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Biochemistry > Quiz 1 Material - Intro, Zaia lectures, Hemoglobin/myoglobin > Flashcards

Quiz 1 Material - Intro, Zaia lectures, Hemoglobin/myoglobin Flashcards

1
Q

Ameloblast

A

Cell Type That Creates the Enamel

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2
Q

Odontoblast

A

Forms Dentin, and Found in Pulp

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3
Q

Dentin Sialophosphoprotein (DSPP)

A

Component in Formation of Dentin,

Gene is seen mutated in Dentinogenesis Imperfecta II and III as well as Dentin Dysplasia II

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4
Q

Anton Van Leeuwenhoek

A

Coined the Term ‘animalcules’ and observed oral bacteria

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5
Q

Robert Hooke

A

Coined the word ‘cells’

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6
Q

Matthias Schleiden

A

Stated all plants are made of cells and come from one cell

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7
Q

Theodor Schwann

A

Worked with Matthias Schleiden and proposed three tenants of the cell theory

  • all organisms are composed of one or more cell
  • the cell is the smallest unit of life
  • cells can come from inorganic materials
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8
Q

Rudolf Virchow

A

Fixes Schleiden and Schwanns third point by saying that cells can only come from previous cells.

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9
Q

Properties of the Archaea

A

Transcription looks like that of eukaryote, but DNA looks like that of a prokaryote

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10
Q

Steps in Endosymbiotic Theory

A

-Large anaerobic Host Took up Small aerobic bacteria
- Large bacteria protects and provides nutrients to small one
- small bacteria generates additional energy for larger bacteria
small bacteria loses ability to proliferate independently

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11
Q

Konstantin Mereschkowski

A

Proposed chloroplasts were distant relative to photosynthetic bacteria

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12
Q

Lynn Margulis

A

Furthered Mereschkowski’s theory and was all over the endosymbiotic theory.

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13
Q

Evidence to Support Endosymbiotic Theory (6)

A
  • mitochondria and chloroplasts can only arise from pre-existing mitochondria and chloroplasts
  • mitochondria and chloroplasts have their own genome that looks like prokaryotes
  • both genomes consist of circular DNA with no histones
  • Mito and Chloro have their own protein assembly machinery
  • antibiotics that black protein synthesis in bacteria also block protein synthesis in mito and chloro
  • inhibitors of protein synthesis in eukaryotes dont have an effect on bacterial proteins
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14
Q

Jared Hara

A

Has Leber’s Hereditary Optic Neruopathy which is a mitochondrial disease that results in blindness

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15
Q

Which came first plant or animal Cells

A

The animal cell because it only contains mitochondria, while plant has chloro and mito

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16
Q

Features in common between prokaryotes and eukaryotes (5)

A
  • Genetic information in DNA
  • The DNA uses common code (ACTG)
  • Mechanism of transcription and translation are strikingly similar
  • Metabolic pathways are conserved
  • chemical energy is stored as ATP
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17
Q

Examining Phylogenetic Tree Reveals (3)

A
  • Life Requires Energy and must conver to useful work
  • Biochemical reactions need a catalyst
  • life depends on info encoded in genes
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18
Q

Watson and Crick

A

Identified the Double Helix using X-Ray Crystallography

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19
Q

Rosalind Franklin and Maurice Wilkins

A

Helped with Double Helix Structure determination with Watson and Crick

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20
Q

How Many Base Pairs are in the Human Genome

A

3 billion

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21
Q

How many protein coding genes are there

A

20,000

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22
Q

What is the central Dogma of molecular Biology

A

DNA -> DNA - Replication
DNA -> RNA - Transcription
DNA -> Protein - Translation

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23
Q

Dentinogenesis Imperfecta (DI) Phenotype

A
  • Discolored Teeth
  • Poorly Mineralized Dentin
  • Fractured Enamel
  • Rapid Wear and Attrition of teeth
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24
Q

