Reading Quiz Ch 7 - 13 Flashcards
(137 cards)
1
Q
The process of gene expression always involves which process(es) described in the central dogma? Why?
a) transcription
b) translation
c) replication
d) transcription and translation
A
a) transcription
some genes that are expressed are functional RNA genes. The RNAs don’t undergo translation to protein because they do their job in the cell as an RNA
2
Q
At which step of gene expression can cells amplify the number of copies a protein made from a single gene? Why?
a) both transcription and translation
b) transcription
c) translation
d) neither transcription nor translation
A
a) both transcription and translation
proteins can be made in large quantities by transcribing many mRNAs from the gene, and then each mRNA can be translated into many copies of the protein. In contrast, if just a few mRNAs are made, only a few copies of the protein are made.
3
Q
Which nucleic acid often base pairs with itself to fold into complex three-dimensional shapes in the cell? Why?
a) RNA
b) neither RNA nor DNA
c) both RNA and DNA
d) DNA
A
a) RNA
RNA is often single-stranded and complementary regions will base pair with each other to form secondary and tertiary structures.
4
Q
What is the difference between the mechanisms of DNA polymerase and RNA polymerase?
A
DNA polymerase needs a primer to provide a base-paired 3’ –OH to catalyze the polymerization reaction. RNA polymerase does not need a base-paired 3’ –OH, it can join two nucleotides together without a primer.
5
Q
Why does RNA polymerase make more mistakes than DNA polymerase?
A
RNA polymerase lacks the ability to proofread its work. If an incorrectly base-paired nucleotide is added, it cannot excise the nucleotide and add the correct one.
6
Q
Which characteristic of a replicating RNA polymerase allows multiple transcripts to be made simultaneously from the same region of DNA?
A
The RNA transcript dissociates from the DNA template immediately once they are made. This allows many RNA polymerases to form a “caravan” on the gene, producing many transcripts.
7
Q
Which RNAs are never translated into protein? What are they collectively called?
A
tRNA, rRNA, and miRNA
noncoding RNAs
8
Q
Shown below is a gene with the direction of transcription noted. How does the RNA polymerase know which strand to use as a template for the RNA, and which strand would it choose in this case?
A
It would use the bottom strand.
RNA polymerase binds to promoter sequences in a specific orientation. The RNA polymerase will then move away from the promoter using the promoter-dictated directionality and uses the 3’ to 5’ strand as a template to make a new RNA in the 5’ to 3’ direction.
9
Q
What performs the function of bacterial sigma factor in eukaryotes?
A
General transcription factors
Sigma factor is an accessory protein to RNA polymerase in bacteria that helps the polymerase bind to the promoter region. In eukaryotes, this function is performed by a set of proteins called the general transcription factors.
10
Q
The splicing of introns out of an mRNA molecule is catalyzed by
A
RNA molecules in the snRNPs that base pair with splice sites. This base-pairing helps promote the rearrangement of bonds to remove the intron.
11
Q
Export of RNA from the nucleus requires the RNA to have which characteristic(s)?
A
RNAs must have the features of a processed mRNA. This includes being properly spliced (no introns), having a 5’ cap and a poly-A tail.
12
Q
The reading frame to use for translating an mRNA into functional protein is determined by the…
A
location of an AUG.
The translation of an mRNA in eukaryotes begins when the initiator tRNA encounters the first AUG in an mRNA. The complex containing the initiator tRNA starts scanning the mRNA from the 5’ end to find the AUG.
13
Q
Show below is a tRNA for tryptophan. Which of the locations on the tRNA accommodates looser base-pairing rules?
a) site 3
b) all of the sites maintain strict base-pairing rules
c) site 2
d) site 1
A
The third base in a codon can base-pair loosely with the corresponding base in an anticodon in a tRNA. This allows specific tRNAs to recognize more than one codon (called wobble base pairing) for a redundant genetic code.
14
Q
How do tRNAs become attached to the correct amino acid?
A
Enzymes called aminoacyl-tRNA synthetases recognize tRNAs with a specific anticodon as well as the amino acid for the tRNA and catalyze a reaction to join them together. This is called “charging” a tRNA.
15
Q
Using the genetic code below, determine the amino acids that a polynucleotide of UC would code for
A
Leu, Ser
16
Q
The catalytic sites for peptide bond formation during translation are found in which part of the ribosome?
