Week 1 Flashcards
(153 cards)
1
Q
ER
A
: protein synthesis and glycosylation, calcium storage, drug metabolism, fatty acid synthesis.
2
Q
Golgi apparatus
A
carbohydrate modification and maturation of membrane and secrectory proteins
3
Q
Lysosomes
A
degradation of cellular components and extracellular particles
4
Q
Plasma membrane
A
interface of cell to external environment
5
Q
Peroxisomes
A
oxidative reactions
6
Q
Nuclear pore complexes
A
Channels for communication between nucleus and cytoplasm
7
Q
Structure and function of intermediate filaments
A
Rope like structure, flexible, strong, non polar, connects cells into sheets, resist force, anchor
8
Q
3 intermediate filaments found in cytoplasm
A
Keratin (hair and nails), Vimentin (muscle cells, connective), Neurofilament (movement, nerve cells)
9
Q
Intermediate filament in nucleus
A
Lamins (structural support nucleus, found in all cells)
10
Q
Why would genetic mutations in keratin gene affect primarily skin?
A
Keratins are only expressed in epithelial cells, such as skin cells, and provide mechanical support and resistance to physical stress. Skin experiences greater amounts of physical stress than most other epithelial tissues.
11
Q
Structure and function of actin
A
flexible, polar, movement of cells/membranes, in bundles linked with proteins, forms microvilli (increase absorptive surface area), bundles, filopedia, contractile ring
12
Q
Where is actin found
A
Plasma membrane (network called cell cortex), muscle (network to generate force)
13
Q
What do actin binding proteins do
A
modify actin structure eg. cap, link, sever
14
Q
How is actin added on?
A
Treadmilling: dynamic assembly and disassembly, add on + end, ATP hydrolyzes, becomes weakly bound and disassociates/leaves on - end
15
Q
Structure and function of microtubules
A
polar, form highways for things to move along and transport on, forms cillia (anchored to basal bodies and have motile and non-motile varieties), flagella, mitotic spindle, points out from the MTOC/centrosome, + end on the plasma membrane outwards, hollow tube made from heterodimers
16
Q
How do microtubules grow
A
Dynamic instability, adding on + side with GTP, it hydroyzes, if + end stops growing the GTP cap disappears and the microtubule becomes unstable and rapidly falls apart
17
Q
What are the different motor proteins, what are they on and how do they work?
A
on microtubules there are kinesins (walk towards + end) and dyneins (walk towards - end) with the walking mechanism; on actin there is myosin
18
Q
Structure of a gene? There are 3 vague parts
A
Promoter (where polymerase and assoc. factors bind), Coding area, Terminator
19
Q
- Why are drugs that affect microtubule dynamics important anti-tumor agents?
A
Answer: Although all cells use microtubules for the placement and movement of organelles, disrupting these functions does not appreciably affect cellular activity. The microtubule dynamics necessary to form the mitotic spindle are highly sensitive to microtubule disrupting drugs. The failure to form a correct spindle will cause problems with chromosome segregation and trigger cell death by apoptosis.
20
Q
- How could a cell regulate the movement of proteins into organelles?
A
Answer: Proteins are targeted to specific organelles by localization sequences in the primary structure of the protein. These localization sequences are recognized by proteins that effect transport into the organelles. Post translational modification of amino acid residues within or near the localization sequence can inhibit or enhance the interaction of the sequence with the transport apparatus. Alternatively, regulatory proteins could bind to the protein and mask the localization sequence. In turn, the activity of these masking proteins is frequently regulated by post translational modification.
21
Q
- How are the structural properties of the different cytoskeletal proteins important for their functions?
A
Answer: Actin and tubulin form polymers by the linear polymerization of monomers. This makes these polymers easy to assemble and disassemble, but also makes them easy to break under stress. Intermediate filaments are formed by the staggered lateral association of filamentous protein subunits. This subunit arrangement makes intermediate filaments much more like a rope, and they are resistant to breakage under stress. This property makes intermediate filaments ideal for providing mechanical support.
22
Q
- Why would a cell need a complex cytoskeletal and motor system to organize cellular organelles?
A
Answer: Due to the crowded environment of the cytoplasm, large structures such as organelles cannot easily diffuse through the space. The cytoskeleton and motor system allows for the positioning of organelles. The actin-myosin cytoskeleton is also important for cell movement.
23
Q
- Why do eukaryotes need three RNA polymerases, when prokaryotes get by with one?
A
Multiple polymerases allows for additional control over the transcription of the different types of genes. This arrangement gives the cell greater control over the level of each type of RNA.
24
Q
What is the advantage to transcribing a gene to include multiple introns in the pre-mRNA?
A
The pre-mRNA can be alternatively spliced to make mRNAs encoding different isoforms of a protein.
25
What advantage does the cell derive by synthesizing ribosomal RNAs as a precursor containing all of the ribosomal RNAs?
Because the RNAs that make up the ribosome must be present in equal amounts, synthesizing them as a single precursor ensures this will occur. The assembly of the ribosome in nucleoli occurs in conjunction with the processing of the precursor RNA. This guarantees the ordered assembly of the ribosome.
26
How can alternative splicing be regulated if the same snRNPs carry out all splicing reactions?
RNA binding proteins that recognize the splice site direct which intron-exon boundaries will be spliced.
27
Characteristics of RNA polymerase
requires DNA template, 5 to 3 polymerase, highly processive
28
what is RNAP I for
transcribes ribosomal RNA
29
what is RNAP II for
transcribes protein coding genes into mRNA, snRNA
30
what is RNAP III for
transcribes tRNA
31
what is POLMRT
single RNA polymerase in mitochondria
32
what are the non template dependent polymerases
polyA polymerase, poly ADP ribose (PARP) used for targeting protein for DNA repair
33
what does mRNA do
carries genetic code from DNA, codes amino acids of polypeptide
34
rRNA
component of ribosome (translates mRNA)
35
tRNA
carry AA into polypeptide chain
36
snRNA
assoc. to specific proteins, processes the precursor mRNA (splicing)
37
snoRNA
rRNA processing
38
miRNA, lncRNA, sncRNA
regulate gene expression
39
how are RNA genes organized on chromosomes
rRNA and tRNA are clustered, mRNA is intersperesed
40
how is rRNA transcribed?
45s precursor is spliced and ITS is taken out, 18s is small and 5.8s and 28s is large (combined with 5s from elsewhere), modified, small and large assembled separately, go into cytoplasm through the nuclear pore complex, join together ready for translation
41
how is tRNA transcribed
tRNAs are synthesized as longer molecules that are trimmed at their ends to form the mature tRNA. Introns are removed. Uracil residues at the 3’ end are removed and replaced by the sequence CCA. The CCA sequence is always on the 3’ end of a tRNA molecule. The amino acid loaded onto the tRNA by aminoacyl tRNA synthetases to form aminoacyl-tRNA is covalently bound to the 3’ hydroxyl group of the CCA tail. Bases modified. Transported through nuclear pore complex
42
how is mRNA transcribed (first steps aka promoters and how is polymerase recruited)
recognition binding sites (TATA, CAAT, GC), TATA is the core promoter, if gene is constitutively expressed it is GC instead, TF bind to the promoter creating the pre-initiation complex which is needed to recruit the polymerase
43
how is mRNA transcribed (RNAP II genes) (what happens after pre-initiation complex is recruited)
mediator complex interacts with pre-initiation and recruits TFs and mediates which genes are active and modulates initiation, enhancers downstream increase or decrease promoter activity, poly A is added after stop codon, transcript is released
44
how is RNAP II transcript or pre-mRNA processed?
co-transcriptionally, 5 end capping, removal of intron (splicing), poly A tail on 3 end
45
how is microRNA processed
capped at 5 end, poly A tail, microprocessor complex cuts long precursor making pre-miRNA, moved into cytoplasm where dicer cleaves, one final strand incorporated with RISC
46
what are some post translational mechanisms for regulating gene expression?
alternative splicing, alternative poly-A
47
1.Many genetic mutations involve a single nucleotide base change in the protein coding portion of the affected gene. How does this lead to the formation of an abnormal protein?
The changed nucleotide in the DNA is reflected in the mRNA encoded by that gene. This base change will change the amino acid specified by the affected codon in the mRNA.
48
2. What are three differences between eukaryotic and prokaryotic translation?
2. The prokaryotic ribosome is smaller and does not contain a 5.8S RNA. In prokaryotes the methionine in the initiator tRNA is formylated. The selection of the start codon is different, eukaryotic ribosomes bind to the 5’ cap structure while prokaryotic ribosomes assembly on the Shine-Dalgarno sequence.
49
3. Why do mRNAs encoding different proteins have different half-lives?
3. Some proteins are only needed transiently so their mRNAs are only needed for a short period of time. Other proteins may need to be constantly present and renewed so their mRNAs will usually have a longer half-life.
50
Characteristics of genetic code?
specific, universal, degenerate (diff codons can code for same AA)
51
How does tRNA read codons?
Codons read by tRNAs; complementary antiparallel binding of anticodons (3 nucleotide sequence) to codons; tRNA covalently attaches to an amino acid by tRNA synthetase -- (called aminoacyl-tRNA) by aminoacyl-tRNA synthase (specific to the amino acid) with 2 ATP - it is then considered “charged.”
52
Describe initiation step in translation
eIF2 initiation factor + initiator tRNA + 40s ribosome subunit = 43 s preinitiation complex; combines with mRNA-cap binding protein complex; RNA helicase unwinds mRNA using ATP, ribosome scans for start codon AUG (in prokaryotes it binds to shine dalgarno instead), large ribosome binds with tRNA
53
What does it mean for some mRNA to be cap independent
doesnt need the cap binding protein because it isn't binding to cap, the complex binds at IRES (internal ribosome entry site)
54
How does elongation of translation work aka amino acids forming polypeptide chain?
cyclic binding of aminoacyl tRNA to ribosome to form peptide bond; tRNA bound to E1Fa-GTP attached to the AA binds to ribosome at the A site, A site amino acid binds to P site amino acid at the A site now (elongation), EF2-GTP moves the chain over to the P site
55
how much energy required in elongation?
2 GTP for each amino acid added, 2 ATP to charge each tRNA
56
how does termination step of translation work after polypeptide chain is elongated
when stop codon enters the A site, tRNA doesnt bind to stop codon and a protein releases release factors that cause hydrolysis of peptide chain from the final tRNA, ribosome subunits dissociate
57
what are examples of regulation of translation?
influencing rate of initation, repressing translation, and induced degradation of mRNA; heme regulates globin mRNA translation, regulation ferritin (storage of iron), stability of mRNA through cap and polyA tail to prevent degradation, microRNAs can block translation or degrade; growth factors activate mTOR which lead to protein synthesis
58
how does heme regulation work
to make sure that the amount of globin produced is the same as heme produced; when heme is low, the HRI (heme regulated kinase) is activated and stops the synthesis of globin
59
how does regulation of ferritin work
ferritin stores iron and transferrin receptors transport iron into the cell, in iron poor situation, no iron binds to IRE-BP (iron response element binding protein) --> so no ferritin is made because IRE-BP (cystolic aconitase) is bound to the ferritin mRNA blocking its translation; & transferrin to be made instead. when we have iron it binds to IRE-BP, removing it, allowing translation of ferritin
60
how do viruses control translation
take over the machinery, control initiation (eg. decap, modify ribosome subunity, modify eif4), elongation (inhibit translocation), termination (change the stop codon)
61
1. Why are SNARES required for membrane fusion events?
The head groups of phospholipids carry a net negative charge so the membranes of the vesicle and the target compartment will repel each other. Membrane fusion requires the close approach of the membranes. SNARES pull the membranes together overcoming the repulsive forces of the charge on the membrane surfaces.
62
2. Why are clathrin and COP coats important for some types of vesicle formation?
The coat proteins help the vesicle to form, they assist in the concentration of specific molecules in the vesicle, and they can help direct the vesicle to the correct target compartment.
63
3. Is the lumen of the ER topologically equivalent to the inside or the outside of the cell?
The outside. The lumen of all membrane bound compartments that are part of the secretory or endocytic pathways are considered to be topologically the “outside” of the cell since their fusion with or budding from the plasma membrane connects their lumens to the outside of the cell.
64
4. Why is the branched carbohydrate tree on dolichol phosphate synthesized on the cytoplasmic side of the ER and then flipped into the ER lumen?
The sugar precursors that are used to synthesize the carbohydrate tree are made in the cytoplasm or transported into the cytoplasm through the plasma membrane. The ER membrane lacks the sugar transporters to move monosaccharides from the cytoplasm to the ER lumen.
65
5. Continuous flow of ER membranes through the secretory pathway would be expected to rapidly deplete ER proteins. How is the concentration of ER-associated proteins maintained?
Answer: Specific receptor proteins (mainly the KDEL receptor) bind signal sequences (KDEL) on resident ER proteins and recycle them back to the ER.
66
how are proteins in the ER moved there
Signal Recognition Particle recognizes the ER signal sequence on the growing mRNA and brings the ribosome to the SRP receptor in the ER
o Different combinations of signal sequences determine the membrane protein topology-the orientation that the protein is in with regards to the membrane - i.e. like N side in cytosol/ how many transmembrane regions
67
example of how protein in ER is modified?
N-linked glycosylation: attachment of complex oligosaccharide onto asparagine residues, added on dolichol in cytoplasm, flipped into ER lumen, transferred sugar from dolichol to protein
68
a way membrane proteins in the ER are modified?
replace COOH end with GPI anchor
69
how are proteins in ER lumen folded?
sugar is modified -- important for quality control; glucose transferase and calnexin, other chaperones
70
role of golgi in protein processing?
process, package, sort for secretion or targeting
71
proteins involved with vesicle formation, targeting, fusion
coat proteins / receptors for coat assembly and cargo selection (clathrin), RAb on vesicle identified by tethering protein on membrane, v and t snares dock and fuse
72
what proteins help transport membrane vesicle move among intracellular compartments
process is same as vesicle to membrane, but COP I for golgi to ER and COP II for ER to golgi
73
what helps move golgi clusters
microtubules and motor proteins
74
what is KDEL sequence
sequence on ER resident proteins that will be recognized to send the protein back to ER
75
golgi to lysosome: how are enzymes sent to lysosome (lysosomal hydrolases)
lysosomal precursor + M6P signal + phosphorylation --> binds to the M6P receptor; clathrin coat forms vesicle; sent to endosome which becomes lysosome; phosphate removed and receptor is recylced
76
Identify the different types of endocytosis and the role of each in trafficking of macromolecules.
Pinocytosis: small bits of PM, Important for blood brain barrier, maternal antibodies, viral infection, prion disease; Phagocytosis: Engulfment of large particles, Requires actin cytoskeleton; Receptor mediated endocytosis: ligand bound receptors (LDL receptors) cluster and form clathrin coated vesicles
77
what happens to receptors that are endocytosed (3 options)
degraded in lysosome, transcytosis to other side of membrane, recycled in transport vesicle
78
exocytosis -- what is it and what is unregulated vs regulated
intracellular components sent out of cell; unregulated is all at once and no outside influence; regulated requires hormone or NT
79
1. Many genetic mutations involve a single nucleotide base change in the protein coding portion of the affected gene. How does this lead to the formation of an abnormal protein?
The changed nucleotide in the DNA is reflected in the mRNA encoded by that gene. This base change will change the amino acid specified by the affected codon in the mRNA.
80
2. Under starvation conditions, a cell begins to recycle amino acids and nucleotides from pre-existing molecules. What mechanism do you think is used?
: Autophagy. This pathway is used to scavenge pre-existing molecules to obtain precursors under stress conditions.
81
3. Protein homeostasis is tightly coupled to cell growth and proliferation. How do growth factors regulate protein levels to allow cells to grow?
A serine/threonine protein kinase called mTOR (mammalian Target of Rapamycin) integrates the input from upstream pathways, including insulin, growth factors (such as IGF-1 and IGF-2), and amino acids. mTOR also senses cellular nutrient, oxygen, and energy levels. Activated mTOR inhibits protein degradation and stimulates protein translation.
