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FB 1 (my cards) > Biochemistry-Midterm > Flashcards

Biochemistry-Midterm Flashcards

1
Q

Octamer complex

A

H2A, H2B, H3, and H4 dimers

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2
Q

H1 protein

A

Binds to the 30 bp linker so that the DNA doesn’t become a mess

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3
Q

Denaturation of DNA is at…

A

95 degrees Celsius

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4
Q

Renaturation of DNA is at…

A

37 degrees Celsius

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5
Q

Melting temperature

A

Temperature at which half of the DNA is denatured

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6
Q

Hybridization

A

Uses renaturation and denaturation to see how similar the genetic material of two species is

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7
Q

Polymerase chain reaction (PCR)

A

Uses denaturation and renaturation to amplify a target sequence to make a specific protein

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8
Q

Introns

A

In between exons

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9
Q

Origin of replication (ori)

A

Full of AT rich sequences

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10
Q

DNAa

A

Binds to the ori and stretches it to break the hydrogen bonds

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11
Q

Helicase

A

Unwinds the DNA by breaking the hydrogen bonds

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12
Q

Single strand binding proteins (SSBP)

A

Binds to the unwound strands so that they won’t get back together. Also protects genetic material from being degraded by nucleases

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13
Q

Primase

A

Synthesizes the RNA primer

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14
Q

Integrase

A

Helps paste the DNA transposon to the new location

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15
Q

Topoisomerase I

A

Relieves stress of the supercooled DNA on one strand by cutting, unwinding, and resealing

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16
Q

Topoisomerase II

A

Helps relieve stress on the supercoiled DNA on both strands by cutting, unwinding, and resealing

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17
Q

DNA polymerase III

A

A holoenzyme consisting of 10 subunits. Includes:
5’-3’ polymerase
3’-5’ exonuclease

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18
Q

5’-3’ polymerase

A

Adds nucleotides to the growing strand

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19
Q

3’-5’ exonuclease

A

Proofreads DNA to check for errors

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20
Q

Leading strand

A

Needs one RNA primer and goes towards the replication fork

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21
Q

Lagging strand

A

Needs multiple RNA primers and goes way from the replication fork. Segments are discontinuous and are called Okazaki fragments

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22
Q

Replication bubble/fork

A

Y-shaped opening that opens up the DNA to being replication

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23
Q

DNA polymerase I

A

Works on the lagging strand after DNA polymerase III adds nucleotides

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24
Q

5’-3’ exonuclease

A

Gets rid of the RNA primers on the lagging strand

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25
Q

Ligase

A

Joins the discontinuous fragments

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26
Q

Polymerase alpha

A

Primase in eukaryotes

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27
Q

Polymerase epsilon

A

Synthesizes the leading strand and fills in the gaps in between the primers on the lagging strand

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28
Q

Polymerase delta

A

Synthesizes the lagging strand

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29
Q

RNase and flap endonuclease 1 (FEN1)

A

Removes the primers

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30
Q

Tandem (satellite)

A

Repeated sequences right next to each other

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31
Q

Interspersed (transposons)

A

Respected at different sections of the DNA

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32
Q

Telomeres don’t shorten in…

A

Cancer, germ, and stem cells

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33
Q

Didanosine

A

Analog of adenine that fails to form a phosphodiester bond since it has H instead of OH. HIV/AIDs drug

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34
Q

Azidothymidine (AZT)

A

Analog of thymine that has an acidosis group instead of an OH. Doesn’t form a phosphodiester bond and is and HIV/AIDs drug

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35
Q

Camptothecin (CPT)

A

Inhibits topoisomerase I from binding to its site. A cancer drug

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36
Q

Eptoposide

A

Topoisomerase II inhibitor and a cancer drug

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37
Q

DNA polymerase proofreading errors

A

Mutations in the 3’ to 5’ exonuclease

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38
Q

Depurination

A

Removing the purines and so 3’-5’ skips over it. Results in deletion mutation

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39
Q

Deamination

A

Removal of amine group. Transition mutation.

Cytosine-> uracil
Guanine-> xanthine
Adenine-> hypo-xanthine
5’methylcytosine-> thymine

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40
Q

Transition mutation

A

Changing from purine to purine or pyrimidine to pyrimidine

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41
Q

Transversion mutation

A

Changing from purine to pyrimidine

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42
Q

ROS

A

ROS binds to DNA and damages it. 8-hydroxyl guanosine changes to thymine

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43
Q

Thymine dimers

A

Thymines next to each other bind and leads to structural damage

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44
Q

Point mutation

A

Change in one nucleotide

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45
Q

Structural damage

A

Breaks backbone

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46
Q

Base excision repair

A

Fixes deamination

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47
Q

Nucleotide excision repair

A

Fixes thymine diners

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48
Q

Mismatch repair

A

Fixes misincorporated bases. Uses MutS, MutL, and MutH

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49
Q

Missense mutation

A

Changes nucleotide leading to different amino acid

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50
Q

Nonsense mutation

A

Puts a premature stop codon

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51
Q

Frame shift mutation

A

Either an insertion or deletion

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52
Q

Silent mutation

A

Change in nucleotide but no change in amino acid coded

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53
Q

Xeroderma pigmantosium

A

Autosomal recessive condition where people are photosensitive. Results in mutation in nucleotide excision repair which corrects for thymine dimers

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54
Q

Ataxia-telangiectasia

A

Mutation in ATM gene which tells that there is an issue. Due to no correction in ROS. Degenerative motor condition due to failure to repair ROS in the cerebellum. Can’t call base excision repair system

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55
Q

Hereditary non-polyposis colon cancer (HNPCC)

A

Mutation in mismatch repair system

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56
Q

Restriction enzymes (endonucleases)

A

Cleave specific DNA sequences

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57
Q

Staggered cuts

A

Produces sticky ends/cohesive ends that have H bonds. Ligand can connect them together