A
large subunit RNAs
The catalysis of the peptide bonds in the growing polypeptide chain during translation is performed by the rRNA of the large subunit. The ribosome is a ribozyme; proteins play a largely structural role.
17
Q
What recognizes the stop codons in an mRNA?
A
release factor
When the ribosome encounters a stop codon, instead of a tRNA binding, a protein called release factor binds and catalyzes the addition of a water molecules to the carboxyl end of the polypeptide and releases it
18
Q
What is the benefit of protein synthesis in polyribisomes?
A
More protein can be produced from a single RNA.
19
Q
What is the name of the complex that degrades proteins that have reached the end of their lifespan, are damaged or are misfolded?
A
proteasome
20
Q
The structure of the proteasome is shown below. What group is recognized by region A to indicate that the protein is marked to be eliminated? What are the functions of B and D?
A
Proteins marked for elimination have a chain of ubiquitin groups added to them.
This is recognized by region A and the protein is then threaded into the central cylindaer (B) to be degraded by the protease active sites (D).
21
Q
Protein concentration can be regulated by all of the steps listed EXCEPT
a) DNA replication
b) RNA processing
c) mRNA stability
d) nuclear export
A
DNA replication
22
Q
Why do we think RNA may have been a primitive autocatalytic system on early Earth?
A
RNA carries/stores information and through base-pairing rules, can act as a template for self-replication. It also had the ability to catalyze reactions.
23
Q
Why is RNA thought to predate DNA in evolution?
a) RNA is less stable than DNA
b) RNA forms many different types of functional molecules, like snRNA, rRNA, and tRNA
c) The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth.
d) rRNA genes are more conserved through evolution
A
c) The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth.
Although the other selections are true, the sugar in RNA, ribose, is more easily produced from formaldehyde, which was abundant in the early environment of Earth.
24
Q
DNA is a better molecule for long-term storage of genetic information than RNA because…
A
The deoxyribose sugar stabilizes the DNA chains; it allows the nucleotide chains to grow to longer lengths. In addition, the presence of thymine (rather than uracil) facilitates the detection and repair of damage.
25
Transplanting the nucleus of an epithelial cell into an egg cell lacking genetic information leads to the formation of
a) a hybrid cell that has characteristics of both embryonic cells and epithelial cells
b) another epithelial cell
c) a normally developing embryo
d) a dead cell
c) a normally developing embryo
Nuclear transplantation experiments took different types of adult body cells and placed them in egg cells without any DNA and these cells developed into normal embryos and then into a normal animal. This showed that differentiated cells contain all the genetic information for many any other type of cell.
26
A housekeeping gene is a gene whose cellular function is
a) involved in the removal of waste products from cells
b) turned off periodically for maintenance
c) important for processes found in all cell types
d) critical for specialized activities in a specific cell type
Housekeeping genes code proteins that play critical roles in basic cellular processes that are found in all cell types. They include the genes that encode the enzymes of glycolysis, gene expression, metabolism, and basic cell structure.
27
Which of the following is the main point of control for regulating gene expression levels?
a) transcription
b) protein degradation
c) mRNA degradation
d) translation
a) transcription
Inhibiting the transcription of genes that are not currently needed help keep unnecessary intermediates from being synthesized.
28
Mutations in which of the following elements would abrogate RNA polymerase's ability to activate gene expression?
a) transcription termination site
b) regulatory DNA sequence region
c) promoter
d) major groove
RNA polymerase binds to the promoter, a specialized sequence that orients the enzyme in the direction of transcription.
Transcription will then start further downstream of the promoter at the transcription initiation site.
29
Excess amounts of the amino acid tryptophan result in the downregulation of the expression of the enzymes required for its synthesis due to ...
the amino acid binding to the repressor protein, which activates it and enables it to bind to the operator sequence near the promoter. The binding of the repressor in the proximity of the promoter inhibits the binding of RNA polymerase, and thus the expression of the trp genes.
30
Generally, bacterial promoters that are regulated by transcriptional activators bind _____ to RNA polymerase, but promoters that are regulated with transcriptional repressors bind _____ to RNA polymerase.
weakly; strongly
Transcriptional activators in bacteria bind to an activator binding site to help the RNA polymerase bind to the promoter. Without this aid, the binding of the polymerase to the promoter is weak and does not activate transcription at high frequency.