Dentinogenesis Imperfecta Types and Cause

A

I - mutation in Collagen gene, and usually associated with Osteogenesis Imperfecta (OI)
II - Have a mutation in the DSPP Gene
III - Aka Brandywine Isolate, and also have mutation in DSPP gene

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25
Q

Dentin Defects (4)

A

Dentinogenesis Imperfecta
Dentin Dysplasia (DD)
Hypophasia
Ehlers Danlos Syndrom (ED)

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26
Q

Dentin Dysplasia Type II Cause

A

Has a DSPP mutation

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27
Q

Amelogenesis Imperfecta (AI) Phenotype

A

Thin Enamel
Hypomineralization (not enough mineral)
Enamel Abrades Easily
Very Sensitive Teeth

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28
Q

Amelogenesis Imperfecta (AI) Mutations

A 
AMELX - amelogenin 
ENAM - Enamelin
MMP20
KLK4
FAM83H
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29
Q

Hypodontia (Cause and Effect)

A

Cengenital Missing teeth caused by disfunction in MSX1 and PAX9 transcription factor problems

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30
Q

Vitamin D Purpose (3)

A

Calcium absorption
Mineral Homeostatis
Bone Health

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31
Q

Bisphenol A (BPA) effects

A

Hypomineralization

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32
Q

Vitamin D Deficiency Effects

A

Low Mineral bone density (osteopenia and osteoporosis)
Infectious disease and inflammatory disease
cancer
Periodontal disease and tooth loss
Poor birth outcomes
Alzheimer, Schizophrenia and depression
Cardiovascular disease

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33
Q

Stages of Periodontal Disease

A

Norma, Gingivitis, Periodontitis, Advanced Periodontitis

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34
Q

Periodontal Disease Causes

A

Bacteria are not actually a good indicator as each host reacts differently.
Environment factors are actually huge
and inflammation of periodontium is very common.

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35
Q

Tumor Necrosis Factor Alpha (TNF α)

A

pro inflammatory cytokine leading to inflammation seen in the relation between obesity and periodontal disease. TNF suppresses insulin action

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36
Q

PubMed

A

Database of Scientific Papers

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37
Q

OMiM

A

Database of human genes and genetic disorders

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38
Q

Cn3D

A

Database to see the three dimensional structures of molecule

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39
Q

First Law of Thermodynamics

A

Energy is not created nor destroyed and constant in a system

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40
Q

Second Law of Thermodynamics

A

Entropy always increases

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41
Q

Gibbs Free Energy Equation

A 
ΔG = ΔH - T ΔS 
H = Chemical Bond Energy 
S = Entropy
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42
Q

ΔH when negative

A

Negative when reactants have more energy than products (gives off energy)

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43
Q

ΔS when it is positive

A

Is positive when when more disorder

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44
Q

When is ΔG always Spontaneous

A

When ΔH is negative (gives off energy) and ΔS is positive (more disorder)

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45
Q

How ΔS and heat transferred relate

A

When ΔS increases than the heat transferred out goes up

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46
Q

How Temperature and ΔS are related

A

When Temperature goes up then it is hard to transfer heat out so the ΔS goes down

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47
Q

What determines the reaction speed

A

Activation Energy, and not the Spontaneity

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48
Q

How many water molecules can H-Bond to a water

A

4

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49
Q

Van Der Waals’ Force Definition

A

A weak force created by the transient nature of electron clouds when molecules nearby naturally attract

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50
Q

Driving Force of Hydophobic Interaction

A

The Disorder increases for water and therefore it is driven by the entropy of water.