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58
Q

Blunt cuts

A

Produce blunt ends that don’t have H bonds. Enzyme in the T4 bacteriophage helps ligase strands together

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59
Q

Gel electrophoresis

A

Electrical field in which DNA goes to the positive side (phosphates of DNA) make it negative. Separated molecules based on size

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60
Q

Requirements of PCR

A

Taq DNA polymerase
Two DNA primers
dNTP
Template DNA

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61
Q

3 steps of PCR

A

Denaturation
Annealing
Extension

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62
Q

Applications of PCR

A

Disease diagnosis
Disease identification
Treatment
DNA sequencing

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63
Q

Melting temperature

A

Tm= 2(# of A&T) + 4(# of G&C)

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64
Q

DNA sequencing

A

Finding out the sequencing of DNA. Two steps:

Generating the sequence
Obtaining the sequence

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65
Q

Maxam Gilbert method

A

Chemical process that has a lot of limitations

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66
Q

Sanger’s method

A

Enzymatic, dNTP, ddNTP, electrophoresis

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67
Q

Pyrosequencing

A

Enzymatic, dNTP, no ddNTP, no electrophoresis

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68
Q

ddNTP color

A

ddATP: green
ddGTP: black
ddCTP: blue
ddTTP: red

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69
Q

DNA sequencing procedure

A

Put all materials in PCR and amplify for 40 cycles. Clean the sample and put in electrophoresis

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70
Q

Applications of DNA sequencing

A

Genetic mutation
Gene function and structure
DNA cloning

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71
Q

RNA

A

Working copy of the DNA

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72
Q

tRNA

A

Makes up 15% of total RNA in the cell. Smallest RNA type in the cell. Decodes the nucleotide sequence to form amino acids at the anticodon loop

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73
Q

rRNA

A

Makes up 80% of total RNA in the cell.

Four different species: 28S, 18S, 5.8S, and 5 S

Attaches to ribosomal proteins

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74
Q

mRNA

A

Most heterogenous RNA in terms of shape and structure. Makes up 3-5% of total RNA.

Has special structures:

  • 5’ cap
  • 5’-3’ UTR
  • poly A tail at 5’ end
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75
Q

Heterochromatin

A

Condensed form of DNA. Genes are inactive. HDAC removes the acetyl group from lysine to form a strong DNA/histone bond

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76
Q

Euchromatin

A

Less condensed structure. Has active genes. HATS adds acetyl group to the lysine to form a loose DNA/histone interaction

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77
Q

RNA polymerase I

A

Transcribes pre-RNA sequences of 28S, 18S, and 5.8S

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78
Q

RNA polymerase II

A

Transcribes mRNA and ncRNA (snRNA, miRNA, scoRNA)

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79
Q

RNA polymerase III

A

Transcribes tRNA and small amounts of snoRNA and snRNA

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80
Q

Promoter region

A

Initiates/promotes transcription

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81
Q

DNA elements

A

Sequences in the promoter region. Two examples:

  • TATA box: 25 nucleotides upstream (down first nucleic acid)
  • CAAT box: 70-89 nucleotides upstream
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82
Q

Transcription factors

A

Binds to the DNA elements

Example: CTF1, SP1, and TFIID (binds to TATA box)

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83
Q

Alpha-amanatin

A

Toxin procure by amanita phaloides mushroom. Binds to RNA polymerase II and is irreversible.

Causes GI disturbances, electrolyte imbalance, and kidney+liver dysfunction

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84
Q

45 S

A

Pre- RNA

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85
Q

Pre- RNA is modified by…

A
  • Cleavage by an endonuclease (RNase)
  • Trimmed by exonucleases
  • Base and nucleotide modification by snoRNA
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86
Q

tRNA modifications

A
  • 16 nucleotide sequence at 5’ end is cleaved
  • 14 nucleotide sequence at anticodon loop is cleaved
  • 3’ end uracil residue is converted into CCA
  • Nucleotide modifications
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87
Q

Primitive mRNA

A

RNA polymerase II transcribes a premature RNA called heterogenous RNA (hnRNA)

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88
Q

hnRNA modifications…

A
  • Cap at 5’ end (co)
  • Poly-A tail at 3’ end (post)
  • Splicing (co or post)
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89
Q

5’ Capping

A

Cap is a 7-methylguanosine which is added backwards frmom 5’ to 5’. Cal is not transcribed from the DNA

Stabilizes mRNA and helps in initiating translation

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90
Q

Guanylyltransferase

A

Adds the GMP (guanosine monophosphate)

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91
Q

7-guonosine methyltransferase

A

Adds the methyl group to the guanosine

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92
Q

Poly- A tail

A

Tail is added after it recognizes the polyadenylation sequence (AAUAAA). Tail ranges from 40-200 nucleotides.

Helps in stabilizing, in translation, and transporting out of the cell

Longer poly-A tail, more stable it is since exonucleases will have to eat more to get to the actual mRNA

Poly A tail sequence is not transcribed from the DNA

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93
Q

Polyadenylation polymerase (poly A pol)

A

Catalyze the poly-A tail. ATP is used as a substrates

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94
Q

Splicing

A

Cutting introns to only ligate the exons

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95
Q

Intron structure

A

5’ end: start with GU
3’ end: start with AG
Branch point A

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96
Q

snRPS

A

Small nuclear ribonuclear proteins. They help in splicing. Contain snRNAs

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97
Q

Splicing mechanism

A

2’OH of branch point A attacks 5’ end of intro closest to exon 1. This forms a 2’ to 5’ bond and lacerates it. The free 3’ end of exon 1 then binds to the 5’ of intron closest to exon 2.

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98
Q

B-knot thalesimia

A

Homozygous mutation in the intron region (5’ or 3’ end) in the hemoglobin gene. This totally abolishes normal splicing and is fatal!

