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M2M > M2M Unit one > Flashcards

M2M Unit one Flashcards

1
Q

What is entropy

A

Disorder or randomness in system

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2
Q

What is enthalpy?

A

Amount of energy (heat or bond energy) in a system

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3
Q

What is free energy?

A

The change in Gibbs free energy is the maximum work that a process can perform under constant pressure

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4
Q

What does a negative Gibbs free energy mean?

A

Reaction is favorable and spontaneous

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5
Q

What are high energy compounds?

A

Compounds that store chemical energy in their bonds which can be used for work on other compounds with relative ease

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6
Q

What is an oxidation-reduction reaction?

A

A reaction where a compound receives or gains electrons (reduced) while a compound that accepts electrons is oxidized.

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7
Q

First law of thermodynamics

A

Energy is neither created nor destroyed

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8
Q

Second law of thermodynamics

A

Entropy in the universe must always increase

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9
Q

What are the four different forms of energy?

A
  1. Radiant
  2. Mechanical
  3. Thermal
  4. Electric
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10
Q

Forms of potential energy?

A
  1. Stored in bonds
  2. Concentration gradients
  3. Electric Fields from charge separation
  4. Movement of charged particles down gradients of electrical potential
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11
Q

Formula for delta G?

A

= delta G0 + RT ln [products]/[reactants]

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12
Q

what is delta G0?

A

free energy change of a reaction under standard conditions (298 K, 1 atm, 1 M, pH=7)

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13
Q

formula for delta G0?

A

= -RTlnKeq = -2.3RTlog Keq = delta H - Tdelta S

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14
Q

formula for Keq

A

[C][D] / [A][B]

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15
Q

Negative H, Negative S = ?

A

spontaneous at low temperatures

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16
Q

Positive H, Negative S = ?

A

reaction is not spontaneous

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17
Q

Numerical conversion between free energy and redox potential?

A

delta G = nFdeltaE
E is the difference in reduction potential in volts
n is number of electrons transferred

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18
Q

What are the purines?

A

two ring nucleotide. Guanine and Adenine

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19
Q

What are the pyrimidines?

A

one ring nucleotide including Thymine and Cytosine

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20
Q

Ribose vs. Deoxyribose?

A

Ribose has a hydroxyl group at the 2’ and 3’ position on the sugar.

Deoxyribose only has a hydroxyl group on the 3’ position of the sugar

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21
Q

Nucleotide

A

includes the nitrogenous base(purine or pyrimidine) attached to 1’ or sugar, sugar, and phosphate attached to the 5’

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22
Q

nucleoside

A

just the nitrogenous base and the sugar. Phosphate is excluded

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23
Q

ribonucleotides

A

Use Uracil instead of Thymine

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24
Q

order the solubility of the following: pyrimidine, purines, bases, nucleotides, nucleosides,

A

pyrimidine > purine; nucleotide > nucleoside > base

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25
Q

Medical Relevance of Gout and Lesch-Nyhan?

A

accumulation of purines which are insoluble in tissues. Causing joint pain

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26
Q

Disease(s) caused by accumulation of purines?

A

Gout and Lesch-Nyhan

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27
Q

Explain polarity of the phosphodiester bond

A

The phosphodiester linkage is between 3’ OH group and the neighboring 5’ phosphate group

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28
Q

Avery, McCloud, and McCarty contribution to science?

A

deduced that DNA is the genetic material through the pneumococcus experiment and killing mice

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29
Q

Rosalind Franklin

A

x ray diffraction suggested that DNA is a helical struture

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30
Q

Watson and Crick

A

DNA is a double helix and can semi conservatively replicate itself

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31
Q

Implications of Chargaff’s Rules?

A

The ratio between G:C and A:T are approximately the same.

Molar ratios between purines (A+G) = pyrimidine (C+T)

The G:C And A:T ratio varies across different organisms

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32
Q

Describe Watson-Crick three dimensional model for DNA structure

A

DNA is a right handed double helix.

The sugar phosphate group is hydrophilic and on the outside of the molecule.

The bases are paired and stacked on the inside due to their hydrophobicity.

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33
Q

Major Groove of DNA vs Minor Groove of DNA

A

Major Groove is the gap between the curve of the same DNA molecule.

Minor groove is the gap between complementary DNA

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34
Q

What contributes to the stability of the double helix DNA in solution?

A

Magnesium ions in the cell neutralize the negative phosphate groups.

hydrogen bonding between base pairs

hydrophobic interaction of base stacking

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35
Q

Ways to further stabilize DNA?