Genes controlled by transcriptional repressors bind polymerase, and this binding can be blocked by the binding of the repressor in the region.
31
If lactose and glucose are both available to a bacterial cell, which carbon source(s) will be used?
Glucose
Bacteria prefer to use glucose whenever it is present. When glucose is present, it will be the only sugar used and expression of the Lac operon genes will be reduced. When only lactose is present, the production of lactose-breakdown enzymes will increase to enable the usage of this alternative carbon source.
32
Eukaryotic repressor proteins can decrease transcription using which of the following mechanisms?
Eukaryotic repressor proteins can act to reduce transcription by inhibiting the assembly of the transcriptional initiation complex, or they can recruit histone-modifying complexes like deacetylases, which remove the activating acetyl groups from nearby histones
33
How do eukaryotic activator proteins regulate chromatin packaging to enhance transcription?
1) attraction of histone-modifying complexes that place activating marks (like acetyl groups) on histones
2) the recruitment of chromatin-remodeling complexes to eject or slide nearby nucleosomes
34
What is the purpose of chromosome loops?
Enhancer sequences act at a distance from their target gene. They are prevent from inappropriately activating the transcription of other nearby genes by the formation of chromosome loops that restrict the engagement of enhancers to just the genes within the same loop
35
What is combinatorial control and how does it differ from operons?
In combinatorial control, transcriptional regulators function together to determine the level of expression of a particular gene.
Operons, on the other hand, are a set of genes under the control of a specific transcriptional regulator, a typical control mechanism in prokaryotes.
36
In eukaryotes, multiple genes can be expressed simultaneously by
a) the binding of a mediator complex to several genes at once
b) the binding of a specific transcriptional regulator to several genes
b) the binding of a specific transcriptional regulator to several genes
In eukaryotes, gene expression is often decided by a committee of transcriptional regulators. A single transcriptional regulator can act as the final voice in the combinatorial control to turn on expression by coordinated binding to several genes at once.
37
What is a reporter gene? What is its use case?
A reporter gene is an experimentally engineered regulatory DNA sequence that has been fused to a gene that encodes a protein that is easily observed.
It provides information into where and when a gene is expressed. The regulatory sequences drive the expression of a gene product that is easily monitored.
38
What is a master transcription regulator?
Master transcription regulators drive the development of a particular cell type and even whole organs by turning on specific genes. The master regulator turns on the expression of other transcriptional regulators that regulate other genes. Results in a cascade of expression, coordinating the formation of an organized group of cells.
39
How do cells maintain their identity through cell divisions?
A master transcription regulator that controls its own expression, as well as the expression of other cell-specific genes can create a positive feedback loop.
Because the regulator is present in the precursor cell before division, the protein will be present in the progeny cells and thus will drive further expression of the regulator.
40
collectively, the processes that alter the levels or activity of a gene product are called...
post-transcriptional control
41
MicroRNAs block the expression of a specific gene product by binding to the _____ and inhibiting \_\_\_\_\_
mRNA; translation
MicroRNAs form a complex with RISC proteins. Once the miRNA forms a complementary base-paired duplex with target RNA, it either targets the mRNA for destruction or reduces the efficiency of translation.
42
Which protein complex mediates the RNA interference (RNAi) process by inhibiting RNA polymerase via histone methylation and heterochromatin formation?
RITS
small interfering RNAs (siRNAs) can form a complex with different protein complexes to lead to different effects on gene expression.
siRNAs that form a complex with RITS (RNA-induced transcriptional silencing0 will bind to the RNA coming from RNA polymerase and will lead to the formation of repressive chromatin structures at that gene region.
43
What are the functions of long noncoding RNAs (lncRNA)?
Long noncoding RNAs (lncRNAs) are known to have functions in regulating gene activity but can also act as a scaffold for protein complex assembly. A prominent example is a lncRNA that helps the telomerase complex assemble.
44
What is a horizontal transfer?
The acquisition of DNA from another organism, which results in genetic change.
45
Which cells contribute to evolutionary changes in an organism? Why?
Mutations in germ-line cells contribute to evolutionary change because they are the cells that go on to form the progeny of the organism.
46
How do point mutations typically arise?
Replication errors
DNA polymerase has a low error rate but mistakes still occur and can be propagated into progeny cells. Other mutagenic phenomena are less common.