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99
Q

B+ thalesimia

A

Point mutation in polyadenylation sequence. Instead of AAUAAA -> AACAAA. Less fatal

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100
Q

Epigenetic change

A

Modification of base pairs that leads to irreversible and hereditary changes. There is no change in bases

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101
Q

Epigenetic changes example

A
  • The way you hold a baby
  • Cellular differentiation
  • Differences in monozygotic twins
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102
Q

Mice example

A

Normal mice has brown fur, is small, and free from disease. Agouti mice has yellow fur, is large, and prone to disease.

When give mother normal diet and B12, folate, choline, and betaine, mice were normal.

When give mother normal diet only, mice were agouti

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103
Q

Bee example

A

Both queen and workers have same genes. However, queen takes royal jelly diet while worker doesn’t take this diet

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104
Q

DNA methylation

A

Silences genes

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105
Q

DNA methyl-tansferase

A

Adds methyl group to 5 part of CpG cytosine.

Can measure these levels in original gene or transcribed target sequences

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106
Q

5mC inhibits gene activity because…

A
  • Harder to break hydrogen bonds
  • Larger is TFs wont attach
  • Strong binding with methyl proteins so won’t bind to TFs
  • Chromatin remodeling
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107
Q

Places where you can get methyl…

A
  • Folic acid
  • Betaine
  • B12
  • B6
  • Choline
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108
Q

Importance of DNA methylation

A
  • DNA imprinting
  • X chromosome inactivation
  • Aging
  • Tissue specialization
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109
Q

H2A and H2B…

A

Leave the cell readily so not important for gene modification

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110
Q

H3 and H4…

A

Stats in cell and is important for gene modification

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111
Q

Histone acetylation

A

Charges of arginine and lysine are suppressed so genes are active

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112
Q

Histone deacetylation

A

Charges if arginine and lysine are activated and genes are inactive

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113
Q

Resveratol

A

Found in red grapes

Removes acetyl group and improves health

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114
Q

Housekeeping genes

A

Need them all the time.

Ex: ribosomal genes, tRNA, actin

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115
Q

Controlled genes

A

Need them at specific times.

Ex:histone, DNA pol, hormones

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116
Q

Regulatory DNA sequences

A

On the DNA and are cis acting elements (come from the same gene). Can enhance/silence gene expression

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117
Q

Regulatory proteins (TFs)

A

Trans-acting DNA proteins that bind to DNA elements. That activate/suppress gene expression

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118
Q

Steroid hormone receptor example

A

Glucocorticoid receptors are separate. When cortisol binds to the receptors, they form a protein dimer. This signals the GRE sequence to come and activate certain genes

Cortisol: DNA binding protein
GRE: DNA sequence

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119
Q

Splice site choice

A

Can choose what regions you want to splice

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120
Q

mRNA editing

A

Change in a nucleotide sequence

Ex: apoprotein B’s real form is actually really long. Change in a nucleotide sequence leads to a premature stop (missense) This protein is found in the liver and small intestine

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121
Q

In iron deficiency…

A

Body thinks transferrin has iron so will increase transcription of transferrin receptors while ferritin receptor transcription will decrease

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122
Q

Proto-oncogene

A

Normal gene. Can become cancerous by accumulation of normal protein or forming an abnormal product

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123
Q

Oncogene

A

Abnormal growth in cells. Can be cause by viral insertion and cellular mechanisms

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124
Q

Viral insertion

A

When a virus enters its genetic material into the cell, it fuses with the cells’ DNA and leads the cell to make a lot of proteins

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125
Q

Point mutation

A

Leads to the change in one amino acid

Ex: in RAS a point mutation leads to a change in only one amino acid

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126
Q

Amplification

A

Usually, when genes are amplified, they are stored in the chromosome as a double minute. Amplification leads to an increase in normal gene product.

Ex: myc oncogenes is found in many neuroblastomas

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127
Q

Chromosomal translocation

A

Can lead to chimeric genes

Ex: translocation between chromosome 9 & 22 leads to a fusion protein called bcr-abl that is defective in normal protein kinase
Abl protooncogene: encodes a tyrosine specific protein kinase

128
Q

src gene

A

Found in the Rous Sarcoma virus and is a protein kinase tyrosine (phosphorylates tyrosine). When the oncogene is activated, it will phosphorylate other proteins as well

129
Q

RAS gene

A

Encodes guanine-nucleotide binding proteins. Activity is controlled by GTP. RAS is activates by a point mutation. When activated, it will lead to enhanced signal induction though Raf-1 serine threonine kinase, ERK-1 AND ERK-2, and induction of transcription of early genes

130
Q

Ribosomes

A

Place where proteins are manufactured.

Have two subunits:

  • Large subunit (catalytic)-cleave
  • Small subunit (decoding)- reading mRNA

Have three functional sites:

  • A: place where elongator aa-tRNA will bind and form the polypeptide
  • P: place where initiator aa-tRNA will bind and accepts peptidyl tRNA
  • E site: where the uncharged tRNA exits

Between the A and P site, there is a hole where the protein will exit from

131
Q

Bacterial ribosomes

A

30S and 50S to make 70S

132
Q

Eukaryotic ribosomes

A

40S and 60S to make 80S

133
Q

tRNA

A

Has unusual bases (T). Have at least 20 tRNAs for each amino acid. Has an acceptor arm (3’ end) for carrying the amino acid and an anticodon loop for decoding the mRNA.

Required for:

  • Activation or polypeptide since peptide bone formation is not feasible in normal environment
  • Sequencing the amino acid in the correct order
134
Q

Initiator tRNA

A

Transports methionine in eukaryotes and f-met in prokaryotes. This is the first amino acid and recognizes it by the sequence AUG

135
Q

aa-tRNA

A

Charging of amino acid with the correct amino acid. Completed by aa-tRNA synthetase which is a proofreading mechanism to make sure correct tRNA and amino acid are selected. Thus activates the COOH group of the amino acid.