A

increase salt concentration to neutralize phosphate negative charge

make DNA longer

increase G:C content

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36
Q

Methylation of Cytosine

A

DNA modification made by enzyme that methylates cytosine at the 5’ position.

Represses transcription

Needs a 3’ G adjacent to it for methylation to occur

Naturally occuring

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37
Q

Deamination

A

Nitrous acid or nitrosamine can be increased in a person that inhales cigarette smoke.

The nitrosamine can then cleave amine group in the DNA (deamination)

If cytosine has been (naturally) mythylated the deamination will make cytosine – > thymine. Thus, there will be a T-G MISMATCH.

Can’t be recognized as mismatch and 50% chance the mutation will remain

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38
Q

Depurination

A

low ph can result in hydrolysis between sugar and the base

phosphate group is now prone to breakage

Can be repaired via DNA repair enzymes

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39
Q

UV cross linking

A

UV light causes covalent attachment of adjacent Thymines on the SAME strand.

Causes kink in DNA that disrupts replication

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40
Q

Mechanism of UV cross linking repair

A

nucleotide excision repair and TF2H

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41
Q

Base Alkylation

A

due to environmental exposure to coal, mustard gas (warfare), and cigarette smoke

nucleophilic reaction leading to alkyl or hydrocarbon being added to nitrogen

Not easily repaired and blocks DNA replication and transcription

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42
Q

Ways that nucleoside analogues can be used as drugs

A
  1. Intercalating drugs insert themselves into DNA and alters DNA double helical structure. Interferes with DNA replication and transcription
  2. Disrupts DNA synthesis (oldest target; today we focuson combination)
  3. Inhibit topoisomerase from relaxing DNA which is necessary for DNA replication and transcription.
  4. Covalently binding to base pairs
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43
Q

Define Semiconservative

A

During DNA replication you have one old strand and one new strand

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44
Q

What does Bi-directional mean?

A

DNA replication occurs in two opposite directions starting at the origin site. ALWAYS 5’ to 3’

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45
Q

Okazaki fragments

A

small fragments of DNA assembled from the lagging template in the 5’-3’ direction and then fused together by ligase

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46
Q

prokaryotes vs eukaryote origin sites

A

prokaryotes only have one origin for replication (they have less to replicate). Eukaryotes have multiple sites of oriin

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47
Q

Origin binding proteins

A

recognize the origin site. MCM in eukaryotes They recognize AT rich sequences

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48
Q

Helicase

A

unwinds just ahead of the replication fork

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49
Q

Single strand binding protein

A

binds to each single strand of DNA and prevents dna from folding on itself or geting degraded

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50
Q

Topoisomerase

A

prevents extreme supercoiling of parental helix due to the unwinding at the replication fork

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51
Q

DNA Gyrase

A

a topoisomerase found only prokaryotes and is inhibited by quinolones (antibiotic)

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52
Q

DNA polymerase

A

adds deoxyribonucleotides to the 3’ hydrolxyl group of the RNA primer and adds dNTs in the 5’ to 3’ direction

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53
Q

DNA polymerase used in prokaryotes?

A

DNA polymerase I and III

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54
Q

DNA polymerase III

A

major replicative enzyme because it has a sliding clamp that keeps it attached = processive

Holoenzyme

Has 3’ to 5’ proofreading ability

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55
Q

DNA polymerase I

A

distributive and dissociates from DNA easily

It has 5’ to 3’ exonuclease activity to remove the RNA primer

replaces RNA primer with DNA in the 5’ to 3’ direction

It also has 3’ to 5’ proofreading ability

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56
Q

Primase

A

A DNA dependent RNA polymerase

needs DNA to add an RNA primer

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57
Q

DNA ligase

A

joins fragments of DNA together

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58
Q

sliding clamp

A

binds to the polymerase III to allow more processitivity. Keeps it tightly bound to DNA

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59
Q

Telomerase

A

an RNA dependent DNA polymerase that maintains chromosomal ends by making the telomeric repeat sequence from an RNA template

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60
Q

Diseases that are caused by mutations in genes that happen to mediate the nucleotide excision repair mechanism

A

Xeroderma pigmentosum
Cockayne Syndrome
Trichothiodystrophy

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61
Q

What causes Thymine dimers

A

UV radiation causing linkage between adjacent thymine residues causing a bulge in the DNA helical structure

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62
Q

Consequences of unrepaired thymine dimer?

A

Disrupts replication because Pol III will fall of and bypass polymerase takes over leading to much more mutations

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63
Q

Best way to repair thymine dimer?

