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501: Foundations I > Exam I > Flashcards

Exam I Flashcards

1
Q

Electronegativity Trend

A

F>O>N>C>H

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2
Q

An amine can ____ a proton to become ____ charged.

A

gain, positively

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3
Q

A carboxylic acid can ____ a proton to become ____ charged.

A

lose, negatively

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4
Q

The larger the Ka is, the ____ it is to dissociate. (____ acid)

A

easier, stronger

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5
Q

The smaller the Ka is, the ____ it is to dissociate. (____ acid)

A

harder, weaker

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6
Q

What is pKa? The value at which there is ____

A

an equal concentration of ionized and unionized species

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7
Q

If pH = pKa, there is ____

A

an equal amount of charged and uncharged species

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8
Q

pKa of Amines

A

pKa ~ 9-10

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9
Q

pKa of Carboxylic Acids

A

pKa ~ 4-5

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10
Q

Phospholipid Structure: ____ Head ____ Tail

A

Hydrophobic Head
Hydrophilic Tail
(Amphipathic Molecules)

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11
Q

____ molecules are more soluble in body fluids.

A

Hydrophobic (Polar)

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12
Q

____ molecules can pass through lipid membranes.

A

Hydrophilic (Non-Polar)

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13
Q

Strengths of Intermolecular Forces

A

Covalent > Electrostatic > Hydrophobic > Hydrogen Bonding > Van der Waals

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14
Q

Partition Coefficient: describes the extent to which an ____ compound dissolves in ____

A

uncharged, an aqueous solvent versus organic solvent

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15
Q

Drugs that are ____ tend to stay in the blood circulation and surrounding interstitial fluid.

A

hydrophilic

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16
Q

Drugs that are ____ tend to get trapped inside the tissue and are slowly eliminated.

A

hydrophobic

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17
Q

Electron-poor atoms

A

Electrophiles

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18
Q

Electron-rich atoms

A

Nucleophiles

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19
Q

Henderson-Hasselbach Equation

A

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

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20
Q

L- vs. D- Amino Acid Configurations

A
  1. Read the word “CORN”.
  2. Clockwise - L Configuration
    Counter-Clockwise - D Configuration
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21
Q

Proteins in humans are synthesized from a set of 20 ____-____- amino acids.

A

L-alpha

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22
Q

Hydrophobic (Non-Polar) Amino Acids (8 total)

A

Alanine, Isoleucine, Leucine, Methionine, Phenylalanine, Proline, Tryptophan, Valine

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23
Q

Hydrophilic (Polar) Amino Acids (7 total)

A

Asparagine, Cysteine, Glutamine, Glycine, Serine, Threonine, Tyrosine

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24
Q

Basic Amino Acids (Positively-Charged) (3 total)

A

Arginine, Histidine, Lysine

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25
Q

Acidic Amino Acids (Negatively-Charged) (2 total)

A

Aspartic Acid, Glutamic Acid

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26
Q

Isoelectric Point: pH value at which a molecule carries no ____

A

electrical charge

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27
Q

Isoelectric Point Equation
When it is an acidic amino acid, use ____.
When it is a basic amino acid, use ____.

A

pI = (pKaC + pKaN) /2

acidic: pI = (pKaC + pKaR) /2
basic: pI = (pKaR + pKaN) /2

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28
Q

Essential Amino Acids (PVT TIM HALL)

A

Phenylalanine, Valine, Threonine
Tryptophan, Isoleucine, Methionine
Histidine, Arginine, Leucine, Lysine

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29
Q

What is the Kreb’s Cycle?

A

The biosynthesis of non-nutritionally essential amino acids used to generate energy through oxidation of Acetyl-CoA

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30
Q

Peptide: a chain of ____ linked via ____

A

amino acid residues, amide bonds

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31
Q

Free amino acids can move from ____ to the brain, gut, kidney (produces ____), or the liver (produces ____ and ____).

A

muscle, NH3, urea, glucose

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32
Q

What is the Urea Cycle?