ATP+tRNA+Amino acid->AMP+ 2pi+ aa-tRNA

136
Q

Selecting a correct amino acid

A
  • Size
  • Thermodynamicity
  • Hydrophilicity or hydrophobicity
  • Acceptor arm
  • C:G 3:70
  • Anticodon arm
137
Q

Double sieve mechanism

A

If size (so thermodynamicity) of two amino acids are similar, need to go to charge

There are two sites in aa-tRNA

  • Catalytic site: hydrophobic
  • Proof reading site: hydrophilic

Amino acid must go through the hydrophobic site. If it goes though the hydrophilic site, it will be thrown out

138
Q

mRNA in prokaryotes

A

Has 5’ to 3’ UTR. Starts are AUG codon. No introns, capping, or poly-A tail. Translation finishes at UAA, UGA, or UAG. Initiator aa-tRNA carries f-meth

139
Q

mRNA in eukaryotes

A

Has capping, poly A tail,and splicing. Cap assembles at the ribosome but translation doesn’t start until the AUG sequence is read in the Kozak sequence. Translation stops at UAA, UAG, and UGA

140
Q

Initiation

A

Happens in two steps:

  • Assembling the 30S subunit
  • Attaching the 30S subunit with the 50S subunit
141
Q

Assembling the 30S subunit

A
  • IF 1 and 3 are bound to the subunit
  • IF 1 blocks the A site
  • IF 3 blocks site for attaching to the 50S subunit
  • IF 2 and 1 take the initiator aa-tRNA and take it to P site
  • IF 2 takes the initiator t-RNA and places it at the P site
142
Q

Binding the 30S subunit to 50S subunit

A

When the initiator aa-tRNA is attached IF 3 disconnects to allow the 50S subunit to attach

143
Q

Elongation

A

Four steps:

  • Putting elongation aa-tRNA on A site
  • Formation of the peptide bond
  • Moving from A to P
  • Moving uncharged tRNA to E site

Have different EFs for prokaryotes and eukaryotes

  • Prokaryotes: eEF-1, eEFG
  • Eukaryotes: EF-Tu, EF-Ts, and EFG
144
Q

Putting elongation aa-tRNA on A site

A
  • EF-Tu is a GTP protein and takes the elongator aa-tRNA and places it at A site. When it is put at the A site, GTP is hydrolyzed and becomes GDP. The protein is now inactive
  • EF-Tu-GDP then binds to EF-Ts and displaces GDP
  • EF-Tu-Ts binds to GTP and displaces Ts
145
Q

Formation of peptide bond

A

Done by peptidyl transferase. Located on 23S in prokaryotes and 28S in eukaryotes. Both are located in the large subunit

146
Q

Transferring from A to P

A

Use EFG (translocase) to move it from A to P.

Some antibiotics inhibit translocation which terminates translation

Antibiotics that bind to A site inhibit translation

147
Q

Streptomycin

A

Binds to 16S on small subunit and prevents binding of initiator aa-tRNA to P site. Leads to polypeptide frame shift. Inhibition in initiation

148
Q

Termination

A

Stop codons UAA, UAG, and UGA don’t have any tRNA association with them

  • RF 1/2 will releases the polypeptide
  • RF3 dissociates it and proofreads it

If a tRNA is put at a stop codon
-RF3 terminates it and RF1/2 releases it
This is post quality control

149
Q

Streptomycin

A

Misreading of mRNA

150
Q

Tetracycline

A

Inhibits elongation

151
Q

Chloramphenicol (pro) or cycloheximide (euk)

A

Inhibits elongation

152
Q

Erythromycin

A

Inhibits elongation

153
Q

Duromycin

A

Inhibits elongation

154
Q

Diphtheria toxin

A

Inhibits translocation

155
Q

Protein reaches its target by…

A
  • Targeting sequence

- Specific modification (protein folding, glycosylation)

156
Q

Protein modification

A
  • Cleavage: make inactive proteins (zymogens) active. Ex: digestive enzymes, preprohormones (insulin)
  • Hydroxylation: collagen
  • Phosphorylation: TFs
  • Lipidation: adding lipid anchors
  • Glycosylation: membrane proteins and secretory proteins
157
Q

Category 1 protein

A

Synthesizes entirely on the free ribosomes

Include: mitochondria, nucleus, proteosomes, and cytoplasm proteins

158
Q

Category 2 proteins

A

Begins synthesis in the free ribosome and then completes it on the rER.

Includes: plasma proteins, ER and Golgi resident proteins, lysosomal proteins, and secretory proteins

159
Q

Category 3 proteins

A

Synesthesia complete on the free ribosome but is then moved to the ER for post-translational modification

160
Q

Mitochondrial proteins

A

Have a target sequence that is on the N-terminus. Is cleaved when the protein reaches the mitochondria

161
Q

Nuclear proteins

A

Has their target sequence on the N-terminus. Is not cleaved when it reaches the nucleus

162
Q

Proteosomal proteins

A

Hydrolyze fat. Have their target sequence on their C-terminus attached to Ser-Lys-Phenalalanine

163
Q

Coupling mechanism

A

Signal peptide (or leading sequence) is located on N-terminus and this will be recognized by signal receptor particles (SRP). SP-SRP complex will slow down translation and bind to SRP receptor on rough ER. Once it binds, GTP will be hydrolzed. Translation will then resume

Sometimes, the signal peptide is cleaved by the ER

164
Q

Modifications in the ER

A
  • Glycosylation
  • Oligomerization
  • Quality control
  • Protein folding
  • Forming disulfide bridges
165
Q

Glycosylation

A

N- linked Glycosylation: attaching complex carbs on the N terminus to Asn

O-linked glycosylation: attaching complex carbs on OH to Ser/Thr

166
Q

Protein folding

A

Chaperones bind to the exposed hydrophobic amino acids to help fold properly

167
Q

Quality control

A

If a protein is not folded properly, glucosyl tranferase will add glucosyl tranferase enzyme. A chaperone called calnexin will fold the protein correctly.

If the protein still isn’t folded correctly, will go to peroxisome.

