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MCAT Biology Flashcards

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1
Q

What is the definition of a virus?

A

It is an obligate intracellular parasite that relies on host machinery whenever possible.

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2
Q

A viral genome may consist of what?

A

DNA or RNA and it can be either ss or ds. The genome can be linear or circular.

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3
Q

If the ratio of base pairs in viral DNA are not one to one, what does this indicate?

A

The viral genome is single stranded

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4
Q

What is an important adaption that has occurred in viruses?

A

They can have overlapping reading frames which allow for multiple proteins to be coded over the same gene sequence.

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5
Q

What are the two different life cycles of bacteriophages?

A

The lytic cycle- “lysis”, all host cells die

The lysogenic cycle- host cell replicates with viral genome incorporated into the bacterial genome. Eventually the viral genome becomes activated and the prophage enters the lytic cycle.

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6
Q

What is the difference between phases and viruses?

A

Phases are viruses the infect bacterial cells.

Viruses infect animal cells.

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7
Q

What is the lifecycle of a phage and virus?

A 
It binds to a proper host cell
It injects its genome into the host cell
Takes over the host replication machinery
Replicates it’s genome
Synthesizes capsid components
Assembles itself
Escapes to infect new cells
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8
Q

What comprises the enveloped virus? What kind of proteins are in the envelope?

A

The virus is encapsulated in a membrane taken from the host cell. It may contain proteins that were present in the host cell membrane and some viral encoded proteins that allow for absorption onto host cells.

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9
Q

How do viruses enter animal cells?

A

Receptor specific endocytosis

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10
Q

What is the term for the process of a virus to become enveloped?

A

Budding

Occurs when the virus exits the host cell and acquires some of the plasma membrane.

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11
Q

What are the the three life cycles of viruses?

A

Lytic
Productive- where budding occurs
Lysogenic

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12
Q

Describe +RNA Viruses?

A

Must encode RNA dependent RNA pol

Single stranded RNA genome that must encode RNA dependent RNA polymerase
Viral RNA pol will transcribe a -RNA template strand intermediate in order to synthesize the + strand.

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13
Q

Describe -RNA viruses

A

Must carry an RNA dependent RNA pol in the capsid.

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14
Q

Describe retroviruses

A

Must encode an enzyme for reverse transcriptase. These viruses integrate into host dsDNA thus they must be converted from ssRNA to DNA.

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15
Q

Describe dsDNA Viruses

A

Must encode enzymes to make dNTP’s and DNA replication

Needs to produce ingredients for DNA replication, the cell does not do this often compared to transcription which is always occurring.

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16
Q

What are the main distinctions between prokaryotes and eukaryotes?

A

Prokaryotes have no membrane bound organelles

Transcription and translation occur at the same place and at the same time

Pros have plasmids

Pros have a cell wall outside the lipid bilayer

Bacterium flagellum has a different structure than eukaryotes

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17
Q

What is a polyribosome?

A

The complex of many ribosomes translating a single piece of mRNA in prokaryotes. Translation occurs before transcription is even finished.

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18
Q

What is a plasmid in prokaryotes?

A

Extrachromosomal genetic material besides the circular Genome which may offer advantages

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19
Q

What is diffusion?

A

Movement of solute towards equilibrium. Solute always moves down its concentration gradient -high to low.

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20
Q

What is osmosis?

A

The movement of solvent towards equilibrium. Need a semipermeable membrane. Water moves from a region of low solute concentration to a region of higher solute concentration in an effort to dilute the higher concentration.

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21
Q

Describe the different osmotic gradient environments a cell can encounter

A

Isotonic- environment in relation to the cell has the same solute concentration

Hypertonic/hyperosmotic-the solution has more total dissolved solutes than the cell.

Hypotonic/hypoosmotic-the solution has a lower solute concentration compared to the cell

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22
Q

Gram negative bacteria has what?

A

An additional outer membrane that encompasses the cell wall which prevents the uptake of stain

Structure:

Outer membrane

Periplasmic space with peptidoglycan cell wall

Plasma membrane

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23
Q

What structures of bacteria facilitate adherence to surfaces?

