Molec Cell > Exam 2 > Flashcards

Exam 2 Flashcards

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1
Q

Where does the energy to form a phosphodiester bond come from?

A

The breaking of a P-P bond (phosphoanhydride) in dNTP

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2
Q

What is econuclease activity?

A

proofreading in the 3’ to 5’ direction (opposite synthesis) done by DNA polymerase

DNA polymerase will then correct it in the 5’-3’ direction

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3
Q

Why can DNA not be synthesized in the 3’-5’ direction?

A

It would make proofreading impossible because the phosphoanhydride bond it on the 5’ end of the nucleotide, so if it was removed during proofreading, there would be no high energy bond available for the addition of the next nucleotide.

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4
Q

What happens if there is no mismatch repair in synthesized DNA?

A

It can lead to permanent substitutions in a one strand of newly synthesized DNA

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5
Q

What happens in incorrect mismatch repair?

A

DNA polymerase replaces the wrong base (template strand) during proofreading leading to two new DNA with permanent substitutions

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6
Q

Give an example of a point mutation

A

Sickle cell anemia is caused by a single nucleotide substitution in DNA which alters the tertiary structure of beta-globin

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7
Q

How does the cell know which strand is newly synthesized (which strands in mismatched repair is wrong)?

A

The new strand is made of Okazaki fragments which leave nicks in the strand.

Repair has to be done BEFORE nick repair

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8
Q

List the steps for mismatch repair

A
  1. DNA mismatch repair proteins recognize the mismatched pair due to topological disturbance
  2. DNA is scanned for nearby nicks to determine new strand
  3. the nicked strand is removed from the mismatch site to the nick
  4. DNA polymerase and DNA ligase complete the repair
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9
Q

What is hereditary nonpolyposis colorectal cancer (HNPCC)?

A

cancer caused by defects in MutS or MutL genes which code for mismatch repair proteins which results in higher mutations in other genes
1/200 people

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10
Q

What is cytosine deamination?

A

cytosine pairs with guanine and uracil pairs with adenine in DNA replication (similar to mismatched pair)

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11
Q

What is a UV-indiced thymine dimer?

A

a radiation induced mutation caused by UV radiation causing a cyclobutane ring to form between adjacent thymine bases. These thymines cannot be paired with adenines

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12
Q

What is the basis for UV decontamination?

A

UV-induced thymine dimer

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13
Q

What are the categories of repair mechanisms for spontaneous mutations?

A
  1. Direct reversal of DNA damage
  2. Base excision repair
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14
Q

What is direct reversal?

A

Fixes the altered molecule by reversing the chemical transformation. It required specific enzymes for each individual lesion

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15
Q

How can some organisms reverse thymine dimers?

A

By using a specific photo reactivating enzyme

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16
Q

What is base excision repair?

A

A general mechanism for repairing nucleotide mismatches through spontaneous mutations. The damaged base/s are replaced BEFORE DNA replication occurs

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17
Q

What are the steps of base excision repair?

A
  1. DNA glycosylase removes the damaged base leaving only the sugar and phosphate backbone

an endonuclease cleaves the phosphodiester bond

a deoxyribosephosphodiesterase removes the remaining sugar and phosphate

  1. DNA polymerase places a new nucleotide
  2. DNA ligase seals the nick
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18
Q

What are DNA rearrangements?

A

recombination events that alter the arrangement of genes within chromosomes

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19
Q

What is site specific recombination?

A

Specific proteins recognized the homologous sequences and mediate somatic recombination.

Occurs between specific DNA sequences that share partial sequence homology (similarity)

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20
Q

What are immunoglobulins and where are they produced?

A

They are antibodies and are produced B lymphocytes

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21
Q

What is the structure of immunoglobulins?

A

Made of two heavy chains and two light chains which are connected by disulfide bonds

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22
Q

What is the structure of the chains in immunoglobulin?

A

They all have a constant (C) region and a variable region (N) which is made of the variable and joining segments

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23
Q

How is immunoglobulin diversity generated?

A

By site-specific recombination and splicing of primary RNA transcripts

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24
Q

How many V, J, and C regions are there for light chains?

A

250 V regions for N-terminal

4J regions for C-terminal end of variable region

a single C region which codes for the constant region

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25
How does site specific recombination work in light chains?
site specific recombination joins one of the V regions with one of the J regions. After transcription, all other J regions are removed by splicing to generate the mature mRNA
26
Give an example of site specific recombination in yeast
There are two mating types of yeast on chromosome 3 of Saccharomyces cerevisiae. HML and HMR contain silent copies of the two MAT genes. Yeast mating types can be switched by replacing the allele on the MAT locus with one of the silent copies.
27
Who was Barbara McClintock?
She pioneered the field of cytogenetics and discovered transposition in corn
28
What is nonreplicative transposition? (aka cut and paste)
enzyme transposase cleaves the insertion sequence at the ends of the inverted repeats. It then makes cute on the non specific target sequence the insertion sequence is then cut from the donor site and pasted into the target site
29
What is replicative transposition? (aka copy and paste)
a copy of the insertion sequence is made by DNA replication and pasted into the target site
30
What is retrotransposition?
the synthesis of a copy of a retrotransposition catalyzed by reverse transcriptase (RT). Results in multiple copies of the retrotransposition and caused many interspersed repeats in the eukaryotic genome
31
What is the process of retrotransposition?
1. the retrotransposition is transcribed to an RNA molecule catalyzed by RNA polymerase 2. a complementary DNA strand is synthesized, catalyzed by RT creating a DNA-RNA double stranded hybrid 3. the RNA strand is destroyed and replaced with a new strand of DNA (catalyzed by RT), making a double stranded copy that can be inserted into the genome
32
What is Barbara McClintock's findings?
the expression of a gene necessary for the pigment Anthocyanin can be supressed by a control element called a dissociator (which is a transposable element) When the dissociator is moved it suppressed the gene for making Anthocyanin The transposition of the dissociator is controlled by another transpositional control element called an activator which allows for pigment expression This results in mosaic patterns in kernals
33
What is hematopoiesis?
differentiation of blood cells from multipotent stem cells
34
What is epigenetics?
the study of changes and variations in phenotypes that are potentially heritable but are not caused by permanent changes in DNA base sequences ex: non-genetic cellular memory like cell differentiation
35
Give a summary of the combinatorial controls that regulate expression of eukaryotic genes?
transcription regulators bind to specific regulatory DNA sequence elements and work with general transcription factors and RNA polymerase to form the transcription initiation complex
36
What is one of the impacts of transcription regulators being combinatorial?
the addition of a single missing protein can complete a complex that switches a gene ON. the protein could also be the same one for transcription initiation complexes for several genes, switching multiple ON or OFF ex: glucocorticoid receptor activates transcription of several gene when cortisol binds to it
37
Which transcription gene is responsible for muscle cells?
MyoD - makes cells into myoblasts (precursor muscle cells) which fuse to myotubes and become muscle fibers
38
What are two examples of transdifferentiation?
MyoD is artificially expressed in fibroblasts (similar to muscle cells) those cells start to form muscle-like cells since they already have some transitional regulators for muscles liver cells can be converted to neurons with the artificial introduction of three neuron-specific transcription regulators
39
Explain the transcription regulator Ey in Drosophila
Ey controls the expression of many genes that are expressed differentially in all the cell types of the composite eye of the fly. If it is ectopically expressed in larval cells of the area that normally gives rise to a leg, an ectopic eye like structure develops on the leg
40
What is epimorphic limb regeneration?
adult cells dedifferentiate to become neoblasts, rapid cell division occurs, and the neoblasts become re-specified to form the missing adult structures ex: limb regeneration in salamanders
41
What are the mechanisms of inheritance of patterns of gene expression? (forms of epigenetic inheritance)
1. feedback loop circuits involving transcription regulators 2. the preservation of covalent histone modifications and chromatin condensation patterns 3. the preservation of DNA methylation patterns
42
What is histone acetylation?
reversible modification of DNA involving histone proteins. Adds a acetyl group to the lysine tail which eliminates the positive charge, stimulating transcription HAT: histone acetyltransferase HDAC: histone deacetylase
43
How does histone acetylation stimulate transcription?
positive lysine tails in histones interact with negative charges of phosphate groups in DNA when they are neutralized, interactions weaken and transcription factors can bind to DNA
44
How are histone modification patterns inherited?
the tissue specific histone modifying enzyme is preserved throughout cell division and passed on to daughter cells.
45
What is DNA methylation?
occurs of cytosines that are immediately followed by a guanine (CG sequence). Turn off gene expression by attracting proteins that block transcription
46
what does maintenance methyltransferase do?
recognizes only already methylated CG sequences and catalyzes the methylation of the corresponding CGs in the new complementary strand
47
What are de novo methyltransferases?
establish new DNA methylations patterns during development or in response to external cues from the environment ex: bees eating royal jelly silences the Dnmt3 (methylate) that suppresses queen genes
48
What is the germ line?
the cell lineage that contributes to the formation of the next generation by producing gametes
49
What happens if a mutation appears in a germ cell after the germ line is set aside?
the mutation will not impact the individual, but may be passed to the next generation and result in a heritable trait
50
What impact do regulatory regions have on gene expression?
related genes may take different developmental pathways due to differences in regulatory DNA. ex: in organism A transcription regulator ninds to gene 3 and in the other one it binds to gene 2. Difference between dog/anteater
51
What is an example of a mutation in regulatory DNA?
ectopic expression of the Antennapedia gene in the head of Drosophila due to mutation in regulatory DNA Ability to digest lactose is due to a mutation in the regulatory DNA of the lactase gene
52
What is a gene family?
groups of genes that originate from a common ancestral gene. Grouped by similarities in structure/function
53
What is the globin gene family?
genes that code for subunits of hemoglobin - they all have the same structure but different versions are expressed at different life stages (fetal, embryonic, adult)
53
What is an example of gene duplication?
the globin gene family
54
What globin subunits make up the adult hemoglobin?
two a (alpha) clusters on chromosome 16 and two B (beta) clusters on chromosome 11 *embryonic/fetal globins have higher oxygen affinities
55
What is one way gene duplication can occur?
unequal crossing over due to short repeated sequences within homologous chromosomes which can cause misalignments of cromosomes during crossing over
56
What happens during exon transposition by mobile genetic elements?
if two similar mobile genetic elements happen to be next to each other on a chromosome, then the transposition element may pick them both up as if they were one and place them in a new place. If these mobile genetic elements have a gene between them, then that gets moved too.
57
What is one result of exon shuffling?
can result in new proteins by piecing together fragments of different genes. (makes new proteins with multiple functional domains)
58
What is conjugation?
transfer of DNA from one bacterium to another through a sex pilus without reproduction
59
What causes Amyotrophic lateral sclerosis (ALS)?
an ancient virus (human endogenous retrovirus K/HERV-K) that was incorporated into human DNA HERVs infect neurons and germ cells
60
What are amphipathic molecules mean?
they have both polar and nonpolar regions. ex: phospholipids, glycolipids, cholesterol
61
What makes up a phospholipid?
glycerol, two fatty acids, a phosphate group, and either a polar group or a charged group
62
What makes a glycolipid?
a glycerol with an extra -OH group, two fatty acids, and one or more sugar groups
63
What makes up cholesterol?
steroid strucure with 4 rings, an -OH group, and a hydrophobic tail
64
What is the role of cholesterol in a lipid bilayer?
It is inserted into pre-formed lipid bilayers low temps - interferes with interactions between fatty acids, maintaining fluidity and preventing membrane hardening high temps - cholesterol interferes with the lateral movements of fatty acids, making membrane less fluid
65
Where are the lipids found in the cell membrane?
distribution is asymmetric glycolipids in outer layer charged phospholipids (phosphatidylserine/phosphatidylinositol) in the inner layer cholesterol in both layers
66
What are the protein components of the cell membrane?
transporters and channels (ex: ion channels) anchors for extracellular matrix and/or cytoskeletal proteins (ex: cadherin) surface receptors (ex: hormone receptors) enzymes (ex: lactase) they are restricted because of the tight junctions
67
What is a tight junction?
cell-to-cell junction that binds adjacent epithelial cells together, preventing the passage of dissolved molecules from one side of the epithelial sheet to the other fromed with occludin and claudin proteins
68
What is passive (simple) diffusion?
diffusion of gases, small hydrophobic molecules, and small polar molecules through the cell membrane no energy direction depends on concentrations on both sides of the membrane
69
What is facilitated passive transport?
passage of molecules without energy mediated by channels and passive transporters (carriers). Direction depends on concentration large polar molecules, charged molecules, ions
70
What is active transport?
transport of molecules against the concentration gradient of the molecule using active transporters (pumps). requires energy large polar molecules, charged molecules, ions
71
How do carriers (passive transporters) and pumps (active transporters) work?
carriers use a conformation change pumps require energy to make a conformation change
72
What is membrane potential (membrane voltage)?
an electrical property of the membrane - plasma membranes at rest have a negative voltage (-Vm) with more negative charges on the cytoplasmic side (inside) than the outside can change when ion currents travel through the membrane
73
How does the Na+/K+ pump work?
Uses ATP to transfer Na+ outside of the cell and K+ to the inside of the cell, against their gradients 3 Na+ ions bind to the cytoplasmic cites, a Pi is attached to the pump causing a transformation change which moves them outside, 2 K+ ions bind to the extracellular cites, and the pump is dephosphorylated causing a return to the original conformation and the release of the K+ ions inside. consumes ~25% of all ATP by animal cells
74
Why is the Na+/K+ pump important?
they counterbalance the high concentration of organic molecules inside the cell which would drive an inward flow of water by osmosis and cause the cell to burst. Also maintains correct membrane voltage/osmotic balance necessary for retention of molecular components inside the cell
75
Explain glucose transport?
It is coupled with Na+ down its concentration gradient with glucose against its concentration gradient glucose is moved to the bloodstream by facilitated diffusion through the basolateral membrane
76
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