A

A process which converts toxic ammonia into urea by use of amino acids and a series of enzymes

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33
Q

Protein Synthesis:

DNA –1–> mRNA –2–> Proteins –> Post-Translational Modifications

A
  1. Transcription (occurs in Nucleus)

2. Translation (occurs in Cytosol)

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34
Q

Steps of Translation (3 total)

A
  1. Initiation
  2. Elongation
  3. Termination
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35
Q

Primary Structure

A

amino acid sequence

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36
Q

Secondary Structure

A

folding of segments of polypeptides into geometrically ordered units (alpha-helix or beta-sheets); governed by hydrogen bonds

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37
Q

Tertiary Structure

A

the assembly of secondary structural units into larger functional units such as the mature protein and its components domains; governed by non-covalent bonds and disulfide bridges

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38
Q

Quaternary Structure

A

the number and types of polypeptide units of oligomeric proteins and their spatial arrangements

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39
Q

Post-Translational Modifications of Proteins

1. Proteolysis

A

PRODUCT: protein cleavage
INVOLVED ENZYME: proteases
PURPOSE: protein maturation

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40
Q

Post-Translational Modifications of Proteins

2. Acetylation Deacetylation

A

PRODUCT: acetyl N-terminal, acetyl side chain of Lys residues
INVOLVED ENZYME: acetylase
PURPOSE: change charge binding; histone and gene regulation

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41
Q

Post-Translational Modifications of Proteins
3. Phosphorylation
Dephosphorylation

A 
PRODUCT: Ser-OH --> Ser-OP3
                    Thr-OH --> Thr-OP3
                    Tyr-OH --> Tyr-OP3
INVOLVED ENZYME: kinase phosphatase
PURPOSE: change charge; cell signaling
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42
Q

Post-Translational Modifications of Proteins

4. Lipid Attachment

A

PRODUCT: farnesylation
INVOLVED ENZYME: lipid transferase
PURPOSE: anchor proteins to membrane for regulation

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43
Q

Post-Translational Modifications of Proteins

5. Glycosylation

A

PRODUCT: addition of carbohydrates to Asn, Ser, Thr
INVOLVED ENZYME: glycosyl transferase
PURPOSE: glycoproteins; protection of cell surface

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44
Q

In what ways does glycosylation affect a protein? (6 total)

A

Affects solubility, stability, cellular localization, trafficking and clearance, immunogenicity, and self-recognition

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45
Q
  1. What classification of proteins contain keratins, cytoskeletal proteins, and extracellular matrix proteins?
  2. What are two examples of cytoskeletal proteins?
  3. What are four examples of extracellular matrix proteins?
A
  1. Structural Proteins (Fibrous)
  2. Actin and Myosins
  3. Collagens, Fibronectin, Laminin, Proteoglycans
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46
Q

What classification of proteins contains enzymes, receptors for signal transduction, antibodies, transcription factors, chaperons, carrier proteins, and growth factors?

A

Functional Proteins (Globular)

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47
Q

What is the function of myoglobin?

A

Stores oxygen in muscle

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48
Q

What is the function of hemoglobin?

A

Stores and transports oxygen in blood

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49
Q

Cytochrom C: heme-containing ____ localized in the ____ inner membrane and is involved in production of ____ via the ____ (oxidative phosphorylation)

A

protein, mitochondria, ATP, electron transport chain

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50
Q

Metabolic Disorders

1. Type I Diabetes

A

CAUSE / DEFICIENCY IN: insulin because immune system attacks insulin producing cell
TREATMENT: insulin

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51
Q

Metabolic Disorders

2. Type II Diabetes Mellitus

A

CAUSE / DEFICIENCY IN: either low insulin or insulin resistance
TREATMENT: insulin, diet, glucose-lowering medicine

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52
Q

Metabolic Disorders

3. Urea Cycle Disorder

A

CAUSE / DEFICIENCY IN: N-acetyl glutamate synthase; carbamoyl phosphate synthase, ornithine transcarbamylase; argininsuccinate synthase
TREATMENT: give the down stream metabolite

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53
Q

Metabolic Disorders

4. Phenylketonuria

A

CAUSE / DEFICIENCY IN: phenylalanine hydroxylase

TREATMENT: diet, enzyme substitutes

54
Q

Metabolic Disorders

5. Gaucher’s Disease

A

CAUSE / DEFICIENCY IN: beta-glucoereberosidase

TREATMENT: enzyme replacement therapy

55
Q

Metabolic Disorders

6. Lactose Intolerance

A

CAUSE / DEFICIENCY IN: lactase

TREATMENT: diet, enzyme substitutes

56
Q

Dimerizing Receptors: lead to downstream ____ of ____-binding proteins and regulation of gene expression

A

phosphorylation of DNA

57
Q

What are the two pathways of protein degradation?

A

ATP-Independent and ATP + Ubiquitin Dependent

58
Q

Describe ATP-dependent protein degradation.