A

Capsule- sugary goo outside of cell

Fimbria- small structures similar to pili but not for locomotion

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24
Q

Describe the 4 types of bacteria

A

Note autotrophs acquire carbon from CO2, heterotrophs acquire carbon from organic molecules created by other organisms.

Chemoautotrophs- get carbon from CO2, get energy from chemicals

Chemoheterotrophs-get carbon and energy from organic molecules

Photoautotrophs- get energy from sunlight, carbon sourced from CO2

Photoheterotrophs- energy from light but require organic molecules as carbon source

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25
Q

What does minimal medium mean?

A

Agar supplemented with only glucose

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26
Q

What is a wild type strain of bacteria?

A

One that has all the characteristics normal to that particular species.

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27
Q

What is an auxotroph bacterium?

A

One that can not survive in minimal medium. It requires an auxiliary trophies substance to live.

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28
Q

What do you call bacteria that require oxygen for metabolism?

A

Obligate Aerobes

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29
Q

List and differentiate the different classes of anaerobes

A

Facultative anaerobes-will use oxygen if it’s around but don’t need it

Tolerant anaerobes- can live in the presence of oxygen but do not use it for metabolism

Obligative anaerobes- will die in the presence of oxygen

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30
Q

What is the main component of bacterial cell walls?

A

Peptidoglycan

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31
Q

Bacteria reproduce how?

What is this term called?

A

asexual

Binary fission

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32
Q

Describe binary fission

A

The method in which bacteria reproduce. They simply create enough cellular components for two cells and then divide.

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33
Q

The stationary phase on the bacterial reproduction graph refers to?

A

The max population of bacteria in which cells cease to divide due to a lack of nutrients in the medium.

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34
Q

What are the 3 methods bacteria have evolved to facilitate increasing genetic diversity?

A

Transduction-via viruses
Transformation-via heat shock
Conjugation-via bridges

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35
Q

Replication forks grow in what direction in relation to the ORI?

A

Away

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36
Q

The separated strands of DNA with all the associated proteins for DNA replication is referred to as?

A

Open complex

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37
Q

What are the common DNA replication rules to memorize?

A

Polymerization occurs in the 5’ to 3’ direction

DNA polymerase requires a template

DNA pol requires a primer (which is made of RNA)

Each replication fork contains a leading and lagging strand

Replication on leading strand is continuous where as replication on lagging is discontinuous(Okazaki fragments)

All RNA primers are replaced with DNA and fragments are joined by DNA Ligase

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38
Q

What are the two functions of DNA pol 3

A

5’ to 3’ polymerase activity

3’ to 5’ exonuclease activity- proof reading activity

No known repair activity, just replication

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39
Q

What are the functions of DNA pol1?

A

Initiates Polymerase activity at the primer/ORI, then pol3 takes over.

DNA pol 1 removes the RNA primer via 5’ to 3’ exonuclease activity while replacing it with DNA

Also capable of proofreading in the 3’ to 5’ direction

Responsible for removing RNA primer segments on the lagging strand

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40
Q

What is the term that describes replication in prokaryotes due to their circular genome and only one ORI?

A

Theta replication

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41
Q

What is the function of telomerase?

A

It adds repetitive nucleotide sequences to the end of chromosomes thus lengthening telomeres and preventing chromosome degradation.

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42
Q

Describe the process of telomerase?

A

It is a protein that contains a RNA primer within the ribonucleoprotein complex. It has a reverse transcriptase function and converts the RNA primer sequence into a repetitive DNA sequence 5’-TTAAGGG3’ over and over again.

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43
Q

How does Telomere extension facilitate cancer?

A

Prevents signaling the cell for apoptosis, prevents the cell from aging and can immortalize the cell.

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44
Q

What is a nonsense mutation and what are the results?

A

A stop codon replaces a regular codon

The protein is is shorten in length

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45
Q

What is a missense mutation?

A

When one amino acid is coded for another. Can be silent or could have a negative impact on protein function.

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46
Q

What is a silent mutation?

A

The codon is changed to a new codon but still codes for the same amino acid. Protein is not impacted by the mutation.

47
Q

What are the three types of point mutations?

A

Silent mutation
Nonsense mutation
Missense mutation

48
Q

What is a frame shift mutation

A

A mutation that changes the reading frame of a gene sequence which results in leftover or not enough nucleotides to complete a codon.
Results in serious significant change in structure and function of protein!

49
Q

Are all insertions and deletion mutations frameshift mutations?

A

No, because as long as the insertion or deletion results in whole codons you end up removing or adding amino acids.

Of course the sequence may not code for the appropriate protein

50
Q

What is the definition of equilibrium?

A

When a reaction is at equilibrium, the rate of the forward reaction equals the rate of the reverse reaction.

51
Q

Equilibria occur in what systems?

A

Closed systems

52
Q

Are solids and pure liquids included in equilibrium constant expressions?

A

No, equilibrium expressions use concentrations

53
Q

If the reactants are gaseous in a chemical equation and you need to calculate Keq what do you use?

A

Partial pressures of the gas. Kp

54
Q

The value of Keq for a given reaction is constant at a given what?

A

Temperature

Keq of the reaction changes if the temperature changes.

55
Q

The value of Keq tells you what?

A

The direction the chemical reaction favors at equilibrium, whether there are more reactants or products at equilibrium.

56
Q

If the Keq is less than one then?

A

The reaction favors the reactants and there is more reactants than products at equilibrium.

57
Q

If Keq equals 1 then?

A

then there is roughly equal reactants and products at equilibrium

58
Q

If Keq is greater than one then?

A

the reaction favors products and there are more products than reactants at equilibrium

59
Q

What are the 3 differentiating characteristics of RNA?

A

1) single stranded
2) sugar is ribose vs 2-deoxy-ribose
3) Uracil is used vs Thymidine

60
Q

Is RNA more or less stable than DNA? Why?

A

Less stable, the 2’ OH group on sugar can nucleophillic attack phosphate backbone of RNA

61
Q

The reduced stability of RNA is not a problem why?

A

B/c RNA is a transient molecule that is transcribed, translated and then destroyed.

62
Q

What is the only type of coding RNA?

A

mRNA

63
Q

What are the 3 regions of mRNA and their functions?

A

5’ UTR-region is not translated-important for initiation and regulation

open reading frame-begins at start codon and ends at stop codon-codes for protein

3’ region- not translated, important for post transcriptional modifications

64
Q

Eukaryotic mRNA is monocistronic, what does this mean?

A

ORF codes for only one peptide

65
Q

Prokaryotic mRNA is polycistronic, what does this mean?

A

each strand of mRNA codes for more than one peptide

66
Q

What is the name of premature mRNA

A

heterogenous nuclear RNA (hnRNA)

Once hnRNA undergoes post-transcritptional modifications it becomes mRNA

67
Q

What are the two types of noncoding RNA?

A

Transfer RNA-brings amino acids from cytoplasm to the ribosome
Ribosomal RNA

68
Q

The thermodynamic driving force for DNA replication and RNA synthesis (transcription) is?

A

The hydrolysis of pyrophosphate from each nucleotide added to the chain

69
Q

What are two differences between DNA replication and transcription?

A

Transcription does not require an RNA primer to start RNA polymerization

RNA Polymerase does not have any 3’-5’ exonuclease/proof reading activity. Thus Transcription is a lower fidelity process than DNA replication.

70
Q

Does RNA transcription require a DNA template?

A

Yes, it is a template driven synthesis

71
Q

What are the various terms for the DNA template strand used in transcription?

A

non-coding, transcribed, antisense strand.

The other DNA strand “coding strand/sense strand” has the same sequence as the transcript with exception of U for T.

72
Q

What DNA strand has the same sequence as the transcript in transcription?

Is this strand used as the template for transcription?

A

Coding strand

No

73
Q

The sigma factor is an additional subunit required for RNA pol to do what?

A

Initiate transcription via binding via increasing the affinity of RNA pol to bind to ssDNA

74
Q

What are the 3 stages of transcription?