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51
Q

Kw Equation

A

Kw = [H+]{OH-]

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52
Q

pH Equation

A

pH = -log[H+]

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53
Q

Ka Equation

A

Ka = [H+][A-]/[HA]

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54
Q

What is a pKa

A

The pH when the reactants are half dissociated, and it is the - log of the Ka

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55
Q

Henderson Hasselbach Equation

A

pH = pKa + log [A-]/[HA]

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56
Q

Result of Fluoride Treatment

A

Hydroxylapatite converts to fluorapatite and impedes demineralization

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57
Q

How to Calculate pI

A

Average the two pKas flanking the new neutral form of the peptide chain, this will be the net neutral pH (Practice this)

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58
Q

pKa of terminal Carboxyl Group

A

~3

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59
Q

pKa of terminal amino group

A

~8

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60
Q

Hydroxyapatite Structure

A

Calcium, phosphate and OH, interacts with protein for shape, and has a woven structure

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61
Q

What Configuration are Amino Acids in

A

L-Configuration

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62
Q

Glycine (chirality, when seen, collagen)

A

Gly, G
achiral, Small, nonpolar, neutral
in the middle of hydrophobicity and hydrophillic
seen when need space and flexibility
because of collagens form of a triple helix there must be a glycine every 3 residues

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63
Q

Alanine

A

Ala, A

Small Neutral and nonpolar, and hydrophobic

64
Q

Valine

A

Val, V
Neutral, nonpolar, hydrophobic
seen interior of proteins

65
Q

Leucine

A

Leu, L
Neutral Nonpolar hydrophobic
seen in interior of protein

66
Q

Isoleucine

A

Ile, I
nonpolar and hydrophobic
Has a chiral Beta Carbon in R Group

67
Q

Methionine

A

Met, M
Non-polar and hydrophobic
Rare
easily oxidized to sulfoxide and sulfone

68
Q

Phenylalanine

A

Phe, F

aromatic, very non-polar, hydrophobic

69
Q

Tyrosine

A

Tyr, Y
Aromatic, hydrophobic and phillic grey area, polar and non polar
absorbs at 280nm
phosphorylates at the OH

70
Q

Tryptophan

A 
Trp, W
aromatic, very large, and hydrophobic, and nonpolar
rare
absorbs at 280nm
only AA that fluoresces
71
Q

Serine

A

Ser, S
Polar and hydrophillic,
phosphorylates and O-glycosylates post translationally

72
Q

Threonine

A

Thr, T
Polar, more hydrophobic
has chiral side chain
post translationally modifies by phosphorylation and o-glycosylation

73
Q

Cysteine

A

Cys, C
has a SH group and is super reactive
oxidizes in presence of oxygen
nucelophillic
must be alkylated when sequencing and analyzing
reacts in metal reactions and is seen in metalloproteins
oxidize to disulfide bonds
forms parts of antioxidants such as glutothione

74
Q

Arginine

A

Arg, R
Positively Charged base,
hydrophillic polar

75
Q

Lysine

A

Positive charged and basic

hydrophillic and polar

76
Q

Histidine

A

His, H
Neutral and polar but basic
HYDROPHOBIC grey area
participates in acid base reactions

77
Q

Aspartate

A

Asp, D
Acidic negative charged, hydrophilic and polar
can esterify to glutathion

78
Q

Glutamate

A

Glu, E
Acidic negative charge, very polar
can have esterification

79
Q

Asparagine

A

Asn, N
polar, and hydrophillic
can deaminate to aspartate,
does not give or remove H

80
Q

Glutamine

A

Gln, Q
Polar and hydrophiliic
does not give or remove H,
can deaminate to glutamate

81
Q

Proline

A 
Pro, P
is an imino Acid 
no rotation around the N and alpha carbon
no resonance of amide bond
usually cis, 
breaks helices
82
Q

Aliphatic

A

Means it does not have a ring

83
Q

Non-Polar Amino Acids

A

Gly, Ala, Val, Leu, Ile, Phe, Pro (some others are in the grey area)

84
Q

Hydrophobic amino Acids

A

Ala, Val, Leu, Ile, Met, phe, Tyr, Trp His Thr

85
Q

Polar Amino Acids

A

Ser, Thre, Csy, Asn, Gln, Lys, Arg, his Asp Glu Tyr (has some polar character)