47
A mutation in the _____ of the gene encoding the enzyme lactase enables the expression of this gene in adults.
regulatory sequence
Normally, lactase is expressed only in infancy to help digest milk sugars. A mutation in the regulatory DNA sequences arose about 10,000 years ago that caused the expression of this enzyme in adults, allowing them to consume and digest milk for nutrition.
48
Shown here are regions of two homologous chromosomes. If homologous recombination occurred between the short repetitive sequence after the gene in Chromosome 1 and the short repetitive sequence before the gene in Chromosome 2, what would be the result?
The duplication of the gene would occur on Chromosome 1 and deletion would occur on Chromosome 2.
49
What are mobile genetic elements? How do they promote gene duplication and exon shuffling?
Mobile genetic elements have similar sequences to each other and are found throughout the genome. They serve as targets for unequal homologous recombination.
50
What percentage of human genes have clearly recognizable homologs in the fruit fly?
50%
These genes likely have common ancestry and have been more resistant to change over the years due to the need to preserve an important function.
51
Germ-line mutations that are deleterious are likely to be...
a) preserved or lost depending on chance
b) lost from a population
c) preserved in a population
b) lost in a population
Deleterious mutations in the germ-line have negative consequences on the organism, decreasing the likelihood of that organism to successfully reproduce and pass on the mutation. These types of mutations are likely to be lost in the population over time.
52
Which of the following DNA sequences is the LEAST likely to accommodate mutations? Why?
a) regulatory DNA sequences
b) ribosomal RNA sequence
c) DNA sequences found between genes
d) the coding sequence of a duplicated gene
b) ribosomal RNA sequence
genes that encode products with a specific and unique function cannot accommodate mutations easily. Many mutations will alter their function and lead to deleterious consequences.
53
What is conserved synteny? What does it suggest?
conserved synteny refers to the conservation of the order of genes on a region of a chromosome between species. This suggests that despite all the shuffling that genomes are subject to, these regions were resistant to change.
54
What is replicative transposition?
DNA-only transposition that involves the replication of the transposon DNA before mobilization and insertion at another location. Thus, the original copy remains in place.
55
What are L1 elements and Alu sequences? What are their differences?
L1 elements and Alu sequences are retrotransposons. They make up 15% and 10% of the human genome, respectively.
L1 elements encode their own reverse transcriptase for mobilization; Alu sequences do not.
56
Name the similarity and difference between viruses and mobile genetic elements.
Both viruses and mobile genetic elements can replicate themselves and insert into genomes, either using the cell's machinery or sometimes enzymes provided by the genetic material of the virus or genetic element.
Only viruses can escape the cell to move to other organisms.
57
The transcription of a retroviral DNA supplies what products for the replication virus?
more copies of the genome and protein for the viral coat/envelope
58
The total size of the human genome is approximately _____ base pairs.
3.2 billion
59
\_\_\_\_\_ of human DNA is in protein-coding exon sequences compared to _____ that is in repetitive elements, including mobile genetic elements.
a) 1.5%; 50%
60
Which organism has the densest distribution of genes in their chromosomes? Why?
a) flies
b) humans
c) yeast
c) yeast
Less complex organisms have less sequence between genes and fewer introns and regulatory sequences. Humans have genes that are very sparsely distributed in the genome.
61
What best describes how some plants have more protein-coding genes than humans?
Generally, more complex organisms like humans have more protein-coding genes. However, humans have a small number of genes compared to some plants due to plants having undergone many genome duplications. Plants have existed for long periods of time as polyploids. Humans also have a great variation in the number of ways a single gene can be expressed.
62
An open reading frame (ORF) is determined as a sequence that has about 100 codons that lack stop codons. Why is finding ORFs helpful in determining the number of genes in an unknown sequence?
To estimate the number of genes in a DNA sequence stretches of nucleotide codons without stop codons are found using a computer. If they are longer than 100 codons, the sequence is a likely candidate for a gene since a stop codon is expected by chance every 20 codons.
63
RNA sequencing can give a more accurate estimate of the number of genes in a genome than finding ORFs because
RNA sequencing will provide information as to which sequences in the genome are actually transcribed into RNAs (rule out ORFs that are not transcribed). This method will also identify functional or regulatory RNA genes.
64
What are restriction enzymes?