A

requires ATP, ubiquitin, and ubiquitinating enzymes

59
Q

Describe ATP-independent protein degradation.

A

specific to blood circulating proteins; first they are deglycosylated then degraded by lysosomes in liver cells

60
Q 
Lipid Class
Fatty Acids (FA)
A

produce energy, synthesis of triglycerides and phospholipids

61
Q

Lipid Class

Triglycerides (TG)

A

lipid storage (unused calories)

62
Q

Lipid Class

Phospholipids

A

cell membranes, cell signaling

63
Q

Lipid Class

Cholesterol

A

cell membranes, steroids, vitamin D, and bile acid synthesis

64
Q

Lipid Class

Bile Acids

A

solubilize dietary fat and oil and help with their intestinal absorption

65
Q

Lipid Class

Eicosanoids

A

signaling, regulation of inflammation

66
Q

Lipid Class

Sphingolipids

A

cell signaling; cell membrane stabilization; protection against harmful chemicals

67
Q

What are fatty acids? They occur in the body mainly as ____, and are present in natural fats, and contain an ____ number of carbons

A

esters, even

68
Q

What are Omega 3 Fatty Acids and what is their function?

A

essential polyunsaturated fatty acids,

decrease inflammation and glucose in the body

69
Q

Triglycerides: storage form of ____ in ____

A

fatty acids, tissues

70
Q

What is Hypertriglyceridemia?

A

high levels of T.G. that could lead to complications such as heart attacks, diseases, strokes, obesity, and metabolic syndromes

71
Q

Classes of Phospholipids (4 total)

A

Choline, Ethanolamine, Serine, Inositol

72
Q

Platelet Activating Factors (PAF): functions as a mediator of ____, acute ____ reactions, and _____ shock

A

hypersensitivity, inflammatory, anaphylactic

73
Q

Fatty Acid Synthesis: completed via ____ involving ____ and requires ____

A

elongation, acyl-CoA, ATP

74
Q

Fatty Acid Beta-Oxidation (Degradation): occurs in the ____ for fatty acids less than ____ carbons

A

mitochondria, 18

75
Q

Functions of Cholesterol (4 total)

A
  1. component of the plasma membrane
  2. regulates membrane fluidity
  3. involved in biosynthesis of steroid hormones
  4. component of lipoproteins (VLDL, LDL, and HDL)
76
Q

What can Cholesterol be metabolized into? (3 total)

A

Steroid Hormones, Vitamin D, and Bile Acids

77
Q

What is Hypercholesterolemia?

And why are Statins prescribed to treat it?

A

Hypercholesterolemia is high levels of circulating cholesterol. Statins inhibit the first step in cholesterol synthesis.

78
Q

What are Eicosanoids? Give three examples.

A

Eicosanoids are derived from arachidonic acid. They regulate inflammation, immune response, cell growth, and blood pressure. They can also cause fever and contribute to the perception of pain.
Examples - Prostaglandins, Leukotrienes, and Thromboxanes

79
Q

Monosaccharides (Formula)

80
Q 
Classifications of Monosaccharides
KETOSES (NUMBER OF CARBONS)
1. Dihydroxyacetone (3) 
2. Erythrulose (4)
3. Ribulose (5)
4. Fructose (6)
5. Sedoheptulose (7)
A 
ALDOSES 
Glycerose (3) 
Erythrose (4)
Ribose (5)
Glucose (6)
------------ (7)
81
Q

Aldoses (Functional Group)

A

Terminal CHO

82
Q

Ketoses (Functional Group)

83
Q

Sugars exist in the ____ - form in the body.

84
Q

alpha-conformation

A

substituent on carbon-1 is in the opposite direction of the substituent on carbon-6

85
Q

beta-conformation

A

substituent on carbon-1 is in the same direction of the substituent on carbon-6

86
Q

Glycosidic Linkages

  1. Starch
  2. Cellulose
  3. Glycogen
A
  1. alpha-(1->4) glycosidic linkage
  2. beta-(1->4) glycosidic linkage
  3. alpha-(1->6) glycosidic linkage
87
Q

What is Glycogenesis? (2 words)

How much ATP does it utilize?

A

Glycogen Synthesis

1 ATP

88
Q 
Cellular Respiration
1 Acetyl-CoA = \_\_\_\_
1 NADH = \_\_\_\_
1 FADH2 = \_\_\_\_
1 molecule of glucose produces \_\_\_\_ molecules of \_\_\_\_
A

1 ATP, 3 NADH, 1 FADH2
2.5 ATP
1.5 ATP
two, pyruvate

89
Q

“N-Linked” Glycan

A

Asn -any amino acid (except Pro)- Ser/Thr

90
Q

“O-Linked” Glycan

A

linkage between the monosaccharide N-Acetylgalactosamine and the side chain of a serine or threonine

91
Q

The extracellular side of the plasma membrane is composed of ____, ____, and ____.