A

Nucleotide excision repair a much more versatile mechanism

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64
Q

Cause of bulky chemical adducts in DNA

A

chemotoxins that bind to DNA helix and disrupt the shape

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65
Q

Repair mechanism for chemical adducts?

A

Nucleotide excision repair

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66
Q

Cause of double strand breaks

A

double break of the phosphodiester back bone because of ionization radiation, oxidatitve damage, and spontaneous events

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67
Q

How to repair double strand breaks?

A

homologous recombination repair or non-homologous end joining

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68
Q

Homologous recombination vs non homologous joining?

A

Homologous recomibination requires extensive sequence homology between broken DNA and the DNA template. Very accurate

Non-homologous joining requires no sequence homology. Often inaccurate leading to deletions/insertions

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69
Q

How does uracil end up in DNA by mistake?

A

cytosine is deaminated and produces uracil in DNA now. Deamination is due to nitrous acid!

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70
Q

How to repair uracil mismatch in DNA?

A

base excision repair!

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71
Q

Consequences of having uracil in the dna?

A

problems with replicating, transcribing this part of the gene and recognition of transcription enzymes

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72
Q

Function of mismatch repair

A

fixes nucleotides that have been mistakenly added during DNA replication

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73
Q

Name the 3 types of excision repair

A

base excision repair
nucleotide excision repair
mismatch excision repair

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74
Q

Main difference between the three excision repair steps?

A

How the mistake is inItially RECOGNIZED

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75
Q

Recognition of a mismatched nucleotide by..

A

MSH and MLH

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76
Q

exonuclease vs endonuclease?

A

endonuclease cleaves the phosphodiester backbone of new strand of DNA

exonuclease CHEWS away the new DNA strand including the mismatch nucleotide.

(alphabetical order)

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77
Q

Steps common to all three types of excision repair

A
  1. Endonuclease-mediated cleaves the phosphodiester backbone flanking the damaged/mismatched nucleotide.
  2. Exonuclease-chews DNA fragment containing the damaged/mismatched nucleotide.
  3. DNA polymerase-mediated synthesis of the missing nucleotides by copying nucleotide sequence from the intact DNA strand.
  4. DNA ligase-mediated sealing of the remaining nick in the phosphodiester backbone.
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78
Q

Hereditary non-polyposis colorectal cancer (HNPCC)

A

caused by mutation in the mismatch repair machinery

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79
Q

How can E.coli differentiate parental strand from daughter strand?

A

Daughter strand has not yet been methylated!

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80
Q

When is nucleotide excision repair used?

A

to remove damages that distort the DNA structure and block polymerase function.

Used to repair thimine dimers and bulky lesions and chemical adducts

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81
Q

Global Genome nucleotide excision repair (NER)

A

protein that recognizes damage anywhere in the genome

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82
Q

Transcription coupled NER

A

protein that only recognizes damage in transcribed regions

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83
Q

Disease caused by mutation in Global Genome NER

A

xeroderma pigmentosum

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84
Q

Disease caused by mutation in Transcription Coupled NER

A

cockayne syndrome

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85
Q

When is based excision repair used

A

To repair DNA lesions that are missed by the NER process

these repairs don’t necessary block polymerase function or distort DNA structure

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86
Q

Protein that recognizes Base excision repair

A

Glycosylase

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87
Q

What is lesion bypass?

A

When cells have too much DNA damage for the “error proof” repair machinery to handle.

Cell uses DNA polymerase with loosened specificity to allow the continuation of replication.

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88
Q

What’s unique about the bypass polymerase?

A

Lacks proofreading 3’ to 5’ and much more errors!

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89
Q

Explain MGMT

A

evolutionary conserved and is an example of “direct reversal” DNA repair.

it removes the methyl group from O6-methyguanine

MGMT is silenced via promoter methylation in 45% of glioblastomas

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90
Q

Cyclin dependent Kinase (CDK)

A

enzyme that is a protein kinase. The CDK subunit requires cyclin inorder to be activated

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91
Q

Retinoblastoma protein (Rb)

A

an inhibitor protein of the cell cycle aka a tumor supprossor

Need Rb inhibited in order for cell to divide and enter S phase

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92
Q

What protein(s) inhibit CDK?

A

CDKN (two types)

I. Cip/Kip Family
2.lnk4 family: p16,p15,p18, p19

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93
Q

What amino acids can be phosphorylated by CDK?

A

Serine, Threonine, and Tyrosine

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94
Q

What is mitogen?

A

proteins and peptides that eventually will cause the production of cyclinD1-3.

results in an increase in cyclinD1-3 proteins and more
CDK4/6-cyclin D1-3 active protein kinase complexes.

