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BIO 2200 > BIO 2200 Exam 2 > Flashcards

BIO 2200 Exam 2 Flashcards

1
Q

What are the 3 components of nucleotide?

A

A nucleotide has three components: a pentose sugar, ribose (RNA) or deoxyribose (DNA), a nitrogen base, and a molecule of phosphate.

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2
Q

What is the difference between purines and pyrimidines? And give examples

A

Purines (two rings) are adenine and guanine while pyrimidines (one ring) are thymine, cytosine, and uracil. Thymine is in DNA and uracil is in RNA

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3
Q

What are the 3 types of RNAs?

A

Messenger RNA (mRNA) carries the genetic information from DNA to the ribosome; Transfer RNA (tRNA) convert the genetic information on mRNA into the language of proteins; Ribosomal RNA (rRNA) is an important catalytic and structural component of the ribosome

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4
Q

What are the 3 stages of molecular processes of genetic information?

A

Replication: DNA double helix is duplicated, producing two double helices; Transcription: Transfer of information from DNA to RNA; Translation: Synthesis of a protein, using the information carried by mRNA

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5
Q

What is denaturation? Which pair melts at higher temperature: GC or AT?

A

Denaturation is when you separate a double stranded DNA (usually by increasing temperature). Since guanine-cytosine pairs have 3 hydrogen bonds, while adenine-thymine pairs have 2 hydrogen bonds, the melting temperature of GC pairs is higher.

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6
Q

What is annealing?

A

Annealing is the process of allowing heated DNA to cool and eventually re-forming a double stranded DNA.

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7
Q

Why is supercoiling and relaxation important and what does DNA gyrase do?

A

DNA gyrase inserts negative supercoils into DNA. Supercoiling is necessary for packing DNA into the cell and relaxation is necessary for DNA replication and transcription.

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8
Q

What is a genome?

A

the total complement of genes in a cell or a virus

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9
Q

What are plasmids and how do they differ from viruses?

A

Plasmids are genetic elements that replicate separately from the chromosome. Plasmids differ from viruses in two ways: 1) they do not cause cellular damage (actually beneficial) and 2) they do not have extracellular forms, while viruses do.

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10
Q

What are transposable elements and why are they important?

A

Transposable elements are segments of DNA that can move from one site on a DNA molecule to another site, either on the same molecule or on a different DNA molecule. They play an important role in genetic variation.

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11
Q

What does is mean when they say DNA replication is semiconservative?

A

after replication, there are one new strand and one old strand. The old strand is a template for the new strand.

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12
Q

What are the leading strand and the lagging strand?

A

Since DNA has to be made in a 5’ to 3’ direction, one strand can be made continuously (leading strand) and the other is made in small pieces, called Okazaki fragment, and then eventually hooked together (lagging strand).

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13
Q

What are the seven major enzymes in DNA replication and what do they do?

A
  1. The enzyme DNA gyrase travel along the DNA ahead of the replication fork and inserts negative supercoils to cancel out the positive supercoils.
  2. Origin binding protein binds to origin of replication and opens up the double helix.
  3. Next, the helicase loader loads helicase at origin and the helicase unwind the double helix at the replication fork.
  4. Primase inserts a primer.
  5. DNA polymerase III catalyzes the addition of the nucleotides to the RNA primer and then to the growing DNA strand.
  6. When replication is well under way, DNA polymerase I chews up the RNA primer and replaces it with DNA.
  7. DNA ligase seals the nicks in DNA.
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14
Q

What is the replisome?

A

a large replication complex that consists of DNA polymerase III, DNA gyrase, DNA helicase and primase, and single-strand binding protein.

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15
Q

What are the 3 ways to fix replication errors?

A

1) Base pairing: DNA polymerase III reads the template nucleotides accurately and usually inserts the correct complementary nucleotide. 2) DNA polymerase III can go back and detect mismatched pairs, and then fix them. This is called proofreading and its possible in all types of cells. 3) Endonucleolytic proteins detect mismatched pairs long after DNA has been replicated and fixes it.

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16
Q

What the 3 stages of transcription?

A

1) Initiation: RNA polymerase must recognize the initiation sites, or promoters, on DNA. The sigma factor recognizes these. 2) Elongation: Sigma factor dissociates, core enzyme moves down the DNA, separating the DNA strands just long enough to allow base pairing. Only one strand is read by the polymerase (coding strand). 3) Termination: The polymerase reaches a sequence in the mRNA called the terminator and falls off the DNA.