If the protein is folded correctly, G molecule will be removed by glucosidase II and will go to Golgi

168
Q

Modifications on the Golgi

A
  • Terminal glycosylation
  • O-linked glycosylation
  • Sorting/packing
169
Q

Sorting lysosomal proteins

A

Lysosomal proteins are tagged with mannose-6 phosphate and its receptor. It is exocytosed to an endosymbiosis which recycles the mannose-6 phosphate and the receptors

170
Q

ER resident proteins

A

Have KDEL. When it goes to Golgi, it will have KDEL receptor to send the protein back to the ER

171
Q

Mucolipidosis II

A

Accumulation of inactive lysosome and so accumulation of mucopolysaccharides in inclusion bodies (mostly in fibroblasts)

172
Q

4 levels of protein structure

A
  • Primary
  • Secondary
  • Tertiary
  • Quaternary
173
Q

Primary structure

A

Linear structure of amino acids that is stabilized by peptide bonds (covalent bonds)

174
Q

Secondary structure

A

Stabilized by H bonds between the amino and carboxyl group.

5 forms:

  • a helices
  • B sheets
  • B turns
  • Repetitive sequences
  • Motifs
175
Q

A helices

A

In a right handed helix. Stabilized by H bonds between the 1st and 4th amino acid respectively.

Also have:

  • a 10 helix: between every third amino acid
  • Pi helix
176
Q

B sheets

A

Formed by two segments of a polypeptide. If it’s formed by two polypeptides, leads to disease. R groups are up or down.

Have two sheets:

  • Antiparallel: segments are coming opposite ways. Major form
  • Parallel: segments at coming from the same way. Minor form
177
Q

B turns

A

Abrupt changes in B sheets. Glycine and proline help stabilize it. Four amino acids make up the turn, of which glycine and proline are present. Bond between 1st and 4th amino acid and 3rd and 4th amino acid

178
Q

Non-repetitive sequences

A

Loops and coils

179
Q

Super secondary structure (motifs)

A

2 or more secondary structures that are connected by loops or turns

  • Helix-turn-helix: major groove binding
  • Helix-bend-helix: TFs
  • B barrels: antiparallel rolled up (bacterial pores)
  • B hairpins: found in globular proteins
  • Helix bundles: transmembrane proteins
180
Q

Tertiary structure

A

Stabilized by ionic bonds, H bonds, hydrophobic interactions, and disulfide bridges

181
Q

Quaternary structure

A

2 or more polypeptides

182
Q

Protein denaturation

A

Disrupts the non-covalent interactions but not the covalent bonds (peptide and disulfide)

Denaturants: pH, heat, urea, organic solvents

183
Q

Enzymes

A

Lower activation energy but don’t change delta G

184
Q

Standard unit

A

1micromol/min.

This is how you measure enzyme activity since you can’t get molar amount of enzyme

185
Q

Specific activity

A

IU/mg

Measure enzyme purity

186
Q

Isoenzymes

A

Enzymes that catalyze the same reaction in different parts of the body

187
Q

CK2

A

Isoenzyme found in cardiac tissue. Is a diagnosis marker for cardiac tissue damage since damage leads to a lot of CK2 release

188
Q

Cofactors

A

Other substances needed to help in enzymatic activity

2 types:

  • Inorganic
  • Organic: coenzymes
189
Q

Ribozymes

A

Non-protein enzymes that are made of RNA. Help catalyze peptide bond formation

190
Q

Ribonuclearproteins

A

Made of RNA and nucleic acids.

Ex: telomerase

191
Q

Proximity effect

A

Brings enzyme and substrates together

192
Q

Orientation effect

A

Provides correct orientation for catalysis

193
Q

Catalytic effect

A

Provides the correct functional groups (acidic, basic)

194
Q

Energy effect

A

Helps reach transition state

195
Q

Lock and key model

A

Substance fits directly into the enzyme.

Static model

196
Q

Induced fit

A

Enzyme wraps around substance since they are not a perfect fit

Dynamic model

197
Q

V max

A

Maximum rate that is achieved theoretically

198
Q

Km

A

Substance concentration that reached 1/2 v max

199
Q

Reversible inhibitors

A

Bind to enzyme through non-covalent interactions. If you add a diluted solution without inhibitors, inhibitors will be washed off

200
Q

Irreversible inhibitors

A

Covalently binds to the enzyme. Adding the solution won’t wash off the inhibitors

Ex: lead and mercury bind to S on cysteine residues
Ex: malathion (organophosphorus insecticide) and sarin (nerve gas) inhibit acetylcholinesterase

201
Q

Competitive inhibitors

A

Actively competes with the substrate to get to the active site. Higher substrate concentration will displace inhibitor. So max isn’t changed by km is increased

202
Q

Lovastatin

A

Lovastatin inhibits HMG-CoA reductase (synthesizes cholesterols) to reduce cholesterol levels

Good for treatment of hypercholesterolemia

203
Q

Non-competitive inhibitors

A

Binds to the enzyme at a different site than the active site. Leads to change in active site or getting rid of it altogether. Decereases vmax but km is the same

204
Q

Transition state analogs

A

Mimics the 3D structure of the transition state but doesn’t form products. Bind very tightly to the active site

205
Q

Suicide inhibitors

A

Binds to the enzyme but never leaves the active site

Ex: penicillin inhibits glycopeptice transpeptidase by modifying the serine chain -OH group
Ex: aspirin inhibits cyclooxygenase
Ex: allopurional inhibits xanthine oxidase

206
Q

Changing enzyme amount

A
  • Synthesis: slow

- Proteolysis: fast and degrades

207
Q

Changing enzyme activity

A
  • Proteloysis
  • Phosphorylation/dephosphorylation
  • Cooperativity/alosteric regulation
208
Q

Trypsinogen

A

In its inactive form. Be woke active by cleavage (proteolysis) or 6 amino acids. Active ones can then activate other inactive ones

209
Q

Cooperativity

A

Usually when an enzyme has more than one subunit. One substrate binds to active site on one of the subunits and if it’s positive cooperativity rest of the substrates will bind as well.

