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LECOM DSP Biochemistry 2022 > Section III (Chapters 10-15) > Flashcards

Section III (Chapters 10-15) Flashcards

1
Q

What the general sequence for signal transduction?

A
  1. Chemical messenger is secreted from specific cells in response to a stimulus
  2. Messenger diffuses/is transported to target cell
  3. Receptor in target cell specifically binds the messenger
  4. Binding of messenger to receptor elicits a response
  5. Signal ceases and is terminated
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2
Q

Endocrine signaling

A

Travel in blood, longer distancea

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3
Q

Paracrine signaling

A

Travel between nearby cells (think: synapse), specific to only nearby receptors (not every muscle cell with ACh receptors; just the neighbors)

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4
Q

What does paracrine signaling limit?

A

Immune response to specific locations within the body

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5
Q

Autocrine signaling

A

Act on same cell or sometimes same nearby cells

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6
Q

What type of chemical messenger does the nervous system have?

A

Neurotransmitters

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7
Q

Neurotransmitters

A

Contains nitrogen molecules (such as amino acids) or neuropeptides
Can be found at synaptic junctions or within the blood (neurohormones)

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8
Q

What type of chemical messengers does the endocrine system have?

A

Hormones

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9
Q

Hormones

A

Secreted from endocrine glands
Types: polypeptide hormones (insulin), catecholamines (epinephrine), steroid (cholesterol derived), thyroid (tyrosine derived)

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10
Q

What are specialized hormones that is not synthesized in endocrine cells?

A

Retinoids! -> derived from vitamin A & D

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11
Q

What chemical messengers are found in the immune system?

A

Cytokines

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12
Q

Cytokines

A

Small proteins that work to KILL invading microorganisms
Types: interleukins, tumor necrosis factors, interferons, colony-stimulating factors
Secreted via immune cells, and alter behavior of other cells by activating transcription of genes for proteins involved in immune response

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13
Q

Eicosanoids

A

Prostaglandins, thromboxane, and leukotrienes
Control cellular functions in response to injury
Derived from arachidonic acid (fatty acid), usually present as part of membrane lipid phosphatidylcholine

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14
Q

Growth factors

A

Polypeptides that function through stimulation of cellular proliferation or cell size

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15
Q

What type of receptor are nicotinic acetylcholine receptors?

A

Ligand-gated ion channel receptor

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16
Q

What occurs in the chemical synapse with nAChR?

A

Action potential causes changes in Na and K gradients across cell, resulting opening of Ca channel and influx of Ca which triggers fusion of vesicles within plasma membrane, releasing ACh into synaptic cleft, binds to nicotinic ACh receptor which contains a channel within the center of the receptors, causes conformational change opening the channel allowing Na to diffuse in and K to diffuse out which activates action potential down next nerve cell
(Sodium Potassium Pump!!!!)

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17
Q

What occurs in myasthenia gravis molecularly?

A

B & T lymphocytes develop pathogenic antibodies against nicotinic ACh receptors which bind to the receptors and cross-link them which is endocytosed and degraded

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18
Q

What does myasthenia gravis cause?

A

Inability of ACh to stimulate repeated muscle contraction (tirednesses utilizing muscle)

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19
Q

How do we test for myasthenia gravis?

A

Acetylcholinesterase -> edrophonium chloride
Should briefly improve the muscle weaknesses
Repetitive nerve stimulation and EMG can also show partial blockage of ion flux through muscular membranes

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20
Q

What are the treatments for myasthenia gravis?

A

Anticholinesterase agents
Immunosuppressive drugs
Thymectomy
Intravenous immunoglobulin
Plasmapheresis

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21
Q

Plasma membrane receptors

A

Spans plasma membrane containing extracellular binding domain
Types: Ion channel receptors, tyrosine kinase receptors, tyrosine kinase associated receptors, serine-threonine receptors, heptahelical receptors

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22
Q

What are the mechanisms for extracellular binding?

A

Phosphorylation of receptors, conformational changes in signal transducer proteins, or increases in levels of intracellular second messengers

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23
Q

What must the molecules not be able to do when using plasma membrane receptors?

A

Diffuse through cell -> polar molecules

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24
Q

What are intracellular receptors?

A

Utilized for messengers that diffuse into cell
Must be: hydrophobic
Mostly gene-specific transcription factors -> regulate transcription

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25
Q

Ion channel receptors -> nicotinic acetylcholine receptor

A

Similar to ACh receptors in neurotransmitters

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26
Q

Tyrosine kinase receptors -> insulin receptors

A

Present as single monomers that form dimers when messenger binds, Protein kinase transfers a phosphate group from ATP to hydroxyl group of amino acid (tyrosine), which is activated when the messenger binds to extracellular domain, causing phosphorylation of intracellular domain or associated protein, and the message is then propagated downstream through signal transducer proteins

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27
Q

G-protein coupled receptor -> glucagon receptor

A

Contain seven membrane spanning a-helices, when messenger binds to receptor, second messenger such as cAMP accumulate intracellularly, and transmit message

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28
Q

What must be looked over before the quiz?

A

ras-MAP kinase pathway & insulin receptor pathway

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29
Q

ras-MAP kinase pathway (in words)

A

One domain of receptor forms binding site for SH2 domain proteins (Grb2), which undergoes conformational change that activates another binding site called SH3 domain, which binds SOS protein , which catalyzes exchange of GTP for GDP on Ras, causing conformational change in Ras that promotes binding of Raf, triggering phosphorylation cascade, resulting in alteration of gene transcription factor activity

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30
Q

Insulin receptor pathway (in words)

A

Present in membrane as preformed dimer with a and B subunits, B subunits autophosphorylate when insulin binds activating the receptor, which then binds IRS, creating binding sites for SH2 domains, which binds Grb2, leading to activation of Ras and MAP kinase, and binds PI3 which phosphorylates PI4,5 bis to form PI345 trisP, PDK and PKB are recruited and phosphorylated

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31
Q

Tyrosine kinase receptors & serine/threonine kinase receptors similarity

A

Both messengers recruit two monomers to form dimer

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32
Q

Tyrosine kinase receptors & serine-threonine kinase receptors difference

A

Tyrosine kinase receptors binds type II receptor first which recruits type I receptor which is then phosphorylated by the type II receptor; then binds Smad protein which is phosphortylated at serine residue, undergoes conformational change and dissocates, then forms complex with Smad 4 or CoSmad forming Smad Complex which travels to nucleus to alter gene transcription

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33
Q

Where is cAMP synthesized from?

A

ATP

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34
Q

What pathway is this?

A

G-protein coupled signal transduction pathway

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35
Q

Steps for G-protein coupled signal transduction pathway

A

If target protein is adenylyl cyclase;
1. cAMP is synthesized from ATP
allosteric activator of PKA, which phosphorylates CFTR, phosphorylase kinase, and phospholmaban, and transcription factor CREB
2. cAMP is hydrolyzed to AMP by cAMP phosphodiesterase
3. Some heptahelical receptors bind q isoform of Ga subunit, activating phospholipase CB, which hydrolyzes membrane lipid PI 45 Bis into DAG and IP3
4. IP3 has binding site in SR and ER stimulating Ca release and activation of calcium-calmodulin subunits
5. DAG remains in membrane and activates protein kinase C, which propagates response by phosphorylating target proteins

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36
Q

What secondary messengers are produced by adenylate cyclase?

A

cAMP -> activates PKA

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37
Q

What are the two heterotrimeric G protein systems?

A

Adenylate cyclase & phospholipase C

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38
Q

What secondary messengers are produced by phospholipase C?

A

IP3 -> stimulates Ca release and activates Ca-calmodulin subunits
DAG -> activates PKC

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39
Q

What are the different ways to terminate signals?

A

Phosphorylation
Internalization
Degradation
Automatic termination of messages due to hydrolysis of GTP
Degradation of secondary messengers

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40
Q

How does insulin work?

A

Via tyrosine kinase receptors to promote fuel storage

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41
Q

What does epinephrine promote?

A

Fuel mobilization

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42
Q

What is the action of guanylyl cyclase receptors?

A

Convert GTP to second messenger cGMP (analogous to cAMP) directly, unlike heptahelical receptors which use G protein to signal adenylyl cyclase to produce cAMP; activates protein kinase G, phosphorylates targets

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43
Q

What do we use guanylyl cyclase receptors for?

A

Angina pectoris, heart failure, and erectile dysfunction

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44
Q

What occurs in cholera?

A

Watery diarrhea leading to dehydration and hypovolemic shock caused by cholera toxin ADP-ribosylating a class of G-proteins, altering their function and affecting water and salt transport across the intestinal mucosa.
Treatment: glucose electrolyte solution to increase coupled glucose sodium uptake into intestinal epithelial cells, reversing the loss of water from these cells

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45
Q

What occurs in anorexia nervosa?

A

Effects of inadequate nutrition on hormone release and response. Cortisol, glucagon, and epinephrine levels are all increased under these conditions

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46
Q

What are the basic principles of signal transduction?

A

Cells receive and respond to a number of different signals at any given time
Only cells with receptors to a specific signal (chemical messenger) will respond to that signal
One signal can elicit different effects in different cell types

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47
Q

When is the signal transduced?

A

Binding of a chemical messenger to its receptor, amplified in the process

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48
Q

What occurs when insulin binds to receptors on hepatocytes?

A

Glycogen synthesis, fatty acid synthesis, and cholesterol synthesis

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49
Q

What occurs when insulin binds to receptors on skeletal muscle fibers?

A

Stimulate glucose uptake, glycogen synthesis, and other anabolic processes

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50
Q

What is within microchondria?

A

less than .1% of genome DNA, similar to bacteria/prokaryotes, not enclosed within membranes

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51
Q

What is within viruses?

A

contain either DNA or RNA genome, proteins required for pathogenesis or replication, and protein coat, but lack complete DNA systems of replication (must invade and commandeer host DNA)

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52
Q

What is ribose?

A

RNA sugar

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53
Q

What is deoxyribose?

A

DNA sugar

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54
Q

Where is the poly A tail?

A

At the 3’ end of DNA

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55
Q

What are the major & minor grooves?

A

Alternating size around outside in DNA

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56
Q

What is chromatin?

A

DNA complex bound to proteins (nucleosomes)

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57
Q

What does complementary mean?

A

Opposite matching strand sequences

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58
Q

What does anticodon mean?

A

Trinucleotide sequence on tRNA

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59
Q

What does gene mean?