A

initiation at a promoter region
elongation
termination

75
Q

What is the open complex in transcription?

A

When RNA polymerase is bound to the promoter with a region of ssDNA

The closed complex is when RNA pol recognizes the promoter region bust has not unwound the dsDNA

76
Q

What are the two roles of the sigma factor in RNA polymerase?

A

1) helps RNA pol find promoter region
2) decrease the non-specific affinity of the holoenzyme for DNA

sigma factor leaves the RNA pol complex once some phosphodiester bonds have been formed

77
Q

RNA pol unwinds and transcribes along ssDNA in a structure termed?

A

transcription bubble

78
Q

Where does Eukaryote transcription occur?
Post transcription modifications?
Translation?

A

nucleus
nucleus
cytoplasm

79
Q

The primary transcript in prokaryotes is?

The primary transcript in eukaryotes is?

A

mRNA

hnRNA

80
Q

Protein coding regions on hnRNA are called?

A

Exons

81
Q

splicing of hnRNA is performed by what enzyme complex?

A

spliceosome

82
Q

Describe the process of the spliceosome

A

The complex binds to introns
it loops the introns
it then cuts out the loop and splices together exons

83
Q

Eukaryotic hnRNA must be modified how before translation can occur?

A

It must have a 5’ cap added (methylated guanine nucleotide)-essential for translation

It must have a 3’ poly a tail-(string of several hundred adenine residues)
(Both prevent mRNA digestion from exonucleases that are free in the cell)

Splicing out of introns

84
Q

gene regulation primarily occurs at the __________ level?

A

Transcriptional level

85
Q

How many RNA polymerases are there in prokaryotes?

How many RNA pol’s are there in eukaryotes?

A

1

3

86
Q

Name and list the functions of the three RNA pol’s in eukaryotes

A

1) RNA pol 1-transcribes most rRNA
2) RNA pol2- transcribes hnRNA, which equals mRNA,.
Also most snRNA and miRNA
3) RNA pol3 transcribes tRNA, some rRNA

87
Q

The DNA polymerases memorized are for what cells?

The RNA polymerases memorized are for what type of cells?

A

Prokaryotes, too many for eukaryotes

Eukaryotes

88
Q

What type of tertiary structure does tRNA have?
How is tRNA stabilized?
What are at the different ends of the stem and loop tRNA?

A

stem and loop
H bonding between neighboring segments of the looped RNA chain

loop is the anti-codon (complementary to mRNA/amino acid at 3’ end of tRNA)
3’ end is the amino acid binding site

89
Q

Explain wobble base pairing in tRNA

A

Only the first two codon/anticodon base pairs obey normal base pairing rules, the third base pair is more flexible. Thus third base pair may not pair with a complementary base.

90
Q

What are the common wobble base pairs?

A

G-U
inosine=I at 5’ end of anticodon
I-U, I-A, I-C

91
Q

Describe the process of amino acid activation/tRNA loading

A

1) amino acid is activated by attacking ATP and forming an amino acyl AMP + PPi
2) PPi is hydrolyzed in water to form 2 Pi, thus two high energy phosphate bonds have been cleaved or 2 equivalents of ATP, delta G is very negative.
3) The amino acid on the amino acyl AMP is loaded to the tRNA (unfavorable reaction driven by phosphate hydrolysis in previous steps) to form amino acyl tRNA

92
Q

What is the name of the enzyme that performs tRNA loading/ amino acid activation

A

aminoacyl-tRNA synthetase’s (highly specific)

There is one of these enzymes for every amino acid
These enzymes recognize both the tRNA and the amino acid

93
Q

amino acid activation serves two roles, what are they?

A

Deliver the correct amino acid to the tRNA
Thermodynamic activation of the amino acid

Note that peptide bond formation is an endergonic process, must be coupled with the hydrolysis of high energy bonds/activation.

94
Q

Compare the impacts of mutations/errors in DNA versus RNA(any type).