A

Glycolipids, Glycoproteins, and Carbohydrates

92
Q

The intracellular side of the plasma membrane is composed of ____, ____, and ____.

A

Cholesterol, Proteins, and Phospholipids

93
Q

Increased membrane fluidity can be associated with a) saturated fatty acids or b) unsaturated fatty acids?

94
Q

Only CO2, N2, O2, and ____-soluble molecules can pass through the cell membrane.

95
Q

How do other molecules move through the cell membrane?

  1. Large molecules bind to ____.
  2. Glucose binds to ____.
  3. Ions are transported via ____.
A
  1. receptors
  2. ping-pong receptors
  3. pumps or ion channels
96
Q

What is the permeability coefficient?

A

a measure of the ability of a molecule to diffuse across permeability membrane

97
Q

Membrane Transport of Small Molecules
__1.__ (along gradient) __2.__ (against gradient)
__1a.__ __1b.__

A
  1. Passive Transport
    1a. Simple Diffusion
    1b. Facilitated Diffusion
  2. Active Transport
98
Q

Types of Transporters (3 total)

A

Uniport, Symport, Antiport

99
Q

Define ion channels.
Are they always open? (What type are open?)
What affects their permeability?

A

transmembrane proteins that allow the selective entry of various ions

  • not always open except for aquaporins (water channels)
  • permeability dependent on size, extent of hydration, and extent of charge density on the ion
100
Q 
ATP-Driven Active Transporters:
P-Type - signifies \_\_\_\_
F-Type - signifies \_\_\_\_
V-Type - signifies \_\_\_\_
ABC-Type - signifies \_\_\_\_
A

P-Type - signifies phosphorylation
F-Type - signifies energy coupling factors
V-Type - signifies vacuolar
ABC-Type - signifies ATP-binding cassette transporter

101
Q

What are two types of Endocytosis?

A
  1. Fluid-Phase Pinocytosis: random and nondirected
  2. Absorptive (Receptor-Mediated Endocytosis): selective and occurs in coated pits lined with the protein clathrin -> LDL receptors bind and undergo endocytosis and metabolize into amino acids and cholesterol
102
Q

Special Transport Features

  1. localized microdomains rich in specific lipids and signaling proteins
  2. invagination in the plasma membrane formed by the protein caveolin (dimer)
  3. allows direct flow of molecules from one cell to another
A

Special Transport Features

  1. Lipid Rafts
  2. Caveolae
  3. Gap Junctions
103
Q

____ affecting membrane proteins cause cause diseases.

  1. ABNORMALITY: mutations in the gene encoding the fibroblast growth factor receptor 3
  2. ABNORMALITY: mutations in the gene encoding the LDL receptor
  3. ABNORMALITY: mutations in the gene encoding the CFTR protein, a Cl- transporter
A

Mutations

  1. Achondroplasia
  2. Familial Hypercholesterolemia
  3. Cystic Fibrosis
104
Q

Purine or Pyrimidine + Sugar = ____

A

Nucleosides (Ribonucleic Acid or Deoxyribonucleic Acid)

105
Q

Purine or Pyrimidine + Sugar + Phosphates = ____

A

Nucleotides (i.e. Oligonucleotides (DNA, mRNA, miRNA, tRNA), energy (ATP, GTP), if cyclic then messengers (cAMP, cGMP)

106
Q

Purine or Pyrimidine + Vitamins = ____

107
Q

Purine Bases

A

Adenine, Guanine

108
Q

Pyrimidine Bases

A

Cytosine, Uracil, Thymine

109
Q

List three differences between DNA and RNA.

A
  1. Thymine vs. Uracil
  2. 2’-deoxyribose vs. ribose
  3. double-stranded vs. single-stranded
110
Q

How many sets of DNA do humans have?

How many chromosomes do humans have?

A

23 sets of DNA (diploid)

46 chromosomes

111
Q

What direction does DNA Replication occur in?

A

5’ -> 3’ direction

112
Q

Three Major Defects in DNA:

  1. ____ hint: Down Syndrome
  2. ____
  3. ____ hint: Cancer
A
  1. Triosomy 21
  2. Monