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1

What is entropy

Disorder or randomness in system

2

What is enthalpy?

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

3

What is free energy?

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

4

What does a negative Gibbs free energy mean?

Reaction is favorable and spontaneous

5

What are high energy compounds?

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

6

What is an oxidation-reduction reaction?

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

7

First law of thermodynamics

Energy is neither created nor destroyed

8

Second law of thermodynamics

Entropy in the universe must always increase

9

What are the four different forms of energy?

1. Radiant
2. Mechanical
3. Thermal
4. Electric

10

Forms of potential energy?

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

11

Formula for delta G?

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

12

what is delta G0?

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

13

formula for delta G0?

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

14

formula for Keq

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

15

Negative H, Negative S = ?

spontaneous at low temperatures

16

Positive H, Negative S = ?

reaction is not spontaneous

17

Numerical conversion between free energy and redox potential?

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

18

What are the purines?

two ring nucleotide. Guanine and Adenine

19

What are the pyrimidines?

one ring nucleotide including Thymine and Cytosine

20

Ribose vs. Deoxyribose?

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

21

Nucleotide

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

22

nucleoside

just the nitrogenous base and the sugar. Phosphate is excluded

23

ribonucleotides

Use Uracil instead of Thymine

24

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

pyrimidine > purine; nucleotide > nucleoside > base

25

Medical Relevance of Gout and Lesch-Nyhan?

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

26

Disease(s) caused by accumulation of purines?

Gout and Lesch-Nyhan

27

Explain polarity of the phosphodiester bond

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

28

Avery, McCloud, and McCarty contribution to science?

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

29

Rosalind Franklin

x ray diffraction suggested that DNA is a helical struture

30

Watson and Crick

DNA is a double helix and can semi conservatively replicate itself

31

Implications of Chargaff's Rules?

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

32

Describe Watson-Crick three dimensional model for DNA structure

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.

33

Major Groove of DNA vs Minor Groove of DNA

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

Minor groove is the gap between complementary DNA

34

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

Magnesium ions in the cell neutralize the negative phosphate groups.

hydrogen bonding between base pairs

hydrophobic interaction of base stacking

35

Ways to further stabilize DNA?

increase salt concentration to neutralize phosphate negative charge

make DNA longer

increase G:C content

36

Methylation of Cytosine

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

37

Deamination

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

38

Depurination

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

39

UV cross linking

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

Causes kink in DNA that disrupts replication

40

Mechanism of UV cross linking repair

nucleotide excision repair and TF2H

41

Base Alkylation

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

42

Ways that nucleoside analogues can be used as drugs

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

43

Define Semiconservative

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

44

What does Bi-directional mean?

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

45

Okazaki fragments

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

46

prokaryotes vs eukaryote origin sites

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

47

Origin binding proteins

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

48

Helicase

unwinds just ahead of the replication fork

49

Single strand binding protein

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

50

Topoisomerase

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

51

DNA Gyrase

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

52

DNA polymerase

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

53

DNA polymerase used in prokaryotes?

DNA polymerase I and III

54

DNA polymerase III

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

Holoenzyme

Has 3' to 5' proofreading ability

55

DNA polymerase I

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

56

Primase

A DNA dependent RNA polymerase

needs DNA to add an RNA primer

57

DNA ligase

joins fragments of DNA together

58

sliding clamp

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

59

Telomerase

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

60

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

Xeroderma pigmentosum
Cockayne Syndrome
Trichothiodystrophy

61

What causes Thymine dimers

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

62

Consequences of unrepaired thymine dimer?

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

63

Best way to repair thymine dimer?

Nucleotide excision repair a much more versatile mechanism

64

Cause of bulky chemical adducts in DNA

chemotoxins that bind to DNA helix and disrupt the shape

65

Repair mechanism for chemical adducts?

Nucleotide excision repair

66

Cause of double strand breaks

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

67

How to repair double strand breaks?

homologous recombination repair or non-homologous end joining

68

Homologous recombination vs non homologous joining?

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

69

How does uracil end up in DNA by mistake?

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

70

How to repair uracil mismatch in DNA?

base excision repair!

71

Consequences of having uracil in the dna?

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

72

Function of mismatch repair

fixes nucleotides that have been mistakenly added during DNA replication

73

Name the 3 types of excision repair

base excision repair
nucleotide excision repair
mismatch excision repair

74

Main difference between the three excision repair steps?

How the mistake is inItially RECOGNIZED

75

Recognition of a mismatched nucleotide by..

MSH and MLH

76

exonuclease vs endonuclease?

endonuclease cleaves the phosphodiester backbone of new strand of DNA

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

(alphabetical order)

77

Steps common to all three types of excision repair

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.

78

Hereditary non-polyposis colorectal cancer (HNPCC)

caused by mutation in the mismatch repair machinery

79

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

Daughter strand has not yet been methylated!

80

When is nucleotide excision repair used?

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

Used to repair thimine dimers and bulky lesions and chemical adducts

81

Global Genome nucleotide excision repair (NER)

protein that recognizes damage anywhere in the genome

82

Transcription coupled NER

protein that only recognizes damage in transcribed regions

83

Disease caused by mutation in Global Genome NER

xeroderma pigmentosum

84

Disease caused by mutation in Transcription Coupled NER

cockayne syndrome

85

When is based excision repair used

To repair DNA lesions that are missed by the NER process

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

86

Protein that recognizes Base excision repair

Glycosylase

87

What is lesion bypass?

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.

88

What's unique about the bypass polymerase?

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

89

Explain MGMT

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

90

Cyclin dependent Kinase (CDK)

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

91

Retinoblastoma protein (Rb)

an inhibitor protein of the cell cycle aka a tumor supprossor

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

92

What protein(s) inhibit CDK?

CDKN (two types)

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

93

What amino acids can be phosphorylated by CDK?

Serine, Threonine, and Tyrosine

94

What is mitogen?

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.

95

How is the cell size regulated?

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.

96

Ataxia Telangiectasia Mutated (ATM)

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

97

targets of ATM

p53, CHK2, and H2AX

98

Endogenous sources of double strand breaks

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

99

Exogenous sources of double strand breaks

1. Environmental radiation
2. Medical Radiation

100

Explain features of non-homolgous end joining

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

101

What proteins work with non homologous end joining?

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.

102

What does artemis protein do?

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

103

Explain features unique to Homologous Recombination

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

104

When is homologous recombination used?

During meiosis

105

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

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

106

tumor suppressor that regulates homologous recombination?

BRCA1

107

tumor suppressor that regulates non homologous recombination

53BP1

108

What are the 3 classes of RNA in human cell

Structural RNA
Regulatory RNA
Information containing

109

Examples of structural RNA

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

110

Example of Regulatory RNA

miRNA and siRNA (downregulates gene expression)

111

Example of information containing RNA

mRNA

112

Difference between RNA and DNA

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

How does puromycin mimic amino-acyl tRNA?

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

The RNA transcript is equivalent to which DNA strand?

The coding / nontemplate strand

115

E. Coli RNA polymerase does what?

transcribes all RNA in E. coli

116

eukaryotic RNA polymerase I

Makes ribosomal RNA (rRNA)

117

eukaryotic RNA polymerase II

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

118

What is unique about RNA polymerase II

Has a C-terminal domain

119

eukaryotic RNA polymerase III

makes primarily tRNA

120

Which RNA polymerase is most abundant?

RNA polymerase I

121

How does alpha-amanitin block transcription?

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

Non competitive inhibitor

122

How does rifampicin block transcription?

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

123

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

TATA box

124

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

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

125

What's the significance of TFIIH?

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

What is the significance of TFIID?

it is the TATA binding protein for RNA II polymerase!

127

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

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

128

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

1. Splicing
2. 3' processing
3. nuclear export
4. Translation via Eukaryotic Initiation factor F4E

129

5' splice site for pre-mRNA

GU residue

130

3' splice site for pre-mRNA

AG

131

function of U1 in splicing.

recognizes 5' splice site

132

function of U2 snRNA's in splicing.

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

133

function of U2AF (protein)

binds to the 3' splice site AG

134

DNA Control elements

part of DNA sequence that act locally in terms for transcription

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

135

TATA box

determines the site of transcription initiation and directs RNA polymerase II

136

What is Thalassemia?

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

What is Hemophilia B-leyden?

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

What is fragile X syndrome?

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

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

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

140

What are the two classes of transcriptional activators and repressors?

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

2. Co-factors that bind to the sequence specific DNA binding proteins

141

What are the different domains of transcriptional activators?

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

Craniosynostosis

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

143

Androgen Insensitivity syndrome

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

Waardenburg syndrome

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

145

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

Craniosynostosis, Androgen insensitivity, and Waardenburg syndrome.

146

Describe combinatorial control as a mechanism for controlling gene expression

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

Define nucleosome

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

148

What is the role of the Swi/Snf protein?

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

149

What are Histone Acetyl Transferases (HATS)

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

150

Histone Acetylations Diseases

Leukemia and Rbuinstein-Taybi Syndrome

151

tamoxifen

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

Example of how nuclear hormone receptors is controlled

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

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

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

How is β-catenin regulated?

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

Most common cause of colon polyps?

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

156

What is the function of ID proteins?

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

157

Steps to 5' capping

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

158

What is the start codon?

AUG

159

What are the stop codons

UAA, UAG, UGA

160

Define degeneracy

There are multiple codons for a single amino acid

161

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

mismatch repair

162

TFIIH

Functions in transcription and DNA repair (nucleotide excision repair)

163

XPB helicase

part of the TFIIH protein

164

CDK 7

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

165

C terminal domain

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

166

SSB

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

167

RPA

is the eukaryotic SSB protein

168

PCNA

the sliding clamp for eukaryotes

169

What's the eukaryotic equivalent to DNA polymerase III

DNA polymerase gamma and epsilon

170

What's the eukaryotic equivalent to DNA polymerase I

DNA polymerase alpha

171

Marfan's disease

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

172

CD44

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

173

3 types of high energy phosphate bonds?

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

174

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

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

175

Rubinstein-Taybi Syndrome

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

176

Shine Delgarno Sequence

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

177

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

using the Shine Delgarno Sequence

178

First set of initiation factors for bacterial translation to occur

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

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

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

180

Last step in the initiation process of translation in bacteria

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

Binding of 50S subunit can now occur

181

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

GTP hydrolysis

182

What is the Kozak sequence

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

polycistronic

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

184

Aminoacyl tRNA synthetase

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

185

peptidyl transferase center (PTC)

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

186

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

Elongation Factor 2 (EF2) and GTP hydrolysis

187

How much energy is required to make a peptide bond?

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

What terminates translation?

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

EF1A

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

190

EF-Tu

bacterial elongation factor equivalent to EF1A

191

Missense mutation

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

192

Nonsense mutation

Mutation that leads to a premature stop codon

193

Sense mutation

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

194

internal ribosome entry sites (IRES)

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

195

4E-binding proteins (4E-BPs)

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

196

Result from phosphorylating 4E-BPs?

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

197

drug rapamycin

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

m-tor

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

199

Eukaryotic initiation factor 2 alpha (eIF2-alpha)

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

200

What's the outcome of phosphorylating eIF2-alpha

eIF1-alpha activity is inhibited and transcription is stopped.

201

Interferon and eIF2-alpha

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

202

Hemoglobin Wayne

Disorder caused by frameshift mutation

203

Hemoglobin Contant

Disorder caused by a sense mutation where stop codon is removed

204

ApoB

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

protein production in the intestines is shorter than in the liver

205

Transferrin

binds iron

206

Transferrin receptor

transport transferrin/iron into the cell

207

Ferritin

Sequesters excess iron

208

Iron response element

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

209

Iron response binding protein

binds to iron and regulates expression of ferritin and transferrin receptor

210

Hydrophobic amino acids

VAG MIL

Valine
Alanine
Glycine
Methionine
Isoleucine
Leucine

211

Aromatic amino acids

Try Tripping with Phenylalanine

Tyrosine
Tryptophan
Phenylalanine

212

Polar uncharged amino acids

Great Asshole, Please Come Take Shrooms

Glutamine
Asparagine
Proline
Cysteine
Threonine
Serine

213

Polar Positively Charged

Shallow HAL

Histidine
Arginine
Lysine

214

Polar negatively charges

Good ' Ayyy

Glutamate
Aspartate

215

pH

AA is protonated

216

pH> pKA

AA is deprotonated

217

Essential Amino Acids

Private Tim Hall = PVT TIM HALL

Phenylalanine
Valine
Threonine

Tryptophan
Isoleucine
Methionine

Histidine
Arganine
Leucine
Lysine

218

Scurvy disease

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

219

Carboxylation of Glutamate

Important for blood clotting and carried out by Vitamin K

220

Deficiency in Vitamin K

improper blood clotting

221

Warfarin

prevents carboxylation of glutamate and acts as anticoagulant

222

Congenital Disorder of Glycosylation (CDG)

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

223

Gleevec

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

Ubiquitination

Add ubiquitine to mark cell destined for degradation by proteasome

225

Peptide bond characteristic

Has partial double bond and therefore no rotation.

formed from dehydration reaction of COO- and NH3+

226

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

psi bond
free rotation

227

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

free rotation
phi bond

228

Strongest non covalent bond

hydrogen bond

229

Strong helix formers

Alanine and Leucine

230

helix breakers

Proline and Glycine

231

Thalassemia mutant

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

232

Structural fibrous proteins mostly made up of alpha helixes

Keratin,
Myson
Tropmyosin
Fibrinogen

233

Globular proteins made up of alpha helices

Hemoglobin
Myoglobin

234

Structural fibrous proteins mostly made up of beta sheets

Fibroin - silk, spider webs

235

Globular proteins made up of beta sheets

Immunoglobin
Fibroblast
Pepsin

236

Beta turn AA

Dont like to be in Alpha or Beta

Proline and Glycine

237

Amino Acids that prefer Beta conformation

Tryptophan
Isoleucine
Valine

238

Beta turn

Hydrogen bond between 1st and 4th amino acid

239

Proline Isomer

Can be in trans or cis (rarely) conformation

240

AA acids most frequently used in loops and turns

Proline and Glycine

241

Protein domains

multiple stable globular units that have independent functions

242

Quaternary Structure

Formed by multiple polypeptides into a larger functional cluster

243

Collagen Fiber

Each chain has Glycine nad Proline left-handed helix

Together makes a right-handed superhelical triple helix

Tensile strength

244

Explain how to use Kd to represent binding strength.

Kd is the dissociation constant
Kd= [ligand] when 50% of ligands are bound

245

Myoglobin

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

246

positive cooperativity

first binding event increases affinity at remaining sites

247

T state

no oxygen is bound to hemoglobin / low affinity for oxygen

248

R state

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

249

Bohr effect

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

Oxygen is release well at lower pH (tissue)

250

Ribonuclease refolding experiment

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

Levinthal parathox

proteins don’t sample all confirmation to achieve folding state

it would take way too long!

252

Heat Shock Proteins (Hsp70)

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

Chaperonin

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

protein disulfide isomerase (PDI)

reduces improper disulfide bonds and reform them correctly

255

Peptide prolyl isomerases (PPI)

Speeds up process of trans to cis confirmation in proline

256

Parkinson’s

Beta-synuclein misfolds into Lewy Bodies (protein agreggrates)

257

Amyloidosis

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

258

Identify the secondary structure changes in prion disease

alpha -> beta sheets

259

gel filtration chromatography

separates proteins by size

260

ion exchange chromatography

separates by charge