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Bio 116H Dr Balish/Zhao > Exam 2(post ME 2) > Flashcards

Exam 2(post ME 2) Flashcards

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1
Q

Results of transcription, what happens after?

A

mRNA, rRNA and tRNA. These types of RNA then undergo translation

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2
Q

T.H. Morgan

A

Showed that genes are located on chromosomes and that chromosomes have 2 components-DNA and protein.

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3
Q

Frederick Griffith

A

Proved the “transforming principle” of genetic material. He did this in an experiment with 2 types of a virus. S cells killed mice and R cells did not. He found that mice lived when injected with heat-killed S cells but died when injected with a mixture of heat killed S-cells and living R cells. The R cells added carbs, protein and DNA to the heat-killed S-cells

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4
Q

Alfred Hershey and Martha Chase

A

Showed that DNA is the genetic material of a phage in an experiment in which the protein and then the DNA of the phage were radioactively labeled. The phages were allowed to infect a bacterial cells then a centrifugation was performed and the phage protein was found in the liquid whereas the DNA was found in the solid pellet(bacteria)

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5
Q

Rosalind Franklin

A

x-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical. She concluded that there were two outer sugar-phosphate backbones with nitrogenous bases paired in the molecule’s interior

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6
Q

Watson and Crick

A

built models of a double helix to conform to the x-rays and chemistry of DNA, enabled by Rosalind Franklin. Watson built a model in which the backbones were antiparallel

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7
Q

Chargaff’s rules

A
  1. The base composition of DNA varies between species

2. In any species that number of A and T bases are equal and the number of G and C bases are equal

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8
Q

of H bonds in A/T and G/C

A

A and T: 2 H bonds

G and C: 3 H bonds

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9
Q

bases present in DNA and RNA

A

DNA: A, T, G, C

RNA: A, U, G, C

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10
Q

In what direction does DNA grow

A

from the 5’ and 3’

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11
Q

DNA structure

A

double helix with H bonds, complementary strands, antiparallel, more stable than RNA

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12
Q

Models for DNA replication modes

A
  1. Conservative model: two strands reassociate after acting as templates for new strands, thus restoring the parental double helix.
  2. Semiconservative model: two strands of parental molecules separate and each functions as a template for synthesis of a new, complementary strands
  3. Dispersive model: Each strand of both daughter molecules contains a mixtures of old and newly synthesized DNA
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13
Q

Experiment to determine mode of DNA replication

A

Bacteria were cultured in medium with heavy N isotope then transferred to medium with a lighter isotope. The sample was centrifuged twice(once after each replication) and the more dense centrifugations went closer to the bottom of the solution. This proved the semiconservative model correct. This rejected both replications of the conservative model and the second replication of the dispersive model.

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14
Q

What DNA replication looks like in bacteria

A

Happens in a single, circular, chromosome with a single origin of replication

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15
Q

What DNA replication looks like in eukaryotes

A

Multiple, linear chromosomes, much longer than bacterial chromosomes, multiple origins of replications, occurs in both directions

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16
Q

Helicase

A

unwinds parental double helix at replication forks

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17
Q

Single-strand binding protein

A

Binds to and stabilizes single-stranded DNA until it is used as a template

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18
Q

Topoisomerase

A

Relieves overwinding strain ahead of replication fork by breaking, swiveling, and rejoining DNA strands

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19
Q

Primase

A

Synthesizes RNA primer at 5’ end of leading strand and at 5’ end of each okazaki fragment of lagging strand, using parental DNA as a template

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20
Q

DNA polymerase I

A

Removes RNA nucleotides of primer from 5’ end and replaces them with DNA nucleotides adde to the 3’ end of adjacent fragment

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21
Q

DNA polymerase III

A

Using parental DNA as a template, it synthesizes new DNA strand by adding nucleotides to an RNA primer or pre-existing DNA strand, elongates leading strand continuously in the 5’ to 3’ direction as fork progresses

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22
Q

DNA ligase

A

Joins okazaki fragments of lagging strand; on leading strand, join 3’ end of DNA that replaces primer to rest of leading strand DNA. Also performs this function in proofreading and repairing DNA