82
What are the 2 ways damaged proteins are degraded?
lysosomal degradation or ubiquitin proteasome system
83
what is ubiquitin proteasome system how does it work
3 enzyme complex (E1, 2, 3) adds ubiquitin (a small protein that is coupled to lysine post translationally), proteasome (ATP dependent) cap interacts with poly-u tail and protein is unfolded and degraded through the proteasome channel
84
how do aggregates form
when accumulation cant be handled by ubiquitin, created from misfolded proteins OR alternative folding (amyloid)
85
how is amyloid formed and what is its effect? what are prions?
alternative folding, caused by mutations, diseases like alzheimers, ALS, parkinsons' prions are infectious amlyoids that can pass abnormality along
86
what is ER stress caused by
misfolded protein accumulation, stressors like oxidative stress, glucose deprivation, viral infection
87
response to ER stress?
ERAD (ER assoc. degradation) and unfolded protein response (UPR)
88
what is ERAD
eliminates misfolded protein in ER by exporing to cytosol where they are poly-U and then degraded by proteasome
89
what is UPR
triggered by ERAD, chaperones activate programs to induce transcription of more chaperones or inhibit transcription of mRNA to reduce protein influx
90
purpose of autophagy? types of autophagy (3 types)
recycles cell compartments, active under starvation or conditions where aggregates form; macrophagy, microphagy, chaperone mediated autophagy
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what is macrophagy
engulfment of large volumes; membrane from ER forms a vesicle that fuses w lysosome
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what is microphagy
capture of small volumes, the membrane of a lysosome invaginates, can happen in bulk or selectively w hsc70
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what is chaperone mediated autophagy how does it work
soluble protein w KFERQ caught by chaperone brought to LAMP (lysosome assoc membrane protein) and the receptors all aggregate on the membrane forming 'translocation complex' aka a channel
94
1. What thermodynamic property of the TCA cycle reactions drives the cycle?
The reactions catalyzed by the dehydrogenases of the TCA cycle have large negative free energy changes, so the equilibrium for the reactions lies strongly toward the formation of product. Also, because of their sequential arrangement in the cycle, the products of one reaction are quickly used as substrates for the next reaction and they never accumulate to high levels.
95
3. Why do cells lacking mitochondria not utilize the TCA cycle for energy production?
The dehydrogenases of the TCA cycle donate electrons to NAD and FAD. These reduced coenzymes must be oxidized by the OXPHOS enzymes in the mitochondrial matrix. Cells lacking mitochondria are unable to oxidize the large number of reduced coenzymes that would be produced by the TCA cycle.
96
2. What are the four direct metabolic fates of pyruvate? (hint: some of the answers are in other lectures)
1) conversion to acetylCoA by pyruvate dehydrogenase, 2) conversion to oxaloacetate by pyruvate carboxylase, 3) synthesis of alanine by alanine aminotransferase, 4) reduction to lactate by lactate dehydrogenase
97
Purpose of TCA cycle?
2/3 production of ATP from oxidation, uses acetyl CoA from glucose, fatty acids, AA, acetate, ketone; in mitochondrial matrix
98
sources of acetyl CoA
fatty acid catabolism, ketone body acetoacetate, pyruvate to acetyl coA, ethanol
99
what is the role of PDC
pyruvate dehydrogenase complex is the enzyme that links glycolysis to the TCA cycle by oxidizing pyruvate to acetyl coA
100
mechanism of PDC reaction
pyruvate to acetyl coA; CO2 and NADH produced
101
cofactors of PDC?
thiamine, lipoate, coA, FAD, NAD
102
how is pDC regulated
kinase (phosphorylates) inactivates PDC; phosphatase (dephosphorylates) activates; Ca2+ activates PDC by activating phosphatase; during starvation kinase is activated so PDC isn't made, so pyruvate isn't oxidized
103
steps in the TCA cycle?
citrate, isocitrate (+ NADH, CO2), a-ketoglutarate (+ NADH, CO2) , succinyl coA (needs GDP), succinate + GTP, fumarate (+FAD2H), malate, oxaloacetate (+NADH)
104
what happens when citrate is high
it is a product inhibitor, so reaction is slowed
105
what is the free energy of the cycle
large negative free energy in first half of the cycle that drives it forward
106
what is isocitrate dehydrogenase
rate limiting enzyme to make isocitrate into ketoglutarate; allostericaly activated by ADP, inhibited by NADH
107
ketoglutarate dehyrogenase?
not allosteric, activated by Ca, inhibited by NADH, goes from ketoglutarate to succinyl coa
108
malate dehydrogenase
inhibited by NADH, not allosteric, goes from malate to OAA
109
what is made with acetyl coA in the cycle
3 NADH, 1 FAD, 1 GTP
110
what are the biosynthetic functions of the cycle and when do they occur
the intermediates make amino acids, glucose, fatty acids, heme, neutrotransmitters; when the cycle is well fed and low energy consumption and ATP isnt needed
111
how is C added back in
anaplerotic reaction: amino acid to pyruvate to OAA through pyruvate carboxylase; and fatty acid to propionyl CoA to succinyl Coa
112
what does glutamine do
Glutamine can enter the mitochondria where it is converted to alpha-ketoglutarate (via being first converted to glutamate) and can then enter the TCA cycle. Cell signalling, anti-oxidants. Give tumor cells growth advantage
113
explain how gaucher disease is caused
a lysosomal storage disease where deficiency of enzyme (glucocerebrodisase) causes buildup of glucocerebroside, which is cell membranes of damanged red blood cells that are phagocytosed
114
3 major organs affected by gaucher
liver, spleen, bone marrow
115
result of gaucher disease? diseases etc
is therefore these organs that are most affected by the disease: enlargement of liver (hepatomegaly), enlargement of spleen (splenomegaly), abnormal bone modeling and bone pain. The enlargement of the spleen causes it to be “hyperactive,” called hypersplenism, and to remove healthy blood cells from the circulation, resulting in low red blood cell count (anemia) and low platelet count (thrombocytopenia).
116
treatment for gaucher?
Gaucher disease can now be treated by actually replacing the defective enzyme: the human enzyme can be infused intravenously, and is taken up by the macrophages and transported to the lysosomes, where it can hydrolyze glucocerebroside. Very expensive
117
Orphan drug act?
provided incentives for pharma to produce orphan drugs (despite the low use/profit)
118
what is the mechanical, transport and biochemical work of the ATP to ADP cycle
1. Mechanical work: hydrolysis of ATP coupled to conformational changes in proteins.
2. Transport work: ion pumps.
3. Biochemical work: coupling reactions, creation of activated intermediates, protein modification.
119
how does ATP produce energy
high energy bonds are hydrolyzed to form energy; phosphate and high energy intermediates release energy that can be used to do other work
120
why is creatine phosphate relevant
it has high energy phoshpate bonds that stores energy like a bank, and if a lot of ATP is being hydrolyzed, that you can use it to make more ADP
121
what is total adenylate pool
AMP + ADP + ATP
122
what happens in an oxidation reduction reaction
Oxidation-reduction reactions are important for metabolism. These reactions involve the transfer of electrons between two molecules. Oxidation means loss of e, reduction means gain of e. The more highly reduced a molecule is the more energy can be obtained by oxidative metabolism.
123
what does free energy change mean
lower than 0 = exergonic, spontaenous; higher than 0 = needs energy, not spontaenous; depends on concentration of reactants and products
124
1. Why does skeletal muscle have a higher concentration of creatine phosphate than other tissues?
Muscle cells have a high ATP requirement for contraction. Creatine phosphate is a store for high energy phosphate bonds to regenerate ATP without increasing the concentration of adenine nucleotides.
125
2. Why does methane possess greater energy potential than formic acid?
Methane is more reduced than formic acid. The more reduced a molecule, the more energy is available through oxidative metabolism.
126
3. For a reaction with a positive standard free energy change, what would be the effect of increasing the amount of substrate?
For most reactions, the increased substrate would be converted to product until equilibrium was reached.
127
1. Why is the assembly of cohesins on replicated chromosomes important for the repair of some types of DNA damage?
Cohesins form a complex that holds the sister chromatids together following replication. This not only keeps to chromatids in close proximity to increase the efficiency of homologous recombination during DNA damage repair, it also allows the chromosome to condense correctly at mitosis and align the sister chromatids for segregation.
128
2. Which DNA repair mechanisms are active in all nucleated cells?
Homologous recombination is the only repair mechanism that is restricted to cells that are in S or G2 phase because this process requires duplicated chromosomes for homology directed repair. All of the other repair pathways can operate throughout the cell cycle.