A

DNA sequence that encodes components of gene product with regulator

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60
Q

What does hybridization mean?

A

Reannealing/renaturation of DNA strand with self or with RNA

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61
Q

What does ribosome mean?

A

Site of translation, contains rRNA & tRNA

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62
Q

What does histone mean?

A

Proteins that DNA winds around to condense in nucleus

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63
Q

What does double helix mean?

A

General shape of DNA

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64
Q

What does codon mean?

A

Binding spot on mRNA, where tRNA binds to direct translation

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65
Q

What does nucleosome mean?

A

Clusters of histones forming beads on string formation

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66
Q

What does antiparallel mean?

A

Two strands running opposite direction 5 to 3 and 3 to 5

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67
Q

What does nucleotide mean?

A

Sugar, base, and phosphate

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68
Q

What does nucleoside mean?

A

Sugar & base

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69
Q

What are the base pairings

A

A - T
G - C

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70
Q

What is the basic structure of a nucleotide?

A

Heterocyclic nitrogenous base, sugar, and phosphate, linked via 3’ to 5’ phosphodiester bonds

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71
Q

What is the general structure of DNA?

A

Double-stranded with two antiparallel polynucleotide strands, joined via hydrogen bondings within base pairs
Strands run in opposite directions of one another (one 3’ to 5’ and one 5’ to 3’)

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72
Q

What is the importance of base pairing, hydrogen bonds, van der Waals interactions, and the hydrophobic effect in DNA?

A

Base pairing is specific and occurs by hydrogen bonds between two strands
Van der waals and hydrophobic effects stabilize the molecule in stacking of the base pairs

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73
Q

What can cause the denaturation of DNA?

A

Alkali solutions and heat

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74
Q

What do alkali solutions do to DNA?

A

They do not break phosphodiester bonds of DNA, but rather cleave RNA due to hydroxyl group on 2’ carbon losing proton

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75
Q

What does heat do to DNA?

A

Tm represents the temperature in which DNA is 50% seperated
Can be realigned in temperature is lowered!

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76
Q

Prokaryotic DNA

A

Packaged in doubled stranded circle with about 4x10^6 bp, fairly large, 3000 genes

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77
Q

Eukaryotic DNA

A

Packaged in nucleosomes and wound into chromatin, approximately 6 x 10^9 up to 25,000 genes (much bigger!)

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78
Q

What is within a histone?

A

Large amounts of arginine and lysine, binds to DNA to form chromatin

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79
Q

Histone clusters form…

A

Beads on a string formation known as nucleosomes, with 4 x2 histones forming core and a fifth type of histone H1 complexing with the DNA joining the cores

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80
Q

Where are DNA found?

A

Within nucleus in nuclear envelope and in mitochondria via primordial eukaryotic cells

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81
Q

What are plasmids?

A

Small circular DNA molecules that can enter bacteria and replicate autonomously; can be used as tools for microbiological transfer of genes

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82
Q

What is the structure of DNA?

A

Bound to proteins forming chromatin, euchromatin, or heterochromatin
Contains double ring purines AG, single ring pyrimidines CT, and a deoxyribose sugar
Negatively charged due to free OH on phosphate dissociating a H ion

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83
Q

Nucleosides are linked via…

A

N-glycosidic bond to anomeric carbon of sugar

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84
Q

Nucleotides are linked via…

A

The phosphate attached to 5’ hydroxyl group of sugar in ester linkage

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85
Q

What is the function of DNA?

A

Purine on one strand forms hydrogen bond with pyrimidine on other
One strand of DNA can serve as template for synthesis of other strand
Also allows for DNA to serve as template for synthesis of complementary strand of RNA

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86
Q

Where are RNA located?

A

Formed in nucleolus, moving to specialized regions of cytoplasm depending on the type of RNA formed

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87
Q

What is the structure of RNA?

A

Similar 3’ to 5’ phosphodiester bonds forming strands, however uracil replaces pyrimidine thymine
Sugar is ribose instead of deoxyribose, ribose contains hydroxyl group on 2’ carbon , which makes it susceptible to alkaline hydrolysis
Single stranded and lack helical structure, though secondary and tertiary structure can occur due to strand looping back on self

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88
Q

What is thymine replaced with in RNA?

A

Uracil

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89
Q

What are the functions of RNA?

A

mRNA, rRNA, tRNA participate in process of protein synthesis

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90
Q

Define mRNA

A

Contain nucleotide sequence converted to amino acid sequence of protein in process of translation

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91
Q

What is contained with mRNA?

A

contains 5’ cap at end, poly A tail at 3’ end, and coding region between
5’ end has leader sequence with guanosine cap and then later start codon
3’ end contains poly A tail that may be up to 200 nucleotides long
Guanosine cap and poly a tail are posttranscriptionally added

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92
Q

Define rRNA

A

Has extensive internal base pairing and complexes with proteins to form ribosomes, which bind mRNA and tRNA during translation

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93
Q

Define tRNA

A

Activates specific amino acid for insertion into growing polypeptide during translation

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94
Q

What is unique about tRNA?

A

unique trinucleotide sequence on each tRNA is anticodon which binds to complementary codon on mRNA
cloverleaf structure

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95
Q

What is the central dogma?

A

Information flows from DNA to RNA to proteins

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96
Q

What is the exception of the central dogma?