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23
Q

Overall purpose of DNA polymerases

A

Catalyze the synthesis of new DNA by adding nucleotides to the 3’ end of a preexisting chain. They also repair damaged DNA by filling in missing nucleotides, suing the undamaged strand as a template

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24
Q

direction of DNA elongation

A

5’ to 3’, leading strand is elongated continuously in the 5’ to 3’ direction as the fork progresses

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25
Q

synthesis of lagging strand

A

synthesized discontinuously, synthesized as a series of okazaki fragments which are joined together by DNA ligase. Primase makes RNA primer from 5’ to 3’ starting closer to the replication fork and moving away, the DNA pol III makes an okazaki fragment starting at the end of the primer furthest from the fork. Then they both detach and repeat this closer to the replication fork. DNA pol I replaces RNA with DNA, DNA ligase bonds fragments

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26
Q

Ends of leading and lagging strands

A

leading strand is 5’ to 3’, lagging is 3’ to 5’

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27
Q

trombone model

A

a recently supported model of DNA replication in which DNA polymerase molecules “reel in” parental DNA and extrude newly made daughter DNA

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28
Q

nuclease

A

enzyme that cuts damaged DNA strand at 2 point, removing the damaged section

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29
Q

Eukaryotic chromosome structure components from smallest to largest

A
  1. DNA: double helix, 2nm in diameter
  2. nucleosome: 10nm in diameter, histones wrapped in DNA with histone tails sticking out
  3. Fiber: 30 nm in diameter, many nucleosomes
  4. Looped domain: 300 nm in diameter, has scaffolding pattern, fiber
  5. chromatid: 700nm
  6. Chromosome: 1400nm, 2 chromatids
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30
Q

General mechanisms of gene regulation

A
  1. structural and chemical changes to the genetic material
  2. binding of proteins to specific DNA elements to regulate transcription
  3. Mechanisms that modulate translation of mRNA
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31
Q

operons

A

clusters of genes with one promoter, serving several adjacent genes

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32
Q

operator

A

site of DNA that switches operon on or off, resulting in coordinate regulation of genes, part of operon

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33
Q

repressible operon

A

usually on, repressors bind to them to shut off transcription

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34
Q

inactive repressor

A

repressor with no corepressor present

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35
Q

active repressor

A

repressor with corepressor bound

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36
Q

tryptophan

A

a co-repressor that activates the repressor, therefore turning the operon off

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37
Q

inducible operon

A

usually off, inducers inactivates repressor and turns on transcription

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38
Q

Lactose

A

when present, allolactose acts as an inducer to inactive the repressor and turn on the operon. It promotes the transcription of the enzymes that use lactose

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39
Q

histone tails

A

protrude outward from a nucleosome, providing amino acids that are available for chemical modification

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40
Q

Acetylation/unacetylated histone tails

A

acetylation of histone tails promotes loose chromatin structure that permits transcription. Unacetylated histone tails are compact and DNA is not accessible for transcription

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41
Q

Purpose of alternative splicing

A

allows for an increase in the size of the proteome while maintaining the size of the genome, conserves energy by not increasing genome size

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42
Q

miRNA

A

microRNA, binds to target mRNA. If the bases are complementary, the mRNA is degraded, if the match isn’t complete, translation is blocked

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43
Q

What do all viruses have?

A

Genome and a capsid protein coat

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44
Q

Viral genome

A

may consist of either double stranded or single stranded DNA or RNA

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45
Q

What do all viruses NOT have?

A

cell membranes, ribosomes, cell walls, organelles

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46
Q

Viral envelope

A

extra layer of protection found in SOME viruses

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47
Q

How do viruses affect host gene expression?

A

They make the host cell, replicate viral genome, transcribe viral genes and translate viral proteins

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48
Q

HIV

A

Virus that causes AIDS. It is a retrovirus that uses reverse transcriptase and infects helper T cells

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49
Q

CRISPR-Cas system

A
  1. Infection by phage triggers transcription of the CRISPR region of the bacterial DNA, where phage has inserted its DNA.
  2. RNA transcript is processed into short RNA strands
  3. Each short RNA strands binds to a Cas protein, forming a complex
  4. Complementary RNA binds to DNA. Cas protein cuts the phage DNA
  5. Phage DNA can no longer replicate
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50
Q

How do scientist take advantage of viral element that control gene expression?