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17
Q

What are the 2 types of terminations to transcription?

A

Rho Dependent: Rho dependent is as protein that travels behind the RNA polymerase on the newly made RNA. If the polymerase slows down, then the Rho protein catches up and causes it to fall off the DNA; Rho Independent: Inverted repeats in transcribed DNA form a step-loop structure in the RNA that terminates transcription when followed by a run of uracils.

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18
Q

What do amino acids consist of?

A

Amino acids (the building blocks for proteins) contain an amino group (-NH2) and a carboxylic acid group (-COOH) attached to the alpha carbon.

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19
Q

What are the steps to protein synthesis?

A

o Initiation of Translation:
1.Met is bound to the P-site during initiation and is therefore always the first amino acid in every protein in bacteria. (AUG is the start codon)
oElongation and Translocation:
1.Elongation factors use GTP to install the incoming tRNA into the A site.
2.Peptide bond is formed.
3.Translocation of the ribosome along the mRNA from one codon to the next requires hydrolysis of another GTP.
4.The outgoing tRNA is released from the E site.
5.The next charged tRNA binds to the A site and the cycle repeats.
oTermination:
1.Protein synthesis stops when the ribosome reaches a stop codon (nonsense codon). UAA, UAG, and UGA are stop codons.

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20
Q

What are polysomes?

A

In both eukaryotes and prokaryotes a single mRNA can have several ribosomes translating it at the same time and these mRNA/ribosome complexes are called polysomes

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21
Q

What is a primary structure of a protein? Secondary structure?

A

Primary structure is the sequence of amino acids in a peptide or protein; Secondary structure is the repeating conformational patterns formed by twist and fold in a polypeptide.

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22
Q

What are exons and introns?

A

Exons are the coding regions and introns are the noncoding regions.

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23
Q

What is the difference between eukaryotes and prokaryotes when it comes to DNA replication?

A

Unlike prokaryotes, eukaryotes have several linear chromosomes, introns, histones, and a nucleus. Transcription and translation occurs in different compartments. mRNA must be transported out of nucleus to be translated.

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24
Q

What is the problem when replicating linear DNA and how can this be fixed?

A

When replicating linear DNA, the problem is how to replace the RNA primer with DNA at the 5’ end of the strand. Solutions are: 1. Many viruses can circularize their genomes before replication because the ends contain complementary nucleotides. The area where they join is called the cos site. 2. Viruses sometime use protein primers, instead of RNA primers, that are permanently attached to DNA.

25
Q

What is splicing and self-splicing introns?

A

Splicing is when the introns are cut out of RNA and the remaining exons join together and this is done by the spliceosome. Self-splicing introns are introns that fold up to generate three-dimensional structures with ribozyme activity.

26
Q

What are the functions of capping? (3)

A

Protection of the RNA from degradation; ribosome recognition; transportation form the nucleus to cytoplasm

27
Q

What happens when a poly(A) tail is added?

A

This consists of trimming the 3’ end of the primary transcript and adding 100-200 adenylate residues as the poly(A) tail.

28
Q

Why do most DNA-binding proteins interact with DNA in a sequence specific manner?

A

because of the specific amino acid side chains of the proteins and specific chemical groups of the nitrogenous bases and the sugar-phosphate backbone of the DNA

29
Q

What does it mean when they say DNA-binding proteins are homodimeric?

A

they are composed of two identical polypeptide subunits. Each subunit has a domain that interacts specifically with a region of DNA in the major groove.

30
Q

What are the 3 possible structures of DNA-Binding proteins?

A

Helix-Turn-Helix: The first helix is the recognition helix that interacts specifically with DNA, while the second helix, the stabilizing helix, stabilizes the first helix by interacting hydrophobically with it; Zinc Finger: Found in eukaryotes, the zinc finger is a protein that binds a zinc ion. Part of the “finger” of amino acids that is created forms an alpha helix and interacts with DNA in the major groove; Leucine Zipper: Does not interact with DNA itself, but functions to hold two recognition helices in the correct orientation to bind DNA.

31
Q

What is negative control of transcription?

A

Negative control of transcription is control that prevents transcription.

32
Q

What is the difference between repression and induction?

A

Repression is when enzymes that catalyze the synthesis of a specific product are not made if that product is already present. Induction is when an enzyme is made only when its substrate is present.

33
Q

What is an inducer? a corepressor?