A

Retroviruses!
Invade cells, RNA genome is transcribed to produce DNA copy, using reverse transcriptase

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97
Q

What do we use 5-FU in?

A

Cancer treatment
- a pyrimidine base similar to uracil and thymine, which inhibits the synthesis of thymine nucleotides by inhibiting thymidylate synthase as a transition state analog, which normally converts deoxyuridine monophosphate to deoxythymidine monophosphate, which ceases DNA synthesis and therefore cell proliferation in cancer

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98
Q

What do we use ZDV in?

A

Viral replication
- nucleoside analog reverse transcriptase inhibitor, acts as a thymine nucleotide that when attached to growing 3’ end of DNA, due to lacking 3’ OH group, DNA synthesis is terminated, terminating viral replication

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99
Q

Why does azithromycin work for bacterial infections without harming the host?

A

Azithromycin is a macrolide antibiotic
Binds to bacterial rRNA stopping protein synthesis by inhibiting transpeptidation/translocation of protein

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100
Q

What are the side effects of azithromycin?

A

Because it can inhibit mitochondrial protein synthesis, can lead to epigastric distress, diarrhea, or cholestatic jaundice

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101
Q

If there is metastasis from colon to liver, what is palliative?

A

5-FU therapy

102
Q

What must retroviruses do?

A

Invade host cells

103
Q

What occurs in AIDS?

A

Infection by the HIV, a retrovirus containing an RNA genome. Through its growth in immune cells, active infection by the virus leads to an immunocompromised state.
Nucleoside analogs are one class of drugs used to treat people with HIV infections

104
Q

What occurs in adenocarcinoma?

A

Use of nucleotide analogs as chemotherapeutic agents. Specifically, 5-fluorouracil is used to inhibit deoxythymidine monophosphate (dTMP) synthesis by the enzyme thymidylate synthase, which leads to the death of rapidly proliferating cells

105
Q

What occurs in pneumonia?

A

A bacteria-induced illness in the lungs, leads to fever and cough. Treated with anitbiotics. Certain antibiotics target bacterial protein synthesis but may also inhibit mitochondrial protein synthesis

106
Q

DNA synthesis in prokaryotes

A

DnaA protein binds at point of origin (oriC) where DNA coils around DnaA core
With assistance of helicase, gyrase, single stranded binding protein, two parental strand separate
Synthesis occurs at two replication forks that move away from each other
Second round of synthesis can start before other is finished

107
Q

DNA synthesis in eukaryotes

A

Replicates histones with DNA
Multiple points of origin, bubbles appear where fork can proceed in each direction
Many more polymerases and complex proteins

108
Q

What does bidirectional mean in context of DNA?

A

Fork travels in both directions from origin

109
Q

What does semiconservative mean in context of DNA?

A

Each daughter chromosome contains one parental strand and one newly synthesized

110
Q

Origin of replication

A

Start point for prokaryote DNA synthesis where DnaA binds

111
Q

Leading strand

A

Continuous 5’ to 3’ synthesis toward the fork

112
Q

Lagging strand

A

Discontinuous 5’ to 3’ synthesis in short fragments called Okazaki, away from the fork, jointed together by ligase

113
Q

Okazaki fragments

A

Short fragments of discontinuous synthesized DNA

114
Q

Helicase

A

Unwind two parental strands

115
Q

Topoisomerase

A

Unwind two parental strands by breaking phosphodiester bonds and rejoining them to relieve supercoiling (DNA gyrase in prokaryotes)

116
Q

Single-strand binding protein

A

Prevents DNA from “reannealing”, or folding over onto itself, to protect from enzymes that cleave single stranded DNA

117
Q

Primase

A

Synthesizes RNA primer molecule in a 5’ to 3’ direction that copies DNA template strand

118
Q

RNA primer

A

Ribonucleotide sequence added for site where DNA polymerase can add to 3’ end, removed and replaced

119
Q

PCNA

A

Proliferating cell nuclear antigen, organizes and orchestrates replication process on both leading and lagging

120
Q

DNA polymerase

A

Copies each parental template 3’ to 5’ producing new strand 5’ to 3’

121
Q

RNase H

A

Ribonuclease that specifically degrades RNA from RNA-DNA hybrid, can also assist with removal of primers

122
Q

Ligase

A

Joins Okazaki fragments, free 3’ OH to phosphate at 5’ end

123
Q

What phase of the cell cycle does DNA replication occur?

A

S-phase of cell cycle, followed by G2 phase then M, where cell divides creating daughter cell with exact copy of DNA

124
Q

Why are the ends of linear chromosomes lost during replication?

A

Primase cannot lay down a primer at the very end of a chromosome
Results in 3’ overhang regions of template on new strand

125
Q

Telomeres

A

Repeating sequences of bases TTAGGG

126
Q

What is the purpose of telomerase in DNA?

A

An RNA dependent DNA polymerase (like reverse transcriptase), uses own RNA template to synthesis new repeating DNA to lengthen DNA overhang, primase can then bind at long end and synthesize back to end of coding regions, telomere binding proteins protect ends of chromosomes from damage and nuclease attack

127
Q

What is the base-pairing correction in prokaryotes?

A

Pol III (a replication enzyme) performs proofreading, 3’ to 5’ exonuclease activity in addition to polymerase activity
Exonuclease activity: incorrectly base-paired nucleotides are removed before the growing chain is lengthened
Only 1 in a million error

128
Q

What are the mechanisms of eukaryotic repair?