Restriction enzymes are enzymes that recognize and cut specific DNA sequences, whether in cells or in a test tube. The enzymes cut regardless of the DNA's origin.
65
DNA migrates through the pores of an agarose gel toward the _____ electrode. Larger fragments travel more \_\_\_\_\_.
positive; slowly
66
DNA in a gel is most often visualized by
a) staining with a UV-reactive dye
b) using a white-light box
c) using a backlight
d) staining with a blue dye
a) staining with a UV-reactive dye
DNA itself is colorless under visible light or blacklight.
The DNA bands are visualized by adding a UV-reactive dye that intercalates between the bases of DNA molecules and observing under UV light.
67
Which feature of a cloning vector enables bacterial cells to replicate a plasmid?
a) DNA polymerase
b) recombination site
c) restriction enzyme cute site
d) replication origin
d) replication origin
For a piece of DNA to be replicated by the cell's machinery, it requires a replication origin. Investigators take advantage of this phenomenon to isolate many copies of a desired plasmid
68
What is a genomic library?
What is a cDNA library and how is it made?
Genomic library: a collection of plasmids, each containing different chromosomal fragments from the genome of an organism
cDNA library: a library of DNA fragments that are made from reverse transcription of mRNA transcripts. This type of library contains only the coding sequences of each gene, since introns are spliced out of mature mRNAs
69
What are the first and second steps of PCR?
In PCR, the target DNA must first be heated to denature the molecule into single-stranded DNA.
This allows the primers to bind in the second step by base-pairing with their complementary sequence.
70
Approximately how many double-stranded AN molecules will be formed from one starting molecule after 3 rounds of PCR?
8
71
What is required so that PCR can be used to detect small amounts of a DNA virus in a sample of blood?
primers specific to the DNA of the virus
primers are used to amplify the small amount of viral DNA present to an observable level
72
What are short tandem repeats and what is it used for?
Short tandem repeats are noncoding sequences that expand and contract in size between generations and are hypervariable. They are used to identify individuals by DNA analysis (DNA fingerprinting)
73
What is the chain-termination method of sequencing?
Sanger sequencing relies on the formation of partial copies of the DNA fragment. The fragments are produced by random termination with the incorporation of one of four different fluorescently labeled dideoxynucleotides. The fragments are separated by size in a capillary gel matrix. The fluorescent tags are read to reveal the sequence of the DNA molecule.
74
Unlike older methods, third-generation DNA sequencing methods can
detect the attachment of a single nucleotide to a DNA molecule (template).
Sanger and second-generation methods of sequencing require the amplification of the target sequence and the use of chain-terminating dideoxynucleotides to determine the sequence.
75
What are the differences between RNA-seq and in situ hybridization?
RNA-seq can be used to compare expression in different cell samples at different timepoints in development, in different cell types, or in cells subjected to different treatments.
RNA-seq cannot provide data on the local differences of expression in tissue. In situ hybridization can show the levels of a gene product in the tissue.
76
What is the difference between classical (forward) genetics and reverse genetics?
Classical (forward) genetics involves finding mutant organisms with a phenotype of interest and identifying the genes involved in determining that trait.
In reverse genetics, changes are made to a gene of interest, and the subsequent phenotype is observed to determine the function(s) of the gene of interest.
77
What is one function of a double-stranded RNA?
double-stranded RNA (dsRNA) can be introduced to inactivate genes. The molecule is identical in sequence to both strands of the gene to be inactivated. Once expressed, the dsRNA is catabolized into single-stranded, complementary miRNAs, which can hybridize to the RNA transcript of the target gene and promote its destruction by the RNAi pathway.
78
The CRISPR system can be used to activate a gene by altering the Cas9 enzyme in what way?
fusing an inactive Cas9 to a transcriptional activator
Instead of targeting a Cas9 nuclease to a site for making a double-strand break for genome editing, CRISPR can be used to activate various activities at specific locations in the genome. This is done by inactivating the Cas9 so that it is no longer a nuclease, and then attaching a protein with the desired activity.
79
Organisms with a mutation in a specific human disease-causing gene
a) cannot be ethically produced using CRISPR
b) are never able to recapitulate the human disease signs
c) are potential models for that human disease
d) are impossible to make with current technology
c) are potential models for that human disease
Researchers can create specific disease-causing mutations in laboratory animal and cell models to study human diseases. These mutations can be produced using CRISPR and other current technologies, though they are time-consuming and difficult.