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95
Q

How is the cell size regulated?

A

In G1 phase, cell growth is coordinated with cell division at the “R” (restriction point). At the R point, the cell determines whether or not it is big enough to move on to S phase.

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96
Q

Ataxia Telangiectasia Mutated (ATM)

A

A serine/threonine protein kinase activated by DNA double strand breaks. Phosphorylates key proteins that initiate DNA damage checkpoint, leading to cell cycle arrest, DNA repair or apoptosis

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97
Q

targets of ATM

A

p53, CHK2, and H2AX

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98
Q

Endogenous sources of double strand breaks

A
  1. Meiosis
  2. DNA replication single stranded DNA breask
  3. Immune system rearrrangments
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99
Q

Exogenous sources of double strand breaks

A
  1. Environmental radiation

2. Medical Radiation

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100
Q

Explain features of non-homolgous end joining

A

imperfect system wit ha loss of a few nucleotides occuring throughout cell cycle

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101
Q

What proteins work with non homologous end joining?

A

Ku recognizes the double strand break and recruits DNA-pKCs (DNA-dependent kinase). ATM triggers the DNA PKcs to autophosphorylate and recruit and phosphorylate artemis.

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102
Q

What does artemis protein do?

A

artemis is phosphorylated by DNA PKcs and is an endonuclease that cuts hairpins as well as 5’ and 3’ overhangs

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103
Q

Explain features unique to Homologous Recombination

A

perfect pairing
requires a sister chromatid
only available during the G2 and S phase

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104
Q

When is homologous recombination used?

A

During meiosis

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105
Q

What can happen if you lose the ability to us non homologous joining and homologous joining?

A

Results in a loss of heterozygosity (loss of the entire gene and the surrounding chromosomal region)

106
Q

tumor suppressor that regulates homologous recombination?

A

BRCA1

107
Q

tumor suppressor that regulates non homologous recombination

A

53BP1

108
Q

What are the 3 classes of RNA in human cell

A

Structural RNA
Regulatory RNA
Information containing

109
Q

Examples of structural RNA

A

rRNA (RNA in ribosome)
snRNA (splicing and cell modification)
tRNA (moving RNA around)

110
Q

Example of Regulatory RNA

A

miRNA and siRNA (downregulates gene expression)

111
Q

Example of information containing RNA

A

mRNA

112
Q

Difference between RNA and DNA

A

RNA can spontaneously hydrolyze given the extra 2’ OH group thus RNA can be cut up more frequently

RNA may have catalytic function like proteins

113
Q

How does puromycin mimic amino-acyl tRNA?

A

strucuture is very similar to a tRNA carrying an amino acid. It binds to the tRNA acceptor region of the ribosome, transfers peptide, and terminate elongation making a defective protein

114
Q

The RNA transcript is equivalent to which DNA strand?

A

The coding / nontemplate strand

115
Q

E. Coli RNA polymerase does what?

A

transcribes all RNA in E. coli

116
Q

eukaryotic RNA polymerase I

A

Makes ribosomal RNA (rRNA)

117
Q

eukaryotic RNA polymerase II

A

makes messenger RNA (mRNA), small nuclear RNA (snRNA), and micro RNA

118
Q

What is unique about RNA polymerase II

A

Has a C-terminal domain

119
Q

eukaryotic RNA polymerase III

A

makes primarily tRNA

120
Q

Which RNA polymerase is most abundant?

A

RNA polymerase I

121
Q

How does alpha-amanitin block transcription?

A

found in death cap mushrooms and inhibits RNA polymerase II by binding to bridge helix and blocking translocation.

Non competitive inhibitor

122
Q

How does rifampicin block transcription?

A

It binds to bacterial RNA polymerase and block RNA exit channel. Therefore no transcription can occur.

123
Q

What is the sequence characteristic of a promoter site in humans?

A

TATA box

124
Q

Name four components of the RNA polymerase II pre-initiation complex.

A

Transcription factor TFII B,D,E,F, H

125
Q

What’s the significance of TFIIH?

A

It facilitates nucleotide excision repair. Think global NER (xeroderma pigmentosum) and transcribed NER (cockayne’s syndrome).

Acts as a helicase to open up DNA

126
Q

What is the significance of TFIID?

A

it is the TATA binding protein for RNA II polymerase!

127
Q

Three major ways in which most pre-mRNA’s are processed.

A
  1. Capping: Adding 7-methyl Guanosine to the 5’ end
  2. Splicing: introns
  3. Cleavage/Polyadenylation: 3’ end
128
Q

List the functions of the 5’ cap of the mRNA.