Does not follow Michaelis-Mentin curve. Leads to a sigmoid also curve

210
Q

Alosteric regulation

A

Effector binds to place outside of the active site and can be positive or negative effect.

When paired with Cooperativity, activators will stabilize the high energy state and make the curve more hyperbolic

211
Q

V effector

A

Affects vmax parameter and is used when enzyme has higher enzyme concentration

212
Q

Km effector

A

Affects km parameter and is used when enzyme has low substrate concentration

213
Q

Adding phosphate by…

A

Protein kinase with the help of ATP

214
Q

Taking away phosphate…

A

Phosphoprotein phosphatase

215
Q

Protein kinase A

A

Ligand binds to membrane which sends secondary messenger (cAMP) which tells kinase to phosphorylate and become active. Kinase then works on multiple reaction pathways

216
Q

Glycogen phosphorylase

A

When phosphorylated, increases activity

217
Q

Glycogen synthase

A

When phosphorylated, decreases activity

218
Q

Preparing agarose gel

A
  • One gram of agarose in 50 ml of TBE buffer
  • Microwave for 1-2 mins
  • Put under running water
  • Put in casting tray its comb and make sure there are no air bubbles
  • Let it solidify
  • Take out comb
219
Q

PCR method

A
  • Add MgCl2, taq polymerase, dNTP into lambda DNA and primers
  • Centrifuge
  • Add buffer dye (helps see DNA migration)
220
Q

MgCL2

A

Helps in primer binding to DNA

221
Q

Electrophoresis method

A
  • Take 10 micro liters or marker and put in one well
  • Put 20 microliters of sample in one well
  • Run for 1 hr at 60 volts
  • Look at results with UV trasilluminator camera
222
Q

Sickle cell anemia

A

Point mutation in changing glutamate to valine. This makes it stay at the top of gel electrophoresis.

Mutation in B chain of hemoglobin

Normal:

  • Oxygenated: nothin
  • Deoxygenated: pockets

Mutated:

  • oxygenatedm spikes
  • Deoxygenated: spikes and pockets ( so forms clumps when low oxygen which leads to vessel clogging and leads to pain)
223
Q

Prions

A

Change alpha helices to b sheets. Leads to rogue protein which can make enormous protein rogue as well

Exam mad cow disease, CFJ

224
Q

Amyloid precursor protein

A

Not cleaved properly so leads to Alzheimer’s since plaques develop

225
Q

Collagen synthesis

A

In the rough ER. Formed by C terminus and helped by inter and intra H bonds as well as disulfide bridges

In the extracellular space, N and C peptodases will cut off some of the N and C ends

226
Q

Modification of collagen

A
  • Hydroxylation of proline by proloyl hydroxylase with the help of vitamin C
  • Fibril formation by covalent cross-linking of lysine helped by lysine oxidase. Need copper for this
227
Q

OI

A

Change in glycine to a bulky amino acid will result in a weak and brittle collagen and no hydroxylation

228
Q

EDH

A

Caused by mutation

229
Q

UV radiation

A

Degrade collagen and forms wrinkles and premature aging

230
Q

Metabolic pathways

A

All reactions in a cell

231
Q

Cycles

A

Pathways that regenerate a substance

232
Q

Catabolic pathways

A

Breaking down a high energy product (glucose) to a low energy product (CO2)

Produces ATP, NADH, and NADPH

High ATP closes catabolic pathways

233
Q

Anabolic pathways

A

Building up high energy products from low energy products

Use ATP, NADH to provide energy for the buildup

High ATP open anabolic pathways

234
Q

Break reactions into small steps

A
  • Pathways will take place where the enzyme is
  • Compartmentalized into organelles
  • One product will be reactant of the next
235
Q

Intrinsic regulation

A

Based on cells needs. Use ATP, ADP, NADPH, NADP+

236
Q

Extrinsic regulation

A

Based on body’s needs. Use hormones

237
Q

Free energy

A

Energy available to do work. When it’s negative, it’s spontaneous. At equilibrium, delta G is 0.

Can couple a nonspontaneous reaction to a spontaneous one

238
Q

Phosphory-transfer potential

A

Ability to transfer a phosphate group. ATP has can both accept and donate a phosphate group

239
Q

Redox reactions

A

Transferring electrons between substances

240
Q

Redox potential

A

Wanting to gain electrons

241
Q

Reducing equivalent

A

Substance that helps transfer electrons

NADH and NADPH are the come common ones

242
Q

Committed step

A

First reaction in a pathway that is irreversible and has only one unique product. Also known as the rate-limiting step. It’s also the slowest step

243
Q

Feedback inhibition

A

Product of a reaction will inhibit that same reaction

Advantages:

  • Prevent accumulation of toxic waste
  • Prevents wastage if energy
244
Q

Feed forward reaction

A

A product early on in the reaction will activate an enzyme later on in the pathway

245
Q

GLUT isoforms

A

Found on the membrane of cells and allows glucose to enter the cell

246
Q

Glycolysis

A

Beginning of respiration if oxygen is available. If in anaerobic conditions, it’s the only way to get ATP

247
Q

Changing glucose to G6P

A

Phosphorylate glucose using ATP with a hexokinase

This allows:

  • Glucose to be be further metabolized since it was inert
  • Prevents glucose from leaving the cell because now it’s an anion

NOT THE COMMITTED STEPPPP

248
Q

Hexokinase

A

Found in non-hepatic cells

Has a low km so non-hepatic cells can trap glucose

Low vmax so can’t trap phosphorylated glucose or phosphorylate more glucose than it can use

249
Q

Glucokinase

A

Found in the liver

Has high vmax for rapid uptake glucose from bloodstream, gkycogenesis, and prevents hyperglycaemia

Has high km fo rapid synthesis/release of glucose (can leave liver following a big meal), glycogenolysis, and prevents hypoglycemia