80
Transgenic plants can be produced using the ability of plants to
a) efficiently take up naked DNA suspended in culture medium
b) be manipulated to form a mature plant from cultured transgenic cells
c) resist the infection of their cells by Agrobacterium NDA
d) pass transgenes to all the cells of the organism through the roots
b) be manipulated to form a mature plant from cultured transgenic cells
Plant cells can be transfected to form transgenic cells with transgenic DNA using a bacterium called Agrobacterium. These transgenic plant cells can then be manipulated to form a shoot that can develop into an entire transgenic plant.
81
Shown here is an expression vector.
For the gene of interest to be expressed in the cells, the gene of interest must be cloned where in this vector?
Expression vectors contain a promoter that drives transcription of the gene of interest.
Promoters have directionality so for the gene to be expressed the gene must be placed in the proper location relative to the promoter.
82
If a protein with a specific activity is isolated, how can the encoding gene be identified?
mass spectrometry followed by gene database searching
mass spec will allow us to determine many short amino acid sequences from the protein. These sequences can then be compared to a database of all known protein-coding genes to identify the gene that encodes this protein.
83
Which of these macromolecules is NOT commonly found in the plasma membrane?
a) nucleic acids
b) proteins
c) carbohydrates
d) fatty acids
a) nucleic acids
84
Phospholipids assemble into a membrane using
a) assembly proteins
b) enzymes
c) covalent bonds
d) hydrophobic forces
d) hydrophobic forces
85
What kind of lipid molecules is represented in this figure?
phospholipid
86
What are the structural similarities and differences between phospholipids, glycolipids, and triacylglycerol?
Phospholipids, glycolipids, and triacylglycerol all consist of a 3-carbon glycerol molecule with fatty acids attached to two of its carbons.
The molecule attached to the third carbon differs between the three lipid categories: in triacylglycerol, it is another fatty acid, in glycolipids, it is a sugar molecule, in phospholipids, it is a phosphate.
87
Which type of movement is the least common for lipids in a bilayer? When does this movement occur?
Flip-flop
This only happens when catalyzed by transporter proteins.
88
What are the attributes that lead to lower membrane permeability?
high amounts of cholesterol
more saturated fatty acids
longer fatty acid tails
89
Why do cells regulate their membrane fluidity? How do cells regulate their fluidity?
Membrane fluidity can be regulated by cells by changing the lipid composition of the membrane.
This is important to allow membrane proteins to diffuse from their place of insertion to where they are needed for their function. In addition, membrane proteins have to come into contact with other proteins for signaling.
90
Where are new phospholipids made?
Enzymes that are bound to the cytosolic face of the ER membrane make new phospholipids and insert them into the ER membrane.
91
What is the difference between scramblase and flippase?
Newly-made phospholipids are added to the cytosolic side of the ER membrane, and scramblases (a transporter) randomly transfer phospholipids from one monolayer to the other. This allows the membrane to grow as a bilayer in which the two leaflets even out continuously in size and lipid composition.
Most cell membranes are asymmetric: the two halves of the bilayer often include strikingly different sets of phospholipids. Membranes that emerge from the ER with an evenly assorted set of phospholipids are selectively shuffled by flippases in the Golgi membrane.
92
If a phospholipid is located in the outer layer of the bilayer in a vesicle, where will it end up when the vesicle fuses with the plasma membrane?
a) the cytosolic face of the bilayer
b) the extracellular face of the bilayer
c) randomly on one side or another
d) vesicles cannot fuse with the plasma membrane
a) the cytosolic face of the bilayer
When vesicles fuse with the plasma membrane, the lipids on the outside of the vesicle will end up on the cytosolic face of the plasma membrane. Lipids on the inside of the vesicle membrane will face the noncytosolic face of the plasma membrane.
93
\_\_\_\_\_ are the most abundant molecules in the animal cell membrane, whereas _____ make up 50% of the membrane by mass.
Lipids; proteins
94
Plasma membrane proteins that move ions in and out of cells using active transport are called
a) anchors
b) transporters
c) channels
d) receptors
transporters
95
What are the two different ways proteins can associate with the membrane?
1) transmembrane association: proteins are fully inserted into the membrane
2) monolayer associated; proteins are inserted into one of the layers of the bilayer
96
Proteins that are associated with the membrane by noncovalent interactions with other membrane proteins are called _____ proteins.
peripheral membrane proteins
97
What are integral membrane proteins?