A
  1. Splicing
  2. 3’ processing
  3. nuclear export
  4. Translation via Eukaryotic Initiation factor F4E
129
Q

5’ splice site for pre-mRNA

A

GU residue

130
Q

3’ splice site for pre-mRNA

A

AG

131
Q

function of U1 in splicing.

A

recognizes 5’ splice site

132
Q

function of U2 snRNA’s in splicing.

A

recognizes the branch point in pre-mRNA splicing between 5’ and 3’

133
Q

function of U2AF (protein)

A

binds to the 3’ splice site AG

134
Q

DNA Control elements

A

part of DNA sequence that act locally in terms for transcription

  1. promoter
  2. Enhancer
  3. TATA Box / initiator
135
Q

TATA box

A

determines the site of transcription initiation and directs RNA polymerase II

136
Q

What is Thalassemia?

A

Disease associated with mutation in DNA control elements

Leads to inherited anemia (low hemoglobin count) due to a mutation in the b-globin promoter region, resulting in lower production fo the b-globin protein.

137
Q

What is Hemophilia B-leyden?

A

Disease associated with mutation in DNA control elements.

Mutation in Factor IX and associated with mutation in promoter region.

Affects males who don’t make enough of Factor IX to help with blood clotting

138
Q

What is fragile X syndrome?

A

Leads to mental retardation and atypical development of the face with enlarged testicles.

Expansion in the CGG count upstream of the FMR1 gene which results in excessive gene silencing.

139
Q

What are examples of disease caused by mutations in DNA control elements?

A

Thalassemia, Hemophilia B-leyden, and Fragile X syndrome.

140
Q

What are the two classes of transcriptional activators and repressors?

A

Sequence-Specific DNA binding proteins (6-8 bp) sequence

  1. Co-factors that bind to the sequence specific DNA binding proteins
141
Q

What are the different domains of transcriptional activators?

A
  1. DNA binding domain - highly structured/highly conserved and binds to DNA.
  2. Activation or repression domain: fairly unstructured/less conserved. Recruits other proteins
142
Q

Craniosynostosis

A

mutation in the homeodomain protein (helix, turn, helix) causes protein to bind more strongly and causes skull to close more prematurely

143
Q

Androgen Insensitivity syndrome

A

Feminization or undermasculization caused by mutations in the zinc finger (two antiparallel beta turns, zinc, and alpha helix) . The androgen receptor no longer binds as well to the ligand binding domain and downregulates the transcription of genes controlled by male androgens.

144
Q

Waardenburg syndrome

A

Caused by mutation in the MITF gene = deafness and pigmentation defects

145
Q

Diseases caused by mutation in the DNA sequence specific domain binding region

A

Craniosynostosis, Androgen insensitivity, and Waardenburg syndrome.

146
Q

Describe combinatorial control as a mechanism for controlling gene expression

A

The Zinc finger for example can form heterodimers. If each monomer of the heterodimer has a different DNA binding specificity, the formation of heterodimers will increase the number of potential sequences to which that family of sequence specific transcription factors can bind

147
Q

Define nucleosome

A

repeating unit of chromatin that has 147 bp of genomic DNA wrapped around an octamer of histone proteins

148
Q

What is the role of the Swi/Snf protein?

A

Uses energy of ATP hydrolysis to break histone-DNA and expose the parts of DNA needed. Slides the histone octomer along the DNA

149
Q

What are Histone Acetyl Transferases (HATS)

A

unwinds DNA to expose areas for transcription. Changes outer histone proteins from lysine –> acetyl (positive to negative) making DNA less stable

150
Q

Histone Acetylations Diseases

A

Leukemia and Rbuinstein-Taybi Syndrome

151
Q

tamoxifen

A

acts as an antagonist to estrogen, binding to the estrogen receptors as a ligand without providing dimerization– thus effectively preventing estrogen from binding to its site of action and preventing the transcriptional effect of estrogen receptors.

152
Q

Example of how nuclear hormone receptors is controlled

A

estrogen crosses the membrane and binds to estrogen receptor. ER has a DNA binding domain and zinc finger binding motif that recruits other proteins

153
Q

example of a sequence specific DNA binding protein regulated by nuclear entry

A

NF-κB: normally bound to IκB hiding the Nucleus signal (NLS) Under certain conditions, IκB is phosphorylated, which targets it for degradation. Degrading IκB shows the NLS of NF-κB to migrate into the nucleus and affect transcription for inflammation response

154
Q

How is β-catenin regulated?