A

Mutations in DNA have long lasting effects, errors made in RNA during transcription have little impact , not passed onto progeny ( RNA is transcribed/translated and destroyed all the time).

95
Q

What are the components of the ribosome?

A

rRNA and proteins in a quaternary structure. There is a small and large segment.

96
Q

Where are ribosomes found?

A

In the cytoplasm and in the rough endoplasmic reticulum

97
Q

How many special sites do ribosomes have and what are the terms for them?

A

3 sites
A site-(aminoacyl site) where each new tRNA delivers its amino acid
P site-(peptide site) where the amino acid is transferred to the growing polypeptide attached to an tRNA
E site (exit site)- where the now empty tRNA sits before it is released from the ribosome

tRNA’s move through the sites A to P to E.

98
Q

The next codon to be translated in a mRNA sequence is adjacent to which site of the ribosome?

A

the A site

99
Q

Translation occurs in what direction on the mRNA?

A

5’ to 3’. Thus DNA replication, RNA transcription and protein translation all occur in the 5’ to 3’ direction

100
Q

Does prokaryotic translation always start at the 5’ end?

A

No, it can start somewhere in the middle of the mRNA as well. This is because prokaryotic mRNA is polycistronic (codes for multiple proteins) and there will be multiple start sites on the mRNA.

101
Q

Are upstream regulatory initiation sites used in translation similar to transcription?

A

Yes, instead of promoter sites there are ribosome binding sites (Shine Dalgarno sequence, in prokaryotes)

102
Q

List the three stages of translation, including the activation step

A

Activation- 2 high energy bonds required to convert amino acid to amino acyl-AMP to amino acyl-tRNA

Initiation- via ribosomes binding to their binding site (powered by GTP hydrolysis). The large section of ribosome come stock with a modified fmethionine -tRNA which H bonds to the start codon.

Elongation-powered via 1 GTP hydrolysis which enables the tRNA’s to shuffle through the A, P and E sites.

Termination-1 high energy bond is hydrolyzed from the last tRNA-polypeptide

Note* that peptide bond formation during translation does not require GTP hydrolysis because the amino acyl-tRNA bond is a high energy bond itself.

103
Q

What is the energy currency of translation?

A

GTP

104
Q

Describe the termination step in translation?

A

A release factor enters the A site which hydrolyzes the last tRNA from the polypeptide chain. The ribosome separates into its subunits and releases from the mRNA strand.

105
Q

How many high energy bonds does it take to synthesize a a peptide chain with n amino acid’s during translation?

A

4n

106
Q

What are 5 differences between prokaryotic and eukaryotic translation?

A

Eukaryotic ribosomes are larger

Eukaryotes do not use a modified f MET-tRNA (initiator tRNA), they use a regular MET-tRNA

hnMRNA must be processed and modified( spliced, 5’ cap and poly A tail) before translation

mRNA must be transferred to the cytoplasm (transcription and translation do not occur in the same place/time in Eukaryotes)

There are no ribosome binding sites

107
Q

How does methylation of DNA in prokaryotes impact gene expression?

A

It can either inhibit or promote gene expression

108
Q

How does DNA methylation in Eukaryotes impact gene expression?

A

It inhibits gene expression 2 ways

1) It physically blocks the gene from transcriptional enzymes
2) Certain enzymes bind to the site of methylation and recruit chromatin remodeling proteins and form a more densely packed DNA complex

109
Q

What is a strategy that cells use to increase the quantity of a protein?

A

Increasing the gene dose via gene amplification.

110
Q

What are repressible enzymes?

A

Anabolic enzymes whose transcription is repressed in the presence of excess amounts of their products.

Default is ON until repressed

RNA level regulation of of gene expression

111
Q

What are inducible enzymes?

A

Catabolic enzymes whose transcription is stimulated in the presence of abundant substrate

Default is OFF until stimulated

RNA level regulation of gene expression

112
Q

What are the two components of an operon?

A

The protein coding sequence and an upstream regulatory sequence

113
Q

What are the two conditions for the LAC operon to be turned on?

A

Low glucose present and the presence of Lactose

MCAT (3 decks)

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