 ratio of purine and pyrimidine bases. Specifically, A/T and G/C should both be 1.

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2
Q

Does the Watson-Crick structure agree with Chargaf’s rule?

A

Yes

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3
Q

What makes stacking possible?

A
  • Van der Waals Interactions

- Hydrophobic effects

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4
Q

What does the Meselson-Stahl experiment show about replication?

A

-Replication is semiconservation

Method:

  1. Increased density of parent DNA with N15
  2. Put it in an environment of N14 and allowed to divide.
  3. Put forth question: What is the distribution of N14 and N15 in DNA molecules after successive rounds of replication?
  4. Test question via density-gradient sedimentation

Result:
-after 1st generation, there’s a single band detected by absorption of UV light–density of band of DNA is halfway in between density of N14 and N15 –> shows that parent DNA didn’t stay intact and absence of N14 shows that daughter DNA got some of their atoms from parent (hybrid daughter DNA)

-after 2nd generation, there’s 2 bands of DNA; 1 was hybrid and the other N14 DNA

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5
Q

How would you view circular and supercoiled DNA?

A

Electron Microscopy

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6
Q

What is the structural shape of circular/relaxed DNA?

A

Has no helical turns

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7
Q

What is the structural shape of supercoiled DNA? What’re the advantages (2)?

A

Shape: Extreme helix

Advantages:

  1. more compact
  2. may hinder/favor the capacity of double helix to unwind which in turn affects the interactions b/w DNA and other molecules
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8
Q

How can 2 strands of a double helix be separated (in a lab and in an organism) and what’s it called?

A

Methods:

  1. In Lab: a) heating b) addition of acid/alkali to ionize base
  2. In organism: Helicase

Name: Melting
Why: because the separation of the 2 strands occurs abruptly at a specific temperature

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9
Q

What types of intramolecular base pairings occur in single-stranded nucleic acids?

A
  1. Stem-loop structure: when 2 complementary sequences within a single strand come together to form a double-helical structure
  2. Non-Watson-Crick base pairing: complementary bases match up but do not pair up with the one naturally parallel to it; results in bulges coming out of helix and a decrease in structure stability
  3. Trinucleotide complexes: Complexes of 3 bases joined together; gives rigidity to structure and helps to stabilize non-watson-crick base pairing.
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10
Q

What are the key components in DNA replication?

A
  1. DNA polymerase
  2. Primer strand
  3. Activated pre-cursors
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11
Q

Define: DNA polymerase

A

2 Functions:

  1. Enzyme that catalyzes phosphodiester bonds (in order to add nucleotide corresponding to one on DNA template strand) by adding onto the 3’ end of the primer strand
  2. Corrects mistakes in DNA by removing mismatched nucleotides
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12
Q

Define: Primer Strand

A

-A short fragment of RNA that’s created and paired with a part of the DNA strand which the DNA polymerase can build off of

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13
Q

How does DNA polymerase use primer strand for elongation/to form a phosphodiester bridge?

A
  1. 3’ -OH group on the primer attacks the innermost phosphate group on the incoming nucleotide triphosphate
  2. Results in formation of a phosphodiester-bridge and the release of pyrophosphate (PPi) from the incoming nucleotide triphosphate
  3. PPi gets hydrolyzed and results in 2 ions of orthophosphate (Pi)
  4. Pi helps to drive polymerization forward
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14
Q

Define: Activated Pre-Cursors (of DNA)

A

dATP, dCTP, dGTP, dTTP

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15
Q

What are the 2 ways that viruses that store their genetic info in single-stranded RNA replicate?

A
  1. RNA-directed polymerase

2. RNA-directed reverse transcriptase

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16
Q

Define: RNA-directed polymerase

A

RNA is replicated based off of a template

17
Q

RNA is less stable than DNA but this instability proves advantageous to viruses. How so?

A
  • Allows for a higher chance of mutation

- Means that they’re constantly changing which decreases chance of detection and getting caught

18
Q

Define: RNA-directed reverse transcriptase

A
  • Done by Retroviruses

- Overall transforms viral RNA into viral DNA

19
Q

Steps of RNA-directed reverse transcriptase

A
  1. Reverse transcriptase catalyzes addition of a complementary strand of DNA to the viral single stranded RNA–> produces a DNA-RNA hybrid
  2. DNA-RNA hybrid can now be incorporated into chromosomal DNA
  3. From this, reverse transcriptase is used again to separate viral DNA from viral RNA strand
  4. Reverse transcriptase on the viral DNA strand results in a double-helical viral DNA
  5. This can no be inserted into the host and be replicated alongside with host DNA
20
Q

What are the 3 major RNAs involved in gene expression (transcription and translation) and what’s the function of each.