A

APC targets beta-catenin (a cell proliferation activator protein) when APC triggers beta catenin for protease degradation. If there is an APC mutation there is a huge build up of beta-catenin which can now enter the nuclease and cause cell proliferation

155
Q

Most common cause of colon polyps?

A

caused by mutations in the APC gene, resulting in insufficient degradation of (and thus proliferation of) B-catenin.

156
Q

What is the function of ID proteins?

A

inhibitor of the E box proteins and regular helix loop helix protein

157
Q

Steps to 5’ capping

A
  1. Triphosphatase (removes phosphate)
  2. Guanalyltransferase
  3. Guanine 7 methyl transferase
158
Q

What is the start codon?

A

AUG

159
Q

What are the stop codons

A

UAA, UAG, UGA

160
Q

Define degeneracy

A

There are multiple codons for a single amino acid

161
Q

What type of DNA repair mutation causes hereditary non-polypsosis colorectal cancer called Lynch syndrome?

A

mismatch repair

162
Q

TFIIH

A

Functions in transcription and DNA repair (nucleotide excision repair)

163
Q

XPB helicase

A

part of the TFIIH protein

164
Q

CDK 7

A

part of the TFIIH protein that phosphorylates the C terminal domain on RNA polyermase II and triggers promoter clearance

165
Q

C terminal domain

A

unique feature of RNA polymerase II that gets phosphorylated by CDK 7 (part of the TFIIH protein) and triggers promoter clearance

166
Q

SSB

A

single stranded binding protein for e. coli that keeps the DNA from getting cut up during replciation

167
Q

RPA

A

is the eukaryotic SSB protein

168
Q

PCNA

A

the sliding clamp for eukaryotes

169
Q

What’s the eukaryotic equivalent to DNA polymerase III

A

DNA polymerase gamma and epsilon

170
Q

What’s the eukaryotic equivalent to DNA polymerase I

A

DNA polymerase alpha

171
Q

Marfan’s disease

A

caused by mutation that disrupts the splicing of the fibrillin gene (fibrillin is a connective tissue important for integrity of blood vessels)

172
Q

CD44

A

is a cell surface glycoprotein that determines migration of cells. It therefore contributes to tumor metastasis and can e used for diagnostic purposes

173
Q

3 types of high energy phosphate bonds?

A
  1. Phosphoanhydride (ATP)
  2. Phosphocreatine (P-N)
  3. Phosphoenolpyruvate (C-O-P)
174
Q

What is the role of excision endonuclease in nucleotide-excision repair of DNA?

A

They cleave the damaged DNA strand at either side of a lesion.

175
Q

Rubinstein-Taybi Syndrome

A

haploinsufficiency of CREB binding protein (CBP) which is a HAT involved in the activation of many genes. It is a multisystem disorder.

176
Q

Shine Delgarno Sequence

A

Purine rich sequence (AG) that bacterial ribosomes use to indicate the start site for translation. It’s upstream from the AUG codon

177
Q

How does the small subunit (30s) of the ribosome bind to the mRNA

A

using the Shine Delgarno Sequence

178
Q

First set of initiation factors for bacterial translation to occur

A

Recruitment of IF1 and IF3 proteins bind to the 30s subunit

Now mRNA cand bind to the subunit via it’s shine delgarno sequence

AUG start codon now in the 30S subunit P site

179
Q

Second set of initiation factor(s) for bacterial translation to occur

A

IF2 helps deliver a special initiator formylmethionine tRNA which attaches to the AUG start codon

180
Q

Last step in the initiation process of translation in bacteria

A

GTP hydrolysis on IF2 leads to the release of all other initiation factors.

Binding of 50S subunit can now occur

181
Q

What type of energy is used to combine the 50S subunit and 30S subunit for bacteria ribosomes?

A

GTP hydrolysis

182
Q

What is the Kozak sequence

A

A sequence that occurs on Eukaryotic mRNA (gccRccAUGG) recognized by ribosome as a start site.

different start codons have different “strengths” depending
on their Kozak context.

183
Q

polycistronic

A

Applies to prokaryotic mRNA. One transcript alone can encode for many different proteins

184
Q

Aminoacyl tRNA synthetase

A

An enzyme responsible for adding the correct amino acid to the tRNA with the correct anticodon by hydrolysis of ATP.

185
Q

peptidyl transferase center (PTC)

A

resides in the ribosomal large subunit and catalyzes the peptide bond formation using ATP as energy

186
Q

What triggers movement of the mRNA and tRNAs exactly one codon in the 3’ direction?

A

Elongation Factor 2 (EF2) and GTP hydrolysis

187
Q

How much energy is required to make a peptide bond?