Induced by insulin

250
Q

PFK1

A

Changes fructose 6 phosphate to fructose 1,6 biphosphate through phosphorylation

251
Q

Aldose B

A

Cleaves fructose 1,6 biphosphate to glyceraldehyde 3 phosphate

252
Q

Glyceraldehyde 3 phosphate dehydrogenase

A

Changes glyceraldehyde 3 phosphate to 1,3 biphosphoglycerate

This is the first oxidation reduction reaction and produce a NADH

253
Q

Pyruvate kinase

A

Changes PEP to pyruvate and gain an ATP through substrate level phosphorylation

254
Q

Branching of pyruvate

A
  • Oxidative decarboxylation to acetyl CoA
  • Reduction to lactate and ethanol
  • Transformation to alanine
255
Q

Regulation of hexokinase

A

Inhibited by G6P. So make sure that if there is a lot of glycolysis going on (meaning there will be a lot of energy) won’t waste any more glucose

256
Q

Regulation of PFK1

A

Negative: ATP, citrate, H+ from lactate
Positive: fructose 2,6, biphosphate and AMP

257
Q

Fructose 2,6, biphosphate

A

Most important regulator for PFK1. Not an intermediate of glycolysis. Catalysts by PFK-2

258
Q

PFK2

A

Non-phosphorylation form catalyze fructose 2,6 biphosphate

Phosphorylated form: glucagon will bind to membrane causing cclyic aMP to activate protein kinase A which will phosphorylate PFK2. Liver stops consuming glucose and makes glucose (so opposite effect!)

In the heart, the phosphorylated form is active and vice versa

259
Q

Regulation by pyruvate kinase

A

Negative: alanine, ATP
Positive: fructose 1,6 biphosphate: feed forward reaction

260
Q

Fructose accumulation

A

When there’s an aldose B deficiency, accumulation of fructose and deficiency in ATP

Shouldn’t give people fructose or sucrose

261
Q

Classic galactosemia

A

Deficiency of GLAT which changes galactose you glucose so accumulation of galactose and can’t make ATP

262
Q

Get acetyl coA from…

A
  • Pyruvate
  • Fatty acids
  • Proteins
263
Q

Pyruvate dehydrogenase

A

Changes pyruvate to acetyl CoA

Need it to be inactivated so don’t need the protein kinase A

Positive: ATP, NADH
Negative: ADP, NAD+, CoA

264
Q

Oxoacetate

A

Transports CoA to cell

265
Q

Citrate

A

Can move in the mitochondria

ACETYL COA CANT MOVE INSIDE THE MITOCHONDRIA

266
Q

Isocitrate dehydrogenase

A

Rate-limiting step

Negative: ATP and NADH
Positive: ADP, Ca

Uses both NAD and NADP

267
Q

Succinyl coA

A

Metabolic branch point

268
Q

Succinyl thiokinase

A

Makes the GTP

269
Q

Succinate dehydrogenase

A

Complex II in mitochondria electron transport chain. Changes FAD to FADH2

270
Q

Malaga dehydrogenase

A

Generates last NADH

271
Q

Summary of Krebs cycle

A
  • 2 carbons from acetyl CoA released as CO2
  • Make 3 NADH
  • 1 FADH2
  • 1GTP
272
Q

Regulation of Krebs cycle

A
  • Citrate synthase inhibited by citrate

- Allosteric regulators of cycle: Ca2+, ATP, ADP

273
Q

Inner membrane of mitochondria

A

Not permeable to substances. Has five complexes

Four are for transferring electrons
One is for making ATP

Inner membrane is folded to allow the complexes to be on it

274
Q

Intermembrane space

A

Has a lot of H+ ions

275
Q

Matrix

A

Place where the hydrogen ions go

276
Q

Electron transport chain

A

Electrons lost by NADH & FADH2 and go to oxygen and combine with hydrogen to form water

277
Q

Oxidative phosphorylation

A

Using diffusion energy of H+ ions, can make ATP

278
Q

Complex 1

A

NADH dehydrogenase. Has Fe-S centers, FMN, and coenzyme Q

Fe-S will transfer electrons from NADH to coenzyme Q

Allows proteins to go into the intermembrane space

279
Q

Coenzyme Q (ubiquinone)

A

A benzoquinone which is hydrophobic.

Gets one electron to be a emiubiquinone radical and two to become ubiquinone

Small size allows for diffusion across the membrane.

Statin inhibits it’s synthesis

280
Q

Flavoproteins

A

Contain FMN or FAD.

Accept one electron to become semiquinone and 2 to become FMNH2

Can donate two electrons to NAD+ and one to Fe

281
Q

Fe-S

A

Contain 2-8 iron atoms that are complexes with elemental and cysteine S residues

Can only transfer one electron at a time

282
Q

Complex 2

A

Succunate dehydrogenase (like in TCA). Has FAD and Fe-S clusters

Electrons from Coq are given to FAD which reduce it. FAD gives to Fe-S clusters who give it to another Coq

283
Q

Complex 3

A

Cytochrome c reductase. Contains cytochrome c, b1, Coq.