A
  1. rRNA: major component of ribosomes and catalyst for protein synthesis
  2. tRNA: acts as an adapter molecule that recognizes 3 base “codons” and carry aminoacyl groups to ribosome for peptide-bond formation (acts as a translator)
  3. mRNA: template for protein synthesis (messenger)
21
Q

What does RNA polymerase-catalyzed transcription of DNA need?

A
  1. Template: either a single or double stranded DNA
  2. Activated precursors (ATP, GTP, UTP, CTP)
  3. A divalent metal ion (Mg2+ or Mn2+)
22
Q

What is different about RNA polymerase-catalyzed transcription and DNA polymerase-catalyzed transcription.

A

-RNA does not need a PRIMER STRAND

23
Q

How is RNA polymerase-catalyzed transcription similar to DNA polymerase-catalyzed transcription.

A
  1. Synthesis goes in the direction of 5’–>3’
  2. Mechanism of elongation
  3. Synthesis is driven by the hydrolysis of pyrophospate (Pi)
24
Q

Define: Promoter Sites

A

Regions on DNA template where DNA polymerase can bind to

-They determine where transcription begins

25
Q

What is the name of the promoter site in eukaryotic organisms?

A

TATA box or Hogness box

26
Q

Define: Enhancer Sequences

A

Sequences further down from the promoter site that further stimulate transcription of genes

27
Q

Define: Terminator Sequence * not sure

A

A sequence found on the DNA template which when RNA polymerase comes across it, the
newly synthesized RNA spontaneously dissociates from RNA polymerase

2 Types:

  1. Base-pair hairpin structure found in newly synthesized RNA sequence, which disrupts RNA polymerase
  2. Rho factor (an RNA helicase protein complex) that disrupts mRNA-DNA-RNA polymerase ternary complex
28
Q

Can transcription self-terminate?

A

Yes

29
Q

What happens during modification of RNA in eukaryotes and when does it occur?

A

When: After transcription

What happens:
1. A “cap” structure is added to 5’ end
2. A Poly(A) tail is added to the 3’ end
(coding region is in between these 2 modifications)

30
Q

Parts of Structure of tRNA

A
  1. Amino Acid Attachment SIte
    • carboxyl group of amino acid gets esterified to the 3’ hydroxyl group of ribose unit at the 3’ end of tRNA chain
  2. Template Recognition Site
    • made up of a sequence of 3 bases known as an ANTICODON–anticodon will recognize a complementary sequence of 3 bases on mRNA known as CODON
31
Q

What enzyme is used to catalyze the joining of an amino acid to a tRNA molecule?

A

Enzyme: Aminoacyl-tRNA synthetase

Complex: Aminoacyl-tRNA

32
Q

What are 3 characteristics of the genetic code?

A
  1. Degenerate (some codes code for the same amino acid but none code for nothing)
  2. Non-overlapping (letters only occur once ex. ABC, DEF, GHI etc NOT ABC, BCD, CDE)
  3. Punctuationless (just read sequentially from a fixed starting point)
33
Q

Define: Stop Codons

A

3 codons that designate the termination of translation

  • They are UAA, UAG, UGA
  • THey are read by release factors
34
Q

Define: Synonyms

A

Codons that code for the same amino acid

-usually only differ from each other by the last letter

35
Q

Define: Reading Frame

A

-Groups of 3 nonoverlapping nucleotides which get defined starting with initiator AUG codon once AUG has been located by fMet (in prokaryotes) or H2N-Met (in eukaryotes)

36
Q

What are the components of the start signal in mRNA for protein synthesis?

A
  1. Shine-Dalgarno Sequence: a purine rich sequence that base-pairs with complementary ribosomal RNA
  2. AUG
37
Q

Define: Release factor

A

Specific proteins that, when bound to stop codons in ribosome, releases the newly synthesized protein

38
Q

Define: Introns (intervening sequences)

A

Sections of the primary transcript that get removed from RNA strand

-Always start with a GU and end with an AG preceded by a pyrimidine-rich tract

39
Q

Define: Exons (expressed sequences)

A

Sections of the primary transcript that are retained in RNA strand

Chemistry of Living Systems (7 decks)

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