A

The substance that induces enzyme synthesis is called an inducer, while a substance that represses enzyme synthesis is called a corepressor.

34
Q

What is positive control of transcription?

A

Positive control of transcription is when a protein is an activator that activates the binding of RNA polymerase to DNA. For example, when the maltose activator protein binds to DNA, it allows RNA polymerase to begin transcription.

35
Q

What is catabolite repression?

A

A mechanism of global control that decides between different available carbon sources if more than one is present. When more than one sugar is present, E. coli would use glucose first because it already has enzymes for it.

36
Q

What is a diauxic growth?

A

A diauxic growth is when two usable energy sources are available, the cells grow first on the better energy source, stop growing, and then, after a lag period, starts to grow on the other source.

37
Q

What is the two-component regulatory system?

A

The two-component regulatory system consists of a specific sensor kinase protein and a response regulator protein. Sensor kinases detect a signal from the environment and phosphorylate themselves. Then the phosphate is transferred to the response regulator protein (DNA-binding protein).

38
Q

What is quorum sensing?

A

Quorum sensing is a mechanism to assess population density.

39
Q

What is an autoinducer?

A

Each species synthesizes a specific signal molecule called an autoinducer. This molecule diffuses freely across the cell envelope and because of this, the autoinducer reaches high concentrations inside the cell is there are many cells nearby. Inside the cell, the autoinducer binds to a specific activator protein and triggers transcription of specific genes.

40
Q

What is the stringent response?

A

global control triggered by amino acid starvation

41
Q

What is the heat shock response?

A

counteract damage of protein denaturation and help cells recover from temperature stress

42
Q

What are antisense RNAs?

A

small RNA molecules that base pair with other RNA molecules and prevent its translation.

43
Q

What are riboswitches?

A

RNA domains that recognize small molecules and respond by changing their three-dimensional structure. This affects the translation of the mRNA or premature termination of transcription.

44
Q

What is attenuation?

A

a mechanism whereby transcription is controlled after initiation of mRNA synthesis. These mechanisms depend upon alternative stem-loop structure in the mRNA.

45
Q

What are viruses?

A

obligate parasites; self replicating nucleic acid molecules surrounded by a protein coat called a capsid; dormant outside of hst cell

46
Q

What are the viral classifications based on the host? based on the genetic material?

A

host: animal viruses (animals), plant viruses (plants), and bacteriophage (bacteria); genetic material: DNA viruses, RNA viruses, and DNA-RNA viruses (use both as genetic material in different stages of life cycle)

47
Q

Describe the viral structure.

A

size is about 20-200 nm; it has a genome; some have enzymes; a caspid; and some have envelopes

48
Q

How do you grow a virus?

A

to grow viruses, you must provide live and metabolically active host cells; for animal viruses, you must provide living animal cells-tissue culture

49
Q

What is the + strand?

A

it is the RNA strand that is translated by the ribosomes (serves as the mRNA)

50
Q

What are the stages of viral replication?

A

attachment (absorption), penetration (infection), synthesis of nucliec acid and protein, assembly and packaging, and release (lysing)

51
Q

What is homologous recombination?

A

as the genome is being replicated, the partially completed fragments recombine at the homologous regions

52
Q

What are concatamers of DNA?

A

several copies of the viral genome are connected in a single large DNA molecule

53
Q

What is headfull packaging?

A

when the concatamer is fed into the phage head and when the head is filled with DNA, an endonuclease cuts the DNA

54
Q

What are restriction endonucleases?

A

classes of enzymes that recognize and cut foreign DNA; this is a mechanism used by bacteria to protect themselves from bacteriophages

55
Q

What are the two cycles of temperate viruses?

A

lytic cycle (lysis of the cells) and lysogenic cycle (integrates into the chromosome and becomes part of its host)

56
Q

How does lysogenic induction work?

A

Bacterial cells have a special system for repairing damaged DNA called the SOS system. One of the proteins in this system, called RecA, acts as a signal to the virus that the host chromosome is in danger an its host might be dying. At this point, the virus goes into the lytic cycle.

57
Q

What are the types of aniaml virus infections?

A

lytic (cells are lysed/killed); persistent (when assembled, the virus can bud through the membrane without killing the cell); latent (doesn’t causes disease until a later time); transformtion (conversion of normal cells into tumor cells)

58
Q

What is a vaccine?

A

a biological preparation that improves immunity to a particular disease

BIO 2200 (2 decks)

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