86
Q

Hydrophilic Amino Acids

A

Arg, Glu, Asp, Lys, Pro. Cys, Ser, Asn, Gln

87
Q

Charged Amino Acids

A

Asp, Glu, Lys, Arg

88
Q

Basic Amino Acids

A

Lys, Arg, His

89
Q

Acidic Amino Acids

A

Asp, Glu

90
Q

Phi and Psi Angles

A

The two bonds around the Alpha Carbon rotate in specific ways, and if you know these angles for all bonds you will know the three d structures. The phi bond is the N-C bond and psi angle is the C–C

91
Q

Hydrogen Bonding in Alpha Helix

A

Between every N and C=O every 3.6 residues.

92
Q

The pitch of an Alpha Helix

A

of Angstroms that rises per turn

93
Q

Amino Acids not found in Alpha Helix

A

branches (Val Thr Ile,) H-Bonding donating (Ser, Asp, Asn). Do See Glu, and Gln

94
Q

Amino Acids found in Beta Strands

A

Val, Ile, Phe, Tyr, Trp, thr. Tolerates large R groups

Proline breaks strands

95
Q

H Bonds in Parallel vs Antiparellel Beta Strands

A

Straight H-bonds in antiparallel, making more stable (seen on outside of proteins)
Diagonal bonds in parallel, making less stable and seen on inside of proteins

96
Q

Chaperones (examples)

A

Stabilize proteins during folding.
Use ATP (folding on own does not)
GroES and GroEL examples

97
Q

Mucin

A

long polypeptide that is carbohydrate modified and coats mucosal surfaces

98
Q

Non-newtonian Fluid

A

Viscosity changes with pressure
Ex// paint ketchup and saliva
Caused y proteins in the fluid

99
Q

Differential Centrifugation

A

step by step centrifugation and removing of supernatant to isolate parts (organelles) of the cells

100
Q

Dialysis

A

Size based separation in which the volume is kept constant

101
Q

Centrifugal Concetrators

A

centrifugal force will push solution through the dialysis pore, which then decreases the volume

102
Q

Gel-filtration Chromatography

A

Aka size exclusion chromatography,

beads have small pores in side that small proteins get stuck in so large molecules will elute first

103
Q

what absorbance do peptides have

A

220nm

104
Q

Ultracentrifugation

A

forms a sucrose density gradient and then spin the protein down it. The proteins will seperate by S value, which is the sedimentation coefficient, a value representing the density and shape

105
Q

Ion Exchange Chromatography

A

Use beads with charged attachments to catch proteins based on pI
Can change the pH to trap certain proteins
use salt to elute

106
Q

Cation Exchange

A

The positive proteins (cations) will get stuck to a negative beed

107
Q

Anion Exchange

A

Beads are positive and capture the anion (negative protein)

108
Q

Affinity Chromatography

A

Beads have very specific attachments like an antibody, which will catch whichever protein you want
to elute you can add a competitor or denature

109
Q

SDS -PAGE

A

based on size.
protein is put through detergent and coated in negative charge
agarose is dense and so bigger proteins will move slow, and small peptides will move quick

110
Q

Reading SDS -PAGE

A

Position shows MW
Size shows amount
and if there are many bands the protein is not pure

111
Q

Anode and Cathode

A

Anode is positive charged so anions move toward it

Cathode is negative charge and so cations move toward it. in SDS page the anode is at the bottom

112
Q

Two-Dimensional Gel Electrophoresis (and Advantages and Disadvantages)

A

Separate by pI and then MW dimension
Advantages - see multiple proteins and patter
Disadvantage- post translational modifications ruin spots, bad resolution and non reprorducable

113
Q

Fluorescamine

A

After dissolving peptide in acid then react with this in order to fluoresce the amino acids
with this you can look at peaks