A

Nucleotide excision repair, base excision repair, mismatch repair, transcription-coupled repair

129
Q

Nucleotide excision repair

A

Local distortions such as a mismatch in base pairs or damage to bases, specific endonucleases cleave abnormal chain removing distorted region, gap filled by DNA polymerase using intact strand as template, joined by ligase

130
Q

Base excision repair

A

DNA glycosylases recognize a small distortion involving lesions caused by damage to single base, glycosylase cleaves N-glycosidic bond joining damaged base to deoxyribose, then endonuclease cleaves the sugar-phosphate strand at the site, then polymerase fills the gap, ligase joins

131
Q

Mismatch repair

A

Mismatched bases recognized by enzyme complex during replication, removed and replaced

132
Q

Transcription coupled repair

A

RNA polymerase that is transcribing a gene stalls when it encounters a damaged portion, excision repair proteins repair damaged region similar to NER

133
Q

How do bacteria distinguish between new and parental strands?

A

Bacteria parental strands contain methyl groups on adenine bases, new strands are not immediately methylated

134
Q

What damage occurs to DNA via UV light?

A

UV alter base pairing by exciting adjacent pyrimidine bases on DNA strands, causing them to form covalent dimers, usually thymine dimers

135
Q

What DNA damage occurs via cigarette smoking (benzo[α]pyrene)

A

Benzo a pyrene coats airways and lungs, can cross cell membranes, and interact with DNA, causing damage to bases interfering with base pairing, specifically makes bulky adducts with guanine residues in DNA

136
Q

What repair is done to UV light & cigarette smoking damaged DNA?

A

NER repair

137
Q

What are genetic rearrangements?

A

Exchange of segments between DNA molecules

138
Q

What are the 3 major mechanisms of genetic rearrangement?

A

Homologous recombination, translocations, transposons

139
Q

Translocation

A

Chromosomes break and portions randomly become joined to others
Breakage by x-ray or carcinogen, and resealing of parts of different chromosomes

140
Q

Transposon

A

Can move from one site in genome to another or produce copies that can be sent to new site

141
Q

What is contained within transposons?

A

Contain gene for enzyme transposase, cleaves transposon from genome and moves to another location

142
Q

What is occurring here?

A

Homologous recombination

143
Q

Reverse transcriptase mechanism

A

RNA template is transcribed from DNA by RNA polymerase or obtained from RNA virus
RNA template forms cDNA strand, is degraded, and second cDNA strand formed

144
Q

What is the mechanism of dideoxynucleoside NRTIs?

A

No hydroxyl group on either 2’ or 3’ carbon, can be converted to dideoxynucleoside triphosphates in cells, and then when incorporated into growing DNA, termination results due to lack of 3’ hydroxyl group

145
Q

Why can HIV genome rapidly mutate?

A

Reverse transcriptase (the enzyme that converts single stranded RNA to DNA) lacks proofreading ability, so it can mutate at a rapid rate

146
Q

What is faulty in xeroderma pigmentosum?

A

Defect in NER or transcription coupled repair, sun hypersensitivity with high risk of skin cancer, inability to remove thymine dimers

147
Q

What is faulty in cockayne?

A

Transcription coupled repair defect, premature aging, premature cell death due to reduction of gene expression, because damaged genes cannot be translated

148
Q

What is faulty in HNPCC?

A

Mutation in enzyme present in intestinal epithelial cells responsible for mismatch repair, leads to colorectal cancers

149
Q

What is faulty is hereditary breast cancer?

A

Inheritance of mutations in proteins responsible for DNA repair of single strand and double strand breaks

150
Q

What does diabetes put patients at risk for?

A

Infections due to high glucose levels -> perfect culture medium for bacteria

151
Q

Define transcription

A

Synthesis of RNA from DNA template

152
Q

Define template strand

A

DNA strand that directs sequence of nucleotides

153
Q

Define coding strand

A

Nontemplate strand, will be identical to RNA transcript except T changed to U, determines protein sequence

154
Q

Define promoter sequence

A

DNA sequence that defines where gene transcription begins

155
Q

Define primary transcript (hnRNA)

A

Initially generated RNA strand from transcription, receives guanosine cap at 5’ end and poly A tail at 3’ end

156
Q

Define upstream in RNA synthesis

A

To left of start point, or towards 5’ end

157
Q

Define downstream in RNA synthesis

A

To right of start point, or towards 3’ end

158
Q

Introns

A

No coding functions, removed during splicing

159
Q

Exons

A

Expressed part, contain coding sequences for proteins

160
Q

What is the fun thing Aloki likes to say for introns and exons

A

Exons we keep, introns we yeet

161
Q

Coding strand is … to RNA transcription produced, RNA strands dictate… chain

A

Identical, protein

162
Q

Template strand is … strand that has base pairs bond in matching order to … strand

A

Actual, coding

163
Q

How is RNA polymerase different from DNA polymerase?

A

Initiate new synthesis without primer

164
Q

RNA polymerase … polymerization of ribonucleotides

A

Catalyzes

165
Q

What must RNA polymerase be able to do?