A

They give “guide RNA” to a Cas9 protein to target a gene, making a Cas9-guide RNA complex. It will then cut the target part of the gene. The target gene can then be isolated so its function can be studied, or if it has a mutation it can be repaired

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51
Q

siRNA

A

stands for small interfering RNA

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52
Q

Methlyation

A

methylation of DNA increases its density and decreases expression of methylated genes

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53
Q

promoter

A

sequences of DNA(a control element) that are part of the operon where RNA polymerase first binds to start transcription

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54
Q

where do transcription and translation occur?

A

Transcription: nucleus
Translation: cytoplasm

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55
Q

Enhancers

A

Region of DNA(a control element) that can be bound by activators to increase the likelihood that transcription of a particular gene will occur, transcription factors can also bind to enhancers

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56
Q

transcription factor

A

proteins that turn specific genes on or off by binding to nearby DNA.

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57
Q

Activators

A

transcription factors that boost a gene’s transcription

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58
Q

control element

A

region of DNA that allows the regulation of gene expression by binding of transcription factors

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59
Q

Mendel definition of a gene

A

discrete unit of inheritance that affects phenotypic character

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60
Q

Morgan definition of inheritance

A

specific loci on chromosomes

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61
Q

One gene-one enzyme hypothesis

A

Hypothesis by beadle and Tatum, included that not all proteins are enzymes

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62
Q

One gene-one protein hypothesis

A

Many proteins are constructed from two or more different polypeptide chains, and each polypeptide is specified by its own gene

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63
Q

One gene-one polypeptide hypothesis

A

still not entirely accurate, a eukaryotic gene can code for a set of polypeptides via a process called alternative splicing

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64
Q

General definition of transcription

A

Synthesis of RNA using information in DNA, produces mRNA

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65
Q

General definition of translation

A

synthesis of a polypeptide using the information in mRNA

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66
Q

Role of RNA in transcription and translation

A

bridge between genes and proteins for which they code

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67
Q

Role of ribosomes in transcription and translation

A

sites of translating nucleic acid to amino acid

68
Q

DOGMA sequence including transcription and translation

A

DNA➡️transcription➡️RNA➡️translation➡️protein

69
Q

Difference between transcription/translation in prokaryotes vs eukaryotes

A

In prokaryotes, there is no barrier between the two processes and translation can begin in prokaryotes before transcription is finished, eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA, in termination of transcription: RNA passes polyadenylation signal sequence and the transcript is released 10-35 nucleotides past this sequence

70
Q

What separates transcription and translation in eukaryotes?

A

Nuclear envelope

71
Q

Differences between transcription and DNA replication

A

RNA polymerase does not need a primer, uracil is used instead of thymine, DNA is split where one strand is the template strand and one strand is ignored, then strands are rejoined once transcript is made and DNA is left as it originally was before

72
Q

Initiation in transcription

A

RNA pol and transcription factors bind to promoter, DNA strands unwind, polymerase initiates RNA synthesis at the start point on the template strand

73
Q

Elongation in transcription

A

RNA pol moves downstream, unwinding the DNA and elongating the RNA 5’ to 3’(adding to 3’ end), Once RNA pol passes, DNA strands reform double helix and RNA transcription peels away from template strand

74
Q

Termination in transcription

A

RNA transcript is released and polymerase detaches from DNA

75
Q

Eukaryotic promoters in transcription

A

Include a TATA box about 25 nucleotides upstream from the transcription site

76
Q

Role of transcription factors in transcription initiation

A

One recognizes the TATA box and binds to the DNA so RNA pol II can bind in the correct position/orientation, then additional transcription factors form a transcription initiation complex with RNA pol II

77
Q

RNA processing

A

Occurs in eukaryotes in nucleus

  1. A 5’ cap with a modified guanine nucleotide and 3 phosphates is added to 5’ end
  2. 50-250 adenine nucleotides are added to the 3’ end, forming a poly-A-tail
  3. RNA splicing: removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence

These modifications facilitate the export of mRNA to the cytoplasm, protect mRNA from hydrolytic enzymes and help ribosomes attach the 5’ end

78
Q

Spliceosome

A

Large complex made of proteins and small RNAs used in RNA splicing

79
Q

Triplet code

A

The genetic code of different combinations of 3 nucleotides forming 64 different combos that code for polypeptides.