114
Q

Amino Acid Analysis

A

Using Fluorescamine you need a lot of protein and you can compare theoretical and experimental. process is dissolve the peptide and chromotraphy it to seperate and then fluoresce and compare to see if it is diseased

115
Q

Edman Degredation (advantage and disadvantage, and two molecules involved)

A

Used to sequence one AA at a time
phenylisothiocyanate - reacts with n terminus of chain
phenylthiohydantoin clips off AA at the end
advantage - can do multiple mixes and is accurate
disadvantage - its really slow and mass spec is better

116
Q

High Performance Liquid Chromatography (HPLC)

A

Make beads super small. Must apply pressure actually to get the peptides through but the result is really specific separation.

117
Q

Reverse Phase HPLC

A

A specific type of HPLC in which one adds hydrophobic groups to beads. Polar molecules flow through first and an increasing organic solvent gradient is used to elute by hydrophobicity

118
Q

Liquid Chromatography-mass spectrometry

A

using the elution from a chromatography then mass spectrometry in order to get peptide sequences

119
Q

ELISA - Enzyme linked immunosorbent Assay

A

To show amount of protein using antibodies

120
Q

Indirect ELISA

A

Fix protein, use specific antibody, then a general antibody that can be detected
This is challenging because you can get non-specific binding and one needs a good specific antibody

121
Q

Sandwhich ELISA

A

More specific then indirect, but also requires good antibodies. You fix one antibody, then put in the protein to bind. One then tag the protein with another antibody on the other side that can be detected

122
Q

Western Blotting

A

After SDS-PAGE one will transfer the blot to a sheet using electricity. One then uses an antibody to only illuminate the band in question. This can help in comparing phenotypes of diseases

123
Q

Circular dichroism

A

Caused by differences in light absorption between clockwise and counterclockwise vectors of light. Spectrums are created that are specific to proteins and their structure
can compare proteins phenotype using

124
Q

NMR Spectroscopy

A

Magnetizes the molecules and results in spinning of the hydrogen atoms. This data can be analyzed to figure out structure.

125
Q

X-Ray Crystallography

A

Pass X-Ray through the a crystallized protein and observe its diffraction. The x-ray will scatter (due to interactions with electron clouds) and professionals can read this information to determine structure.

126
Q

Trypsin Digest

A

When you digest a peptide with Trypsin it reliables cleaves at Arg and Lys

127
Q

Compare and Contrast Myoglobin, and Hemoglobin

A

Similar - in Structural motifs, carry oxygen, have prosthetic group
Contrast - AA sequence is less than 25% similar and hemoglobin is a quaternary protein

128
Q

Which are the crucial Histidines in hemoglobin

A

F8 and E7

129
Q

Myoglobin Properties

A

Located in muscle
Compact with helical sections
only charges are located on the two histidines

130
Q

What is the prosthetic group in myoglobin and hemoglobin?

A

Ferroprotoporphyrin

131
Q

Methemoglobin

A

If oxygen oxidizes the ferrous to the ferric in the heme it will no longer coordinate with oxygen

132
Q

Histidine E7 (what it does and what happens when mutated)

A

Is the distal histidine that donates H-Bond to the oxygen but also forces bent confirmation
Blocks oxidation of the ferrous
with mutation you get a lot of methemooglobin

133
Q

Ferrous Ion (How Does it Bind)

A

Binds to 6 ligands. Four of which are Nitrogen in the porphyrin ring. 2 are perpendicular to the ring.

134
Q

Carbon Monoxides effect on hemoglobin

A

CO binds more strongly to iron then oxygen. Because of histidines though you can actually has some CO in the body as it will be blocked and oxygen in high concentration can overpower it

135
Q

Histidine F8

A

Binds directly to the Iron

136
Q

Hemoglobin A

A

Found in adults. Has 2 alpha and 2 Beta subunits

137
Q

Mechanism for Cooperativaty

A
  • The T (Deoxy) form has its Iron out of the plane porphrin plane
  • O2 enters and pulls electrons from the ferrous
  • this lowers it in to the plane
  • an actual conformational change happens rotating 15 degrees counterclockwise
  • thus opening the molecule for more cooperation
138
Q

2,3 - diphosphoglycerate affect on hemoglobin

A

Stabilizes deoxyhemoglobin, thus weakening affinity for oxygen

139
Q

H+ ions and CO2 effect on hemoglobin

A

promotes release of oxygen, lower binding affinity by stabalizing deoxy form

140
Q

Bisphosphoglycerate - BPG

A
  • Has a minus five charge
  • Stabalizes the T state (Deoxyhemoglobin)
  • charges interact with positive charges in beta chain
  • BPG moves affinity curve right
  • oxygen must knock BPG out it get in to the hemoglobin (seen in lungs)
141
Q

Hemoglobin F

A

Fetal Hemoglobin containing 2 alpha and 2 gamma subunits

142
Q

BPG in Fetuses

A

Does not exist due to the lack of Beta chain.
Histidine is replaced by Serine in the Gamma subunit and therefore less affinity to the negative BPG
This makes deoxy less stable and affinity curve moves left for oxygen
allows for oxygen to flow from mother to child

143
Q

Bohr Effect

A

Decreasing pH shifts curve right and creates a lower affinity for oxygen

144
Q

Mechanism of Bohr Effect

A
  • When the pH goes down the histidine becomes protonated (His-146)
  • His-146 ion pairs with Asp-94
  • By forming this it pulls His-f8 which then pulls on the iron
  • this removing it from the plane and thus unloading the oxygen
  • this stabilizes the deoxy form
145
Q

The Two Ways Carbon Dioxide lowers Oxygen Affinity

A

1) Co2 becomes bicarb thus releasing protons

2) co2 reacts with the n-terminus amino to form carbamates - which stabilize salt bridges in the T Deoxy state

146
Q

Haldane Effect

A

Deoxygenation of blood increases its ability to carry co2

147
Q

Carbonic Anhydrase

A

Converts Carbon dioxide to bicarbonate and protons. Thus if you were to inhibit this it would shift an affinity curve left for oxygen.

148
Q

Two ways to transport CO2

A

1) Goes to bicarbonate dissolved in the plasma (most of it)

2) Gets put on to hemoglobin making carbamino hemoglobin

149
Q

Pulse Oximeters

A

Measure heart rate and percent hemoglobin that is oxygenated. oxygenated and deoxygenated absorb light differently.

150
Q

Functional Magnetic Resonance Imaging (fMRI)

A

Fully oxy hemoglobin is non-magnetic (diamagnetic)

Deoxy hemoglobin is magnetic (paramagnetic)

151
Q

Glycosylated Hemoglobin (HbA1c)

A

Increase in glucose concentration results in irreversible glycosylated hemoglobin. This is seen in diabetic patients

152
Q

Sickle Cell (Implications, AA Mutation, Malaria effect)

A
  • deformed RBC
  • tends to block capillaries and rupture them, causes bad bone development, gingival lesions, caries, perio disease, anemia, infections, renal failure
  • GTG->GAG so Glu becomes Val (loses the charge)
  • will accelerate destruction of RBC infected by parasites of malaria
  • Tends to aggregate to large fibers
153
Q

Isoelectric Point in Sickle Cell

A

Sickle cell is higher pI and when separating by electrophoresis it moves slower because it does not have the charge from Glu anymore

154
Q

Thalassemia (Dental Effects)

A

imbalance of production of hemoglobin chains can be alpha or beta
Results in malocclusion, caries and gingivitis

155
Q

Beta-Thalassemia

A

B chain of hemoglobin is not produced. So only an alpha chain is there resulting in insolubility and lack of cooperativity

156
Q

Alpha-Thalassemia

A

Alpha chain is not produces enough so hemoglobin only has beta and binds oxygen with high affinity and no cooperativity

Biochemistry (3 decks)

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