Undergoes the Q cycle

284
Q

Q cycle

A

Round 1: CoQ gives electron to Fe-S who gives it to to cytochrome c. Other electron goes to cytochrome b. At this time, CoQ will dock at cytochrome b point and receive this electron to become a radical

Round 2: Another CoQ will come and give electron to cytochrome c. Other will go to cytochrome b to give to quinone radical to become normal again

285
Q

Cytochromes

A

Contain heme which can undergo transition between two iron states

286
Q

Cytochrome c

A

Transfers electrons to complex 4. Has positive amino acids which interact with the negative amino acids in complex 4 which helps it dock

287
Q

Complex 4

A

Cytochrome C will dock on complex 4 and Cu will accepts the electrons and give it to O one at a time

1 e: o radical
2 e: peroxide
3 e: 2 o radical
4 e: water

288
Q

Moving H

A

Complexes will have strong affinity for H in the beginning and then have low affinity which will allow it to release it

289
Q

Complex 5

A

Makes ATP

Has two parts: F1 and F0

290
Q

F0

A

Has a rod (a subunit) and rotating part (c subunit). Protons go up rod and are repelled by c subunit. End of c subunit when bound to rod will allows hydrogen ions to exit leading to a step movement

291
Q

F1

A

In the matrix and makes ATP

Has 3 catalytic sites

Site 1: has ADP and pi
Site 2: has ATP
Site 3: empty

Every rotation is 120 degrees to repeat the cycle after every three rotations

292
Q

Uncouplers

A

Lipid-soluble molecules that will dissipate the electrochemical gradient of H+. H ions will still move but instead of energy being in ATP, it’ll be in heat

Thermogenein (UCP1) is an example

UCP2 and UCP3 lead to weight loss by breaking down fat

293
Q

Mitochondrial diseases

A

From mother. Random selection of mitochondria region leads to some areas having more infectious agents than others

294
Q

Glycogen

A

Stores glucose. Is a branches polysaccharide that is sparsely soluble

Has glycosidic type a 1,4 and 1,6 bonds

Found in liver and muscle. Higher composition in liver but higher mass in muscles.

Muscle glycogen can not give glucose to other tissues since it doesn’t have glucose 6 phosphorylase

295
Q

Phosphoglucomuatse

A

Isomerizes glucose 6 phosphate to glucose 1 phosphate

296
Q

Glycogen synthase

A

Adds glucose to 4’ end on glycogen branch. However, this is thermodynamically unfavorable so first has reaction with UTP and glycogen synthase uses this phosphate to add glucose

Glycogen synthase can only add glucose to an already existing glycogen chain

297
Q

If no glycogen chain…

A

Glucose attaches to tyrosine residue on glycogenin. Glycogenin catalyzes it’s own reaction

After about 7 chains, glycogen synthase can begin acting on it

298
Q

Branching enzyme

A

Takes a residue of about 6-7 branches and attaches it to a terminal carbon 6 group to form an a 1,6 bond

299
Q

Glycogen phosphorylase

A

Breaks down glycogen to form glucose. Cannot break down a glycogen chain that is 4 residues or less

300
Q

Debranching enzyme

A

Breaks down the 4 chain glycogen molecule. Takes three out of the four glucose molecules and adds them to a longer chain. Takes the remaining one and cuts off the bond to form a free glucose molecule

301
Q

Lysosomal degradation of glucose

A

Lysosome has enzymes to break down glycogen. However, breaks down a very negligible amount.

When this enzyme is defected, glycogen accumulates in the lysosome vesicle and leads to glycogen storage disease type II (pompe’s disease)

302
Q

Regulation of glycogen phosphorylase

A

When blood glucose becomes low, glucagon levels become high. So glucagon binds to the receptor and form cAMP. cAMP will activate protein kinase A. PKA will activate the active “a” form of phosphorylase kinase. “A” form of phosphorylase kinase will activate glycogen phosphorylase and break down glycogen

In muscle, epinephrine is used

303
Q

A adrenergic receptors

A

Couple to adenyl cyclase and form cAMP

304
Q

B adrenergic receptors

A

Coupled to G protein. G protein activates phospholipase C. Phospholipase C hydrolyzes PIP2 to form IP3 and DAG

DAG binds to & activates protein kinase C that phosphorylates a lot of molecules including glycogen synthase

IP3 binds to ER receptors to release Ca. Ca will bind with calmodulin and activate phosphorylase kinase

305
Q

In liver, epinephrine…

A

Leads to same Ca cascade

306
Q

In muscle, acetylcholine

A

Will release Ca and go through same cascade. In this way, don’t need pka to activate phosphorylase kinase

AMP also activated phosphorylase kinase

307
Q

Glycogen synthase

A

Exits in active “a” non-phosphorylated form and inactive “b” phosphorylated form

Insulin will activate glycogen synthase and glucagon will inhibit it

308
Q

Pentose phosphate pathway

A

Anabolic reaction that changes 6 carbon sugar (glucose) to 5 carbon sugar (ribose) for nucleotide and nucleic acid synthesis

Also makes NADPH and makes glyceraldehyde-3-phosphate and glucose-6 phosphate

Has 2 steps:

  • Oxidative
  • Non oxidative
309
Q

Oxidative

A

G6P is changed to 6-phosphogluconate and produces NADPH

6-phosphogluconate is changed to ribulose-5 phosphate and produces NADPH

310
Q

NADPH

A

Differs from NADH by one phosphate group. Involved in anabolic reactions

Need it for:

  • Synthesis of fatty acids and cholesterol
  • Changing ribonucleotides to deoxyribonucleotides
  • Reducing glutathione (antioxidant)
311
Q

Non-oxidative stage

A
  • Change ribulose 5P to ribose 5P (make NADPH)

- Make glyceraldehyde 3-phosphate and G6P (to go back to oxidative stage and g9 to glycolysis) (also makes NADPH)

312
Q

Digesting proteins in stomach

A
  • HCl: secreted by parietal cells and first denatures and then cleaves
  • Pepsinogen: gets activated by active pepsin and HCl
313
Q

Digestion by pancreas

A

Zymogens released by cholecystokinin and secretin

Activated by:

  • Enteropeptidase activates trypsinogen
  • Trpsinogen activates everything else
314
Q

Digestion in small intestine

A

Done by aminopeptidase which is an exopeptidase the is found in the lumenal surface of the intestine. Repeatedly cleaves N-terminus from oligopeptides to form smaller peptides and amino acids

315
Q

Absorbing free amino acids

A

Through Na+ linked secondary transport system in RBCs

316
Q

Absorbing di- and tri- peptides

A

Through a H+ transport system

317
Q

Cystinuria

A

Defect in transport system in proximal tubules of kidney to absorb cysteine. Leads to accumulation of cysteine leading to stones in the urinary tract

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