80
Q

AUG

A

start codon

81
Q

Stop codons

A

UAA, UAG, UGA

82
Q

What are ribosomal units(for translation) made of?

A

Proteins and rRNA

83
Q

tRNA

A

Each tRNA molecule enables a translation of a given mRNA codon into a certain amino acid, carries a specific amino acid on one end and an anticodon on the other end

84
Q

Difference between prokaryotic and eukaryotic ribosomes in translation

A

Prokaryotic: 50S and 30S subunit(70S) total

Eukaryotic: 60S and 40S subunit(80S) total

85
Q

Components of ribosome during translation

A

Large subunit, small subunit, exit tunnel through large subunit for polypeptide, mRNA entering and exiting in small subunit, tRNA molecules in the middle for mRNA to pass through

86
Q

binding sites in tRNA

A

P site: holds tRNA that carries the growing polypeptide chain

A site: holds tRNA that carries the next amino acid to be added to the chain

E site: Exit site, discharged tRNAs leave the ribosome

87
Q

In what order is mRNA read in the ribosome?

A

5’ to 3’

88
Q

Amino end

A

first amino acid to be made, at the end of polypeptide chain, opposite of carboxyl end, doesn’t change

89
Q

What is required in all 3 steps of translation?

A

protein factors that aid in the translation process

90
Q

Initiation in translation

A

small ribosomal unit binds to mRNA, initiator tRNA binds at the start codon(AUG) , large ribosomal subunit arrives and uses GTP to bind to small ribosomal unit

91
Q

Met

A

an amino acid called methionine produced by the start codon, AUG

92
Q

Elongation in translation

A

Codon recognition occurs, anticodon of an incoming tRNA base-pairs with complementary mRNA codon in the A site, peptide bonds are formed

93
Q

anticodons

A

located on tRNA, bind to codons of mRNA

94
Q

Carboxyl end

A

end of polypeptide that has been most recently added to the chain in translation, opposite of amino end

95
Q

How are new amino acids attached to the growing polypeptide chain in translation?

A

an rRNA molecule from the large ribosomal subunit catalyzes the formation of a peptide bond between the new amino acid from site A and the growing peptide in the P site

96
Q

What form of energy is used in translation?

A

GTP

97
Q

translocation

A

Ribosome translates tRNA to their next sites using GTP, while the empty site is simultaneously replaced with the next tRNA. mRNA moves along with it’s in bounds tRNA

98
Q

Termination in translation

A

Ribosome reaches stop codon on mRNA, A site accepts a release factor, polypeptide is freed and ribosomal subunits and other components dissociate(uses 2 GTP)

99
Q

Release factor

A

A protein shaped like tRNA, promotes hydrolysis of the bond between tRNA in the P site and the last amino acid of the polypeptide

100
Q

Polyribosomes

A

aka polysomes, this is the result when multiple ribosomes can translate a single mRNA simultaneously, enables cells to make multiple copies of a polypeptide very quickly. This can occur on another level when the same strand of DNA is transcribed multiple times and each strand of resulting mRNA has polysomes

101
Q

Site of polypeptide synthesis

A

Synthesis always starts in cytosol, it finishes in cytosol unless the polypeptide signals the ribosome to attach to the ER. It is attached to the ER by an SRP and a signal-cleaving enzyme cuts of the signal polypeptide

102
Q

Bond between ribosomes and amino acids

A

covalent

103
Q

Glycocalyx

A

A pink coating/layer of molecules external to the cell wall that serves as a protective, adhesive, and receptor functions. It can fit tightly or be loose

104
Q

Bacterial chromosome/nucleoid

A

Composed of condensed DNA

105
Q

Plasmid

A

double-stranded DNA circle containing extra genes

106
Q

Pilus

A

long, hollow appendage used in transfers of DNA to other cells

107
Q

Flagellum

A

Specialized appendage attached to the cell by a basal body that holds a long, rotating filament. The movement pushes the cell forward and provides motility

108
Q

Outer membrane

A

extra membrane similar to cell membrane, except it also contains lipopoly saccharide. It controls flow of materials and portions of it are toxic to mammals when released

109
Q

Gram positive vs gram negative

A

Positive: has a thick cell wall, purple

Negative: pink, thin or no cell wall, more difficult to kill because they have 2 cell membranes

110
Q

What grams stains are and are not useful for

A

Useful in providing info on cell wall and can reveal which antibiotics are useful against a certain type of bacteria. Not useful in classifying bacteria or identifying their ancestry

111
Q

What determines cell shape?