A

4 high energy bonds

2 ATPs to charge TRNA
1 GTP to deliver AA to TRNA Asite (via EF1)
1 GTP to translocate one codon in the 3’ direction

188
Q

What terminates translation?

A

This is a PROTEIN driven event. No TRNA can recognize the stop codon and a release factor comes in and recognizes the stop codon.

GTP hydrolysis causes cleavage

189
Q

EF1A

A

the first elongation factor in Eukaryotes that brings tRNA to the A site

190
Q

EF-Tu

A

bacterial elongation factor equivalent to EF1A

191
Q

Missense mutation

A

The codon is changed so now is encodes a different amino acid.

192
Q

Nonsense mutation

A

Mutation that leads to a premature stop codon

193
Q

Sense mutation

A

Mutation that leads to the removal of a stop codon (opposite of sense)

194
Q

internal ribosome entry sites (IRES)

A

cap independent process in eukaryotes that viruses can take advantage of after shutting down the host’s cell cap dependent process

195
Q

4E-binding proteins (4E-BPs)

A

sequester and bind to eukaryotic initiation factors 4E (EIF4e) and block it from recognizes the 5’ Cap

196
Q

Result from phosphorylating 4E-BPs?

A

These 4E binding proteins can no longer bind to eukaryotic initiation factor 4E. Therefore, EIF4e can recognize 5’ cap for translation to occur

197
Q

drug rapamycin

A

Inhibits m-TOR which normally phosphorylates 4E binding proteins so that EIF4E can bind to 5’ cap and initiate translation.

This drug inhibits cell proliferation

198
Q

m-tor

A

master controller of cellular process that phosphorylates 4Ebinding proteins so they cannot block the function of EIF4E

199
Q

Eukaryotic initiation factor 2 alpha (eIF2-alpha)

A

important for bringing in the initiaor tRNA which attaches to the AUG start codon in the ribosome

200
Q

What’s the outcome of phosphorylating eIF2-alpha

A

eIF1-alpha activity is inhibited and transcription is stopped.

201
Q

Interferon and eIF2-alpha

A

An interferon indicates cell has been infected with virus and triggers phosphorylation of eIF2 to stop viral proteins from being made.

202
Q

Hemoglobin Wayne

A

Disorder caused by frameshift mutation

203
Q

Hemoglobin Contant

A

Disorder caused by a sense mutation where stop codon is removed

204
Q

ApoB

A

An example of how mRNA can be altered after its been made

protein production in the intestines is shorter than in the liver

205
Q

Transferrin

A

binds iron

206
Q

Transferrin receptor

A

transport transferrin/iron into the cell

207
Q

Ferritin

A

Sequesters excess iron

208
Q

Iron response element

A

RNA stem loop structure found in mRNA that can bind to iron response binding protein (when low concentration of iron)

209
Q

Iron response binding protein

A

binds to iron and regulates expression of ferritin and transferrin receptor

210
Q

Hydrophobic amino acids

A

VAG MIL

Valine
Alanine
Glycine
Methionine
Isoleucine
Leucine
211
Q

Aromatic amino acids

A

Try Tripping with Phenylalanine

Tyrosine
Tryptophan
Phenylalanine

212
Q

Polar uncharged amino acids

A

Great Asshole, Please Come Take Shrooms

Glutamine
Asparagine
Proline
Cysteine
Threonine
Serine
213
Q

Polar Positively Charged

A

Shallow HAL

Histidine
Arginine
Lysine

214
Q

Polar negatively charges

A

Good ‘ Ayyy

Glutamate
Aspartate

215
Q

pH

A

AA is protonated

216
Q

pH> pKA

A

AA is deprotonated

217
Q

Essential Amino Acids

A

Private Tim Hall = PVT TIM HALL

Phenylalanine
Valine
Threonine

Tryptophan
Isoleucine
Methionine

Histidine
Arganine
Leucine
Lysine

218
Q

Scurvy disease

A

Break down of collagen which needs hydroxyl group on proline for strength. Vitamin C delivers the hydroxyl group

219
Q

Carboxylation of Glutamate

A

Important for blood clotting and carried out by Vitamin K

220
Q

Deficiency in Vitamin K

A

improper blood clotting

221
Q

Warfarin

A

prevents carboxylation of glutamate and acts as anticoagulant

222
Q

Congenital Disorder of Glycosylation (CDG)

A

glycosylation cannot occur on asparagine and impact hydrophilicity in secreted and cell surface proteins

223
Q

Gleevec

A

An bcr-abl protein kinase inhibitor that binds to the bcr-abl kinase domain so it can no longer bind to its substrate and cause uncontrolled blood cell proliferation