A

Recognize promoters for transcription starting site

166
Q

RNA polymerase lacks…

A

3’ to 5’ endonuclease activity (but has some rudimentary error checking)

167
Q

Prokaryotic RNA polymerase

A

Single RNA polymerase that transcribes DNA to generate all different types of RNA
Five subunits with sigma factor that binds and directs promoter binding

168
Q

Eukaryotic RNA polymerase

A

Three different RNA polymerases, I = rRNA, II = mRNA and microRNA, III = tRNA and 5S rRNA
Different promoters

169
Q

What is a promoter?

A

Composed of boxes or elements that are contiguous with transcribed region, control binding of RNA polymerase and to DNA, identifying start point

170
Q

-10 region in prokaryotes is the

A

TATA box

171
Q

-25 region in eukaryotes is the

A

TATA box

172
Q

-35 region in prokaryotes is the

A

TTGACA sequence

173
Q

What do eukaryotes frequently have?

A

GC rick sequence/BRE, initiator element, downstream promotor, motif ten element

174
Q

What are the proximal promoters regions in eukaryotes?

A

-100 to -200

175
Q

First base of coding strand is …, untranscribed sequence in 5’ flanking region are numbered … and so on

A

+1, -1

176
Q

What is the role of sigma factor in prokaryotic transcription?

A

Binds to RNA polymerase enzyme to direct promoter binding
Binds to TATA box region of promoter, sigma 70

177
Q

What are the 2 mechanisms of termination for sigma factor?

A

Transcription termination signal of either hairpin loop preceding several U residues, or binding of a rho factor protein which causes release of RNA transcript from template

178
Q

Polycistronic transcripts

A

Contains information to produce several different proteins
Usually common in bacteria, several different proteins formed at once (operon)

179
Q

Monocinstronic transcripts

A

Contains information for one protein
Usually common in eukaryotes, requires introns removed and other posttranscriptional modifications

180
Q

What are the posttranscriptional processing events?

A

5’ end capped as it is transcribed: first loses a phosphate becoming a diphosphate which attacks GTP
Methylated guanosine = CAP 0
Addition of methyl group to 2’ carbon = CAP1
Addition of another methyl group to next nucleotide 2’ carbon = CAP2
Methyl groups donated by SAM
3’ end acquires poly A tail
Removal of introns: introns = “nonsense information”: intron barriers, spliceosome

181
Q

What is the importance of splicing eukaryotic transcripts?

A

Consensus sequences at intron/exon boundaries are AGGU which vary to some extent on exon side of boundary, but intron side are fairly invariant
Spliceosome complex forms loop formation cutting out intron, and linking exons together

182
Q

Posttranscriptional processing for tRNA

A

cloverleaf shape that folds into 3D L shape
start with 100 nucleotide precursors off of RNA strand, 5’ and 3’ ends are cleaved
introns removed by endonucleases
uracil methylated by SAM to form thymine
one of double bonds of uracil is reduced to form dihydrouracil
uracil residue is rotated to form pseudouridine

183
Q

Posttranscriptional processing for rRNA

A

large gene exists in many copies in nucleolar organizer region of nucleus
produces large 45S transcript which can be cleaved to form 18S, 28S, and 5.8S
can become methylated which may signal for cleavage

184
Q

What is the difference between eukaryotic and prokaryotic DNA & RNA

A

Eukaryotes have introns, repetitive sequences, histones, and errors occur in nucleus
Prokaryotes are open ring, and errors occur in cytosol

185
Q

What occurs in beta-thalessemia?

A

Decrease or abolish the synthesis of a or B chains in adult hemoglobin A tetramer, which interfere with transcription of B globin transcription, processing, or translation
Mutation within TATA box for B globin gene, reducing accuracy of start point, so only portion of normal protein synthesized, other mutations further upstream in promoter region
Or
Mutation in promoter region of B globin gene, results in significantly decreased rate of synthesis in homozygous
Minor, intermediate, or major: amount of B globin gene affected, which then affects total hemoglobin level = anemia

186
Q

What is the difference between beta-thalassemia and sickle cell anemia?

A

Beta-thalassemia does not cause muscle pain with exacerbation during exertion

187
Q

Mechanism of action of transcription inhibitors rifampicin and alpha-amanitin

A

Inhibits eukaryotic RNA polymerases, especially polymerase II
Lack crucial OH group, so chain cannot be continued after addition to chain

188
Q

What is the genetic code?

A

Groups of 3 nucleotides that code for an amino acid = a codon. There are 64 of these.

189
Q

What are anticodons?

A

Adapters on tRNA that bind directly with an mRNA codon, transferring an amino acid to the growing polypeptide chain

190
Q

What occurs in transcription?

A

The transfer of genetic message from DNA to RNA

191
Q

What occurs in translation?

A

The transfer of genetic message from nucleic acids to amino acids

192
Q

What occurs in replication?

A

The replication of genetic material in DNA

193
Q

Why is the genetic code degenerate, unambiguous, nonoverlapping, and almost always universal?

A

Many amino acids are specified by more than one codon = degenerate
Each codon only specifies one amino acid = unambiguous
No extra nucleotides or punctuation to separate codons- each nucleotide is only read once = nonoverlapping

194
Q

What is always the coding strand unless stated?

A

DNA

195
Q

Point mutation

A

One base in DNA altered producing change in signle base of mRNA codon

196
Q

What are the types of point mutation?

A

Silent, missense, nonsense

197
Q

Missense mutation

A

Amino acid is replaced by other

198
Q

Nonsense mutation

A

Change to stop codon causing premature termination

199
Q

Silent mutation

A

Does not impact amino acid

200
Q

Insertion

A

One or more nucleotides are added to DNA, if stop codon not generated, a protein with more amino acids could be produced

201
Q

Deletion

A

One or more nucleotides added to DNA, if deletion does not affect normal start and stop, shorter protein can be produced

202
Q

Frameshift

A

Number of inserted or deleted is not multiple of three, causes reading frame to shift, beyond point of mutation, amino acids will differ from normal protein

203
Q

What do anticodons on tRNA match with?

A

Three base sequence of codons on mRNA strand

204
Q

What does each tRNA carry?

A

Specific amino acid, thus amino acids are linked in sequence according to mRNA codons

205
Q

Three phases of translation

A

Initiation, elongation, and termination

206
Q

Initiation

A

Formation of a complex containing methionyl tRNA bound to AUG start codon of mRNA and to P site of ribosome, requires GTP and eIFs
Methionine tRNA initially forms complex with IF2 which binds GTP which then binds to ribosome with participation of IF3
IF4F binds 5’ cap

207
Q

Elongation

A

Binding of aminoacyl tRNA to A site on ribosome base pairing with second codon on mRNA, formation of peptide bond between first and second amino acid, translocation of mRNA relative to ribosome so third mRNA codon moves into A site
GTP must be hydrolyzed for tRNA to stay in A site

208
Q

Termination

A

Termination codon aligns with site on ribosome where next aminoacyl tRNA would normally bind, release factors bind instead causing completed protein to be released from ribosome

209
Q

How is the correct 3D conformation of polypeptide achieved?

A

Proteins begin folding as they exit the ribosome
Chaperone proteins help with folding
Disulfide isomerases help disulfide bond formation between cysteines

210
Q

Posttranslational modifications on amino acids

A

Cleavage of methionine or other to form new N terminal amino acids
Acylation of N terminal amino acid
Methylation of lysine
Hydroxylation of proline and lysine
Carboxylation of glutamate
Fatty acylation and prenylation
Transfer of ADP ribose group from NAD+
Phosphate addition or removal
Glycosylation

211
Q

What is the mechanism for protein targeting?

A

Targeting sequences or signal sequences: amino acid sequences that facilitate transport to certain organelles if synthesized in cytosol
Proteins synthesized bound to RER are destined for secretion to organelles or cellular membranes

212
Q

What do the proteins synthesized bound to RER contain?

A

Contain signal peptides near N terminus that do not have common amino acid sequence, with several hydrophobic residues , SRP binds and attaches to SRP receptor in rough ER, signal peptide removed by signal peptidase, then transferred in small vesicles to golgi, golgi sorts and processes proteins such as glycosylation and modification

213
Q

What do the mutations cause the beta-globin transcript to do?

A

Function, shape, and size of beta globin protein is impacted

214
Q

What leads to Tay-Sachs disease?

A

Insertion within the alpha-chain of hexosaminidase A gene
Causes dysfunction of hexosaminidase enzyme which normally degrades glycosphyngolipids like gangliosides
Dysfunction leads to build up of gangliosides and neurological symptoms, vision difficulty

215
Q

What is an E6V mutation?

A

Missense mutation that impacts hemoglobin -> sickle cell
Valine residue replaces glutamic acid at position six of the beta-chain

216
Q

What occurs in I-cell disease?

A

Lysosomal proteins are not sorted properly in golgi and up being secreted from cell, due to mutation of phosphotransferase enzyme which is a required first step to attach lysosomal targeting signal m6p, organelles become clogged with materials that cant be digested, lysosomes swell because enzymes not present to degrade

217
Q

What does streptomycin inhibit?

A

Inhibits translation initiation by binding to three proteins and ribosomal subunit 16S of bacteria

218
Q

What does tetracycline inhibit?

A

Binds to 30S ribosomal subunit of bacteria and prevents aminoactyl tRNA from binding to A site on ribosome

219
Q

What does chloramphenicol inhibit?

A

Binds to ribosomal subunit 50S and prevents binding of amino acid portion, inhibiting peptidyltransferase action

220
Q

What does erythromycin inhibit?

A

Bind to 50S ribosomal subunit near binding site for chloramphenicol, however prevents translocation step so tRNA cannot move from A to P

221
Q

What is the need for cells to regulate expression of its genes?

A

Efficiency and ability to express specific proteins, and ability to adapt to changes in environment

222
Q

What is an operon?

A

Genes of a related function are grouped sequentially and coordinately expressed (all on, or all off)

223
Q

Why is an operon of genes well-suited for regulation of gene expression for prokaryotes?

A

Single polycistronic mRNA produced coding for all proteins of the operon
Allows more adaptability

224
Q

Where does a repressor protein bind?

A

Operator blocking transcription

225
Q

What is an inducer?

A

Stimulates expression of operon by binding to repressor and changing conformation causing release from operator (nutrient or metabolite of nutrient- lac operon)

226
Q

What is a corepressor?

A

Repressor is inactive until corepressor binds which activates it allowing it to bind to the operator preventing RNA polymerase (if product is available, save energy by not transcribing more – trp operon)

227
Q

What is the negative control within the lac operon?

A

Repressor binding to operator

228
Q

What is the positive control within the lac operon?

A

Allolactose binding to repressor

229
Q

How does the existence of different sigma factors that bind RNA polymerase result in prokaryotic gene regulation?

A

Stimulates binding to certain promoters, activating transcription of specific operons, thus specific gene expression

230
Q

Transcriptional attenuation is

A

Interrupting transcription after it has been initiated
As mRNA is being transcribed, hairpin loop forms in mRNA due to speed of translation too high due to high availability of trp
Requires coupled transcription and translation so cannot occur in eukaryotes

231
Q

Most regulations in eukaryotes is…

A

Positive
Very complex with complex functions within each cells that change as development continues, environments change, etc.
Genes must be active to be expressed, no operons/often located on different chromosomes, transcription and translation are separated

232
Q

What is the role of chromatin remodeling?

A

Chromatin must remodel so that not part of a nucleosome, and chromatin is in euchromatin/loose state, not heterochromatin/dense
ATP driven chromatin remodeling complex which uses energy from ATP hydrolysis to unwind sections of DNA from nucleosome core
Covalent modification of histone tails through acylation by histone acetyltransferases, making it easier for DNA to unwind from histones

233
Q

What is the role of DNA methylation?

A

Methylation of cytosine residues located in CG rich sequences, often near promoter regions
Usually less readily transcribed than those that are not methylated

234
Q

What are gene-specific transcription factors?

A

Regulatory proteins that bind directly to DNA sequences
- Activators, inducers, repressors, nuclear receptors

235
Q

What are hormone-binding transcription factors?

A

Steroid hormones that activate or inhibit the transcription of specific genes through binding to nuclear receptors
Nuclear receptors bind to DNA regulatory sequences called hormone response elements and induce or repress transcription

236
Q

Basal transcription factors

A

Basal are bare minimum for transcription
Gene specific enhance basal model for faster expression of specific gene

237
Q

Alternative splicing

A

splicing out of introns to form exon coding regions

238
Q

Polyadenylation

A

poly A tail to 3’ end

239
Q

mRNA editing

A

editing bases or addition or deletion of nucleotides after synthesis

240
Q

What are the mechanisms of regulation at the level of translation and mRNA stability?

A

Initiation of protein synthesis by initiation factors Ifs, which are regulated through mechanisms involving phosphorylation
Transferring moves iron into cells (higher if levels low in blood)
Ferritin stores iron (less if iron levels low in blood)

241
Q

How does a single RNA binding protein, IRE-BP, coordinates the levels of ferritin and the transferrin receptor to ensure that cellular and bodily iron levels are tightly regulated?

A

IRE-BP bind to transcript when low iron, high iron binds to IRE-BP to remove
Ferritin: IRE binds at 5’ end, blocks ribosome
Transferrin: binds to 3’ end to stabilize and prevent degredation

242
Q

How can microRNAs (miRNAs) can posttranscriptionally regulate gene expression?

A

microRNAs can induce degradation of target mRNA or block translation of mRNA
miRNA -> pri-miRNA -> pre-miRNA -> mature miRNA -> incorporation into RISC complex -> RISC blocks translation of target mRNA

243
Q

Non-Hodgkin lymphoma

A

Treatment with multiple drugs, all targeted to inhibiting cell proliferation, but through different mechanisms. DNA synthesis is targeted, as is tubulin action (to block cell division). DNA damage is induced, and thymidine synthesis is also blocked to inhibit further DNA replication

244
Q

CML (chronic myelogenous leukemia)

A

More than 90% of CML arises owing to the generation of the Philadelphia chromosome, which is created by an exchange of genetic material between chromosomes 9 and 22. This translocation creates a unique fusion protein (BCR-abl), which facilitates uncontrolled proliferation of cells which express this fusion protein

245
Q

Anorexia nervosa

A

The patient’s poor diet has led to a hypochromic anemia owing to low iron levels. This leads to a reduction of expression of serum and tissue ferritin, but an increase of expression of the transferrin protein and the transferrin receptor

246
Q

Angelman and Prader–Willi syndrome

A

The use of base methylation, within promoter regions, to regulate gene expression. The methylation of key bases within the promoter leads to nonexpression of the gene and forms the basis for imprinting. This is an example of epigenetic modification of gene expression

247
Q

Fragile X disease

A

A significant number of triplet repeat expansions within a gene may lead to dysfunction of the protein product, leading to disease. In fragile X, impairment of cognitive function is the primary symptom, caused by expansions in the FMR-1 gene on the X chromosome

248
Q

Androgen insensitivity

A

Lack of androgen receptors, leading to default female sexual characteristics. The patient produces androgens but cannot respond to them. These patients have an XY genotype but female sexual characteristics

249
Q

Diphtheria, pertussis

A

Diphtheria toxin catalyzes the ADP-ribosylation of eEF2, a necessary factor for eukaryotic protein synthesis. This results in cell death. Vaccination against pertussis antigens will prevent infection

250
Q

Hutchinson–Gilford Progeria syndrome

A

An example of a silent mutation in terms of amino acid substitution, but the single nucleotide change creates an alternative splice site that leads to a loss of 50 amino acids from the precursor lamin A protein. This leads to altered posttranslational processing and the symptoms of a premature aging disease

LECOM DSP Biochemistry 2022 (11 decks)

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