Transmembrane, monolayer associated, and lipid-linked proteins are all directly associated with the membrane and are called integral membrane proteins.
98
If the backbone of a polypeptide is hydrophilic, how can a transmembrane alpha-helix span the hydrophobic portion of the lipid bilayer?
The amino acid side chains in a transmembrane helix are hydrophobic and interact with the hydrophobic interior of the bilayer. This shields the hydrophilic backbone from unfavorable interactions.
99
Which of the following is a common transmembrane protein structure that can traverse the membrane to form a pore or channel by alternating hydrophobic and hydrophilic amino acids?
beta-barrel
100
What are detergent molecules?
Detergents are amphipathic molecules that bind with membrane proteins and membrane lipids to disrupt their interactions and release the proteins from the membrane.
The detergents' hydrophobic portion disrupts the hydrophobic interaction of lipids with membrane proteins. The hydrophilic region stabilizes the protein in solution by interacting with the aqueous environment.
101
What is the FRAP experiment used for?
To determine the mobility of the protein of interest. The recovery of fluorescence in FRAP experiments is directly related to the amount of mobility the protein exhibits. This can be due to increased fluidity of the membrane, as well as whether the protein is relatively unconstrained by interactions that would impede on its motion.
102
What are the ways cells restrict the lateral movement of membrane proteins?
establishing diffusion barriers in the membrane
tethering to external cell components like the extracellular matrix or adjacent cells
anchoring to internal cell components like actin or other proteins
103
Which molecules does the lipid bilayer allow to pass through? Why?
Which does it not allow to pass through? Why?
nonpolar molecules because they interact favorably with the hydrophobic tails. Polar molecules without charge can pass through at a low rate but are further limited by size constraints.
it excludes ions and charged molecules from passing through because of their interaction with water.
104
What are the differences between transporters and channels?
Transporters can facilitate both active or passive transport of solutes. Transporters are highly selective.
Channels facilitate only passive transport. Channels loosely discriminate between ions when open.
105
Which ion is generally maintained at a high concentration inside the cell? Which is maintained at a high concentration outside?
K+; Na+
106
Cells, compared with the extracellular fluid are
a) slightly negatively charged
b) electrically neutral
c) extremely positively charged
d) slightly positively charged
a) slightly negatively charged
due to the distribution of ions and charges across the membrane
This leads to a slight negative resting membrane potential of cells
107
Which factors determine the force driving the passive transport of charged solutes across the membrane?
a) ATP gradient
b) electrochemical gradient
c) concentration gradient only
d) membrane potential only
b) electrochemical gradient
108
Which of the following is NOT used as a source of energy by a transmembrane pump to actively transport a solute?
a) Na+
b) H+
c) ATP
d) K+
d) K+
109
What is a common intracellular signaling molecule? Why?
Calcium ions
The concentrations in the cell are kept extremely low so that Ca2+ channels can rapidly change the concentration and activate cellular processes
110
What is a selectivity filter?
The pores of ion channels contain a region called the selectivity filter. The selectivity filter's width imparts a size restriction on the ions that can pass through. The charged amino acid residues in this region repel any ions of the wrong charge.
111
The opening of channels can be triggered by what three mechanisms?
ligand-binding (ligand-gated)
membrane potential (voltage-gated)
mechanical forces (mechanically gated)
112
Which cell types in humans use voltage-gated ion channels?
Cells part of the nervous system and cells that respond to nerve stimulation like muscle cells.
113
How are voltage-gated ion channels opened by voltage sensors?
When membrane potential changes sufficiently, the electrical forces of the membrane potential cause voltage sensor domains to change conformation, opening the pore of the channel.
114
How does an action potential spread along the cell membrane?
An action potential spreads along the cell membrane because the change in membrane potential triggers the opening of nearby Na+ channels, which then change the membrane potential in their local vicinity. This continues down the cell membrane in the direction away from the location of the originally stimulated channels.
115
What keeps the action potential from traveling backward along the axonal membrane?
During an action potential, Na+ channels change conformations from closed to open to inactivated, then back to closed.
Channels are in the inactivated state directly after opening, which keeps them from being reactivated immediately, and leads to the movement of the action potential away from the site of activation.
116
What is the role of K+-gated ion channels in an action potential? when do they open?
K+-gated ion channels open after membrane depolarization. K+ moves across the membrane to reestablish resting potential.
117
How is an electrical signal converted to a chemical signal at a nerve terminal?
An electrical signal is converted to a chemical signal at a nerve terminal by the action of voltage-gated Ca2+ channels, which allow the influx of Ca2+. Ca2+ triggers the fusion of neurotransmitter-containing vesicles with the plasma membrane to release the neurotransmitter into the synaptic cleft.
118
What is the molecular target of the antidepressant Prozac?
Prozac binds to and inhibits the Na+-driven symport that drives the reuptake of serotonin. This leads to sustained levels of serotonin signaling in the synaptic cleft.
119
The food molecule whose breakdown generates most of the energy for a majority of animal cells is
glucose
120
Why do cells use enzymes to harvest energy from food molecules rather than by direct oxidation?
Direct oxidation is the release of all the energy in glucose to CO2 and H2O in a single combustion step. This would lead to a massive release of energy as heat.
Instead, cells use enzymes to transfer energy from food to carrier molecules in small steps. The carrier molecules carry energy in usable "packets."
121
The major products of the citric acid cycle are...
CO2 and NADH (from the oxidation of acetyl CoA)
122
During glycolysis, the number of ATP consumed (per glucose molecule) is \_\_\_\_\_, while the number produced is \_\_\_\_\_
two; four
123
What is the function of a kinase?
to add a phosphate group to a molecule
they are very specific to the molecule they phosphorylate. Hexokinase, for instance, phosphorylates the 6-carbon sugar glucose.
124
The first step of glycolysis uses one ATP molecule in order to...
phosphorylate glucose to glucose 6-phosphate
125
What is the purpose of a fermentation process?
To recycle NADH back to NAD+ so that glycolysis can continue in the absence of oxygen.
No ATP is generated and lactic acid is produced
126
What are the products of glycolysis?
pyruvate, ATP, and NADH
127
Refer to the diagram below. If cells that cannot carry out fermentation were grown in anaerobic conditions, at which step would glycolysis halt?
step 6: where NAD+ is converted to NADH
128
Fatty acids can be used to produce energy by conversion to _____ in the _____ of the cell.
acetyl CoA; mitochondria
129
Why is the presence of oxygen required for the citric acid cycle to operate?
because the NADH passes its electrons to oxygen in the electron transport chain to renew NAD+. NAD+ is needed for the reactions of the citric acid cycle.
130
What does each molecule of acetyl-CoA entering the citric acid cycle produce?
acetyl CoA is a 2-carbon molecule; those carbons are oxidized to 2 CO2
In the process of acetyl CoA oxidation, 3 NADH and 1 FADH2 are produced.
131
What is the role of oxygen in the electron transport chain? what happens to it?
Oxygen is the final electron acceptor of the electron-transport chain. It captures the electrons that were transferred from activated carriers. In the process of accepting electrons, oxygen also accepts hydrogen ions and is reduced to H2O
132
Glycolysis produces _____ ATP molecules, whereas the complete oxidation of glucose to water and carbon dioxide produces _____ ATP molecules.
2; 30
glycolysis uses 2 ATP molecules and produces 4, yielding a net of 2 ATPs
complete oxidation of glucose to CO2 by citric acid cycle and oxidative phosphorylation produces about 30 molecules of ATP
133
What are some other uses of pyruvate other than to be converted to acetyl CoA for the citric acid cycle?
synthesis of alanine
ethanol and lactic acid fermentation
134
What is gluconeogenesis?
The synthesis of glucose from pyruvate
135
Gluconeogenesis requires a total of _____ ATP and _____ GTP molecules.
4 ATP; 2 GTP = 6
136
What is phosphofructokinase? How is it inhibited?
Phosphofructokinase is a glycolytic enzyme that catalyzes one of the irreversible steps of glycolysis (the conversion of fructose 6-phosphate to fructose 1,6-bisphosphate).
This enzyme's activity is shut down by feedback inhibition when there are high levels of ATP because if ATP is abundant further glycolysis becomes unnecessary.
137
What is glycogen synthetase, and how is it activated?
Glycogen synthetase is an enzyme that forms glycogen from glucose. The activity of this enzyme is triggered by high levels of glucose 6-phosphate