224
Q

Ubiquitination

A

Add ubiquitine to mark cell destined for degradation by proteasome

225
Q

Peptide bond characteristic

A

Has partial double bond and therefore no rotation.

formed from dehydration reaction of COO- and NH3+

226
Q

Bond from alpha carbon to carbon of peptide bond/carbonyl (C2-C1)

A

psi bond

free rotation

227
Q

Bond from amide nitrogen to alpha carbon (N-C3)

A

free rotation

phi bond

228
Q

Strongest non covalent bond

A

hydrogen bond

229
Q

Strong helix formers

A

Alanine and Leucine

230
Q

helix breakers

A

Proline and Glycine

231
Q

Thalassemia mutant

A

Introduction of proline in the alpha helix causes breaks and destabilization of hemoglobin

232
Q

Structural fibrous proteins mostly made up of alpha helixes

A

Keratin,
Myson
Tropmyosin
Fibrinogen

233
Q

Globular proteins made up of alpha helices

A

Hemoglobin

Myoglobin

234
Q

Structural fibrous proteins mostly made up of beta sheets

A

Fibroin - silk, spider webs

235
Q

Globular proteins made up of beta sheets

A

Immunoglobin
Fibroblast
Pepsin

236
Q

Beta turn AA

A

Dont like to be in Alpha or Beta

Proline and Glycine

237
Q

Amino Acids that prefer Beta conformation

A

Tryptophan
Isoleucine
Valine

238
Q

Beta turn

A

Hydrogen bond between 1st and 4th amino acid

239
Q

Proline Isomer

A

Can be in trans or cis (rarely) conformation

240
Q

AA acids most frequently used in loops and turns

A

Proline and Glycine

241
Q

Protein domains

A

multiple stable globular units that have independent functions

242
Q

Quaternary Structure

A

Formed by multiple polypeptides into a larger functional cluster

243
Q

Collagen Fiber

A

Each chain has Glycine nad Proline left-handed helix

Together makes a right-handed superhelical triple helix

Tensile strength

244
Q

Explain how to use Kd to represent binding strength.

A

Kd is the dissociation constant

Kd= [ligand] when 50% of ligands are bound

245
Q

Myoglobin

A

Main oxygen storage in mammals. Stores heme in the center of protein so no risk of oxidation

246
Q

positive cooperativity

A

first binding event increases affinity at remaining sites

247
Q

T state

A

no oxygen is bound to hemoglobin / low affinity for oxygen

248
Q

R state

A

relaxed state induces conformational change and has high affinity for oxygen now

249
Q

Bohr effect

A

Oxygen binds well at higher pH (like in the lungs)

Oxygen is release well at lower pH (tissue)

250
Q

Ribonuclease refolding experiment

A

Used reducing agent to denature Ribonuclease A, then after dialyzing out the urea it slowly refolded and restored almost 100% of activity

All the information needed to fold the protein correctly is embedded in the primary amino acid sequence

The environment provided by the inside of the cell is not always required in order for proteins to fold correctly

The protein does not explore all possible structures while folding, there is instead a pathway it follows. (Levinthal’s paradox)

251
Q

Levinthal parathox

A

proteins don’t sample all confirmation to achieve folding state

it would take way too long!

252
Q

Heat Shock Proteins (Hsp70)

A

induced at elevated temperatures and binds to hydrophobic region of unfolded proteins to prevent aggregation, can also help transport some proteins across membranes in unfolded states, works with other heat shock proteins

253
Q

Chaperonin

A

consists of a cap and two 7-subunit rings. The hydrophobic region of the unfolded protein binds to the hydrophobic region of the chaperonin then with some ATP and a conformational change of the chaperonin the protein is folded at least partially so that it can only continue to the final native shape.

Ex: GroEL/GroES complex in E. coli.

254
Q

protein disulfide isomerase (PDI)

A

reduces improper disulfide bonds and reform them correctly

255
Q

Peptide prolyl isomerases (PPI)

A

Speeds up process of trans to cis confirmation in proline

256
Q

Parkinson’s

A

Beta-synuclein misfolds into Lewy Bodies (protein agreggrates)

257
Q

Amyloidosis

A

Generalized protein misfolding in the rest of the body leading to a variety of disease (from Type II diabetes to Cardiac amyloidosis)

258
Q

Identify the secondary structure changes in prion disease

A

alpha -> beta sheets

259
Q

gel filtration chromatography

A

separates proteins by size

260
Q

ion exchange chromatography

A

separates by charge

M2M (2 decks)

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