A

the way peptidoglycan is layered around a cell

112
Q

Which part of a bacteria is more selective?

A

the cell membrane

113
Q

What makes gram negative cells pink after a stain is performed?

A

Crystal violet is easily rinsed away, revealing red safranin dye.

114
Q

Why is the cell wall a good target for antibiotics?

A

Humans don’t have cell walls and bacteria do, so there will be less side effects. Targeting organelles present in human cells will cause side effects.

115
Q

Lipopolysaccharides

A

aka LPS, they are embedded in the outer membrane of gram negative cells. Human immune systems are sensitive to LPS and it’s recognized as a foreign substance. This causes gram negative infections to tend to be more harmful

116
Q

What is the result of bacterial cell division

A

In theory, two identical daughter cells

117
Q

What allows bacteria to grow rapidly?

A

They have no nuclear membrane, making division faster and more energetically efficient

118
Q

Which cells have circular chromosomes?

A

bacteria

119
Q

Where can the origins of replication be found in bacterial cell division and why?

A

Anchored on the cell membrane, this happens because there is no mitotic spindle to pull anything apart, the elongation of the cell acts as the pulling force

120
Q

Parts of a growth curve for bacterial population

A
  1. lag phase: cells adjust to new environment
  2. logarithmic phase: aka exponential phase, population grows very rapidly, cells double at maximum rate
  3. Stationary phase: growth plateaus, more cells can’t be supported, population stops increasing due to lack of resources, space or buildup of toxins. Some bacteria population maintain this stage for a very long time, competition has increased
  4. Death phase: not experienced by all cells
121
Q

Events that occur at stationary phase

A
  1. Production of spores/endspores
  2. biofilm production
  3. toxin production
122
Q

Production of endospores

A

endospores receives half of bacterial DNA while the rest of the DNA builds the coat, they have very little water, process of complicated

123
Q

Main type of endospore

A

anthrax

124
Q

Quorum sensing

A

Genes are regulated by an autoinducer and production of proteins in density-dependent. This is what allows stationary phase events to occur

125
Q

Quorum

A

minimum number of individuals needed to make decision in bacterial population

126
Q

Autoinducers

A

signaling molecules produced in response to cell population density, allows interspecies communication, new drug targets

127
Q

Types of autoinducers

A

Autoinducer 1: tends to be species specific

Autoinducer 2: conserved among many bacterial species

128
Q

How do prokaryotic cells target eukaryotic cells?

A

A large number of prokaryotes group up to target a eukaryotic cell to make up for the size difference

129
Q

Vibrio fischeri

A

autoinducer, bioluminescent, lives in light organ of Hawaiin bobtail squid, doesn’t glow when free living, gene expression for glow increases in concentrated numbers

130
Q

What can bacteria produce in large numbers and how are these produced?

A

Biofilm components, enzymes and toxins produced from changes in gene expression

131
Q

Metabolic processes found in both eukaryotes and prokaryotes

A
  1. Oxygenic photosynthesis
  2. Calvin cycle
  3. Aerobic respiration
  4. Citric acid/TCA/Krebs cycle
  5. glycolysis
  6. Lactic acid fermentation
  7. Alcohol fermentation
132
Q

Which metabolic processes take place in the cytoplasm of prokaryotes?

A
  1. Glycolysis
  2. Krebs cycle
  3. Calvin cycle
  4. Fermentation
133
Q

Which metabolic processes take place in the plasma membrane of prokaryotes?

A
  1. ATP synthesis
  2. chemiosmosis
  3. light reactions
134
Q

Most abundant metabolic membrane

A

thylakoid membranes

135
Q

Where do proteins that will be secreted from he cell or function inside cellular compartments go?

A

from the cytosol to the ER lumen

136
Q

What is a common theme among metabolic processes found in ONLY prokaryotes?

A

many them are associated with prokaryotes that do not or can not use oxygen, a lot of them came from ancient earth where there was no oxygen

137
Q

Lithotrophy+example

A

Metabolic process only found in prokaryotes, inorganic molecules are used to generate energy and build cells, example includes ammonia oxidizers, which use ammonia as a source of electrons for production of ATP

138
Q

How do eukaryotes and prokaryotes get nitrogen

A

Some bacteria and archea can fix nitrogen themselves, every other organism gets N from these organisms

139
Q

Why must nitrogen be fixed in order to be made available to most organisms

A

It is unavailable in its atmospheric form to most organisms

140
Q

Sequence of N fixation

A

N2➡️ammonium➡️nitrite➡️nitrate

141
Q

Process of nitrogen fixation

A
  1. Plant releases signal in soil that bacteria respond to
  2. Specific species of bacteria respond
  3. Plant root hair curls around bacterial cells and bacteria enter plant cells via an infection thread
  4. Plant creates anaerobic environment for N fixation
142
Q

Lephemoglobin

A

A protein produced by a plant that binds to oxygen to make an anaerobic environment needed for N fixing bacteria

143
Q

Methanogenesis

A

Production of methane as a waste product, only in archea, found in anaerobic environments, critical to carbon cycle, made by obligate anaerobes

144
Q

Biogas system

A

Organic material is inserted into a digestion tank, producing biogas(heats homes) and co-products(nutrients, compost, livestock bedding)

145
Q

Where is H+ released to when H20 is split in photosystem II

A

the thylakoid space

146
Q

Primary electron acceptor

A

first electron acceptor in the ETC after P680/P700 gets excited

147
Q

In the chemiosmosis gradient in photosynthesis, where are electrons pumped to and from?

A

ETC pumps H+ into the thylakoid space, they H+ drives ATP synthesis as they diffuse back into the stroma

148
Q

Where is there high and low H+ concentrations in photosynthesis?

A

High in thylakoid space low in stroma

149
Q

what occurs in bundle sheath cell

A

CO2 and pyruvate are released by PEP, 1ATP is used ti fix pyruvate in PEP, CO2 undergoes carbon fixation

150
Q

What type of molecule is NAD+?

A

a coenzyme

151
Q

How is energy released in photosynthesis/cellular respiration, or what actually carries the energy?

A

passing electrons to another substance releases energy, electrons hold the energy

152
Q

Number of carbons in pyruvate

A

3

153
Q

Where is the cellular respiration ETC?

A

The inner membrane(cristae) of mitochondria

154
Q

Where do organisms get electrons for cellular respiration?

A

Organic molecules(food) and O2

155
Q

Where is H+ pumped to and from in cellular respiration? Where are there high and low H+ concentrations?

A

Pumped from matrix to intermembrane space, then they go through ATO synthase back into the matrix.

High H+: Intermembrane space

Low H+: matrix

156
Q

What occurs in substrate-level phosphorylation?

A

Phosphate is directly transferred from an organic molecule to ATP

157
Q

What is a main characteristic of fermentation other than ATP production?

A

recycling of NAD+ into NADPH

158
Q

Purines and pyrimidines

A

Purines: adenine, guanine, wider

Pyrimidines: Thymine, Uracil, cytosine, narrower

159
Q

Which nucleotides pair with which?

A

A and T(DNA) and U(RNA)

G and C

160
Q

Which DNA strand is the template in transcription?

A

3’ to 5’

161
Q

tRNA

A

molecule with anticodons on one end, has H bonds and an amino attachment site on the 3’ end

162
Q

Which part of elongation in translation requires GTP?

A

Translocation/movement of tRNA

163
Q

What can possibly occur after translation?

A

protein processing

164
Q

Cell type-specific transcription

A

Certain activators for certain genes are available in certain cells

165
Q

What regulations occurs at initiation of transcription?

A

Promotors/transcription factors, enhancers/activators

Bio 116H Dr Balish/Zhao (6 decks)

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