129
3. Why are topoisomerases required for DNA replication?
The unwinding of the DNA helix during replication induces both positive and negative supercoiling in the DNA adjacent to the replication bubble. In prokaryotes, plasmid DNAs are naturally supercoiled and must be unwound in order to be replicated. The topoisomerases relieve supercoiling.
130
4. Why would mutations in a protein involved in homology directed repair be a source of birth defects?
During the formation of gametes, errors in DNA replication or damage due to genotoxic agents must be repaired to prevent any mutations from becoming part of the embryo’s genome. Homology directed repair (homologous recombination) is the major mechanism for repairing these errors.
131
DNA base pairs?
The DNA double helix forms due to the hydrogen bonding between complementary purine and pyrimidine bases on opposite strands.
1. Adenine-Thymine pairs form 2 hydrogen bonds
2. Guanine-Cytosine pairs form 3 bonds.
132
what is chromatin
DNA-protein-RNA complext, form of packaged DNA in nucleus, structure determined by DNA and histone modification
133
DNA in mitochondria?
circular
134
how does replication of DNA begin
protein ORC (origin replication complex) binds to origin and recruits replication machinery, ORC + DNA proteins = pre-replicative complex; helicase associates and unwinds DNA; single strand DNA binding protein is behind the helicase to protect the single strand
135
how is the parent strand replicated after unwinding
parent strand is read 3 to 5 and so replication strand happens 5 to 3; synthesized by DNA polymerases that are initiated with RNA primer
136
leading vs lagging strands?
leading is in direction of the fork, and lagging is opposite; lagging happens in several pieces called okazaki fragments
137
what happens to DNA after replication strand is made
RNA removed by a different polymerase and ends are joined by ligase
138
what is proofreading
DNA polymerase detects incorrect sequences and removes
139
what is supercoiling and how is it fixed
parts in front of the fork in the DNA can coil up and interfere with unwinding' topoisomerases
140
what is cohesin ring
holds sister chromatids together after replication
141
purpose of telomeres
to stabilize end of linear chromosome and help prevent recombination
142
what is shelterin complex
protein complex assoc. w telomere and maintains its structure
143
why are telomeres shortening
after RNA primer is removed, a gap remains
144
BER
base excision repair -- damage to single base by oxidation/alkylation/hydrolysis/deamination; DNA glycosylase removes base, backbone removed, polymerase fills and ligase seals
145
NER (nucleotide excision repair)
remove helix distorting changes caused by dimers (UV)
146
mismatch repair
errors in dna replication and recombination, recognizes, coat DNA with clamps, machinery, exonuclease cut on each side of machinery, chews up bad strand, polymerase fills in region (imp. to recognize parental vs new strand)
147
how are double strand breaks fixed
non homologous end joining or homology directed repair
148
non homologous end joining vs homology directed repair?
NHEJ preferred during G1, broken ends are brought together with polymerase but this is very error prone because there is no template; HDR happens during and after replication (S) and it uses a sister chromosome has a template; there is a pair of homologous DNA molecules, the bad one is chewed back a little more and the good strand is copied. NHEJ must occur during G1, because the sister chromosomes are not together then. During S, they are held together by cohesin so HR can be used.
149
what is the genome surveillance complex
integrates diff DNA damage repair pathways
150
what is cystolic aconitase doing
it binds to ferritin mRNA blocking its translation to ferritin protein; when comes in, it binds to cystolic aconitase, thus removing it and allowing ferritin to be made; on the other hand, cystolic aconitasae STAbilizes transferrin mRNA so that when there is no iron, it can be made
151
Which of the following best describes the order of events in the initiation and elongation of DNA replication in Eukaryotes?
Replication complex assembles at an origin, DNA helicase unwinds the double helix, RNA Primase lays down an RNA primer, DNA polymerase extends the new strand in the 5’ to 3’ direction
152
tight junction vs desmosomes
Tight junctions mainly function to restrict and regulate what is able to pass from the lumen into the connective tissue between neighboring cells. The main function of desmosomes is cell-cell adhesion; a disruption in this component (possibly due to autoantibodies against desmosomes in certain skin diseases) leads to loosening of cell-cell junctions and blistering in the skin where desmosomes are prominent.
153
what does poly A tail affect
Poly a tail length will only affect how fast the mRNA is degraded, not the protein translated, as it is located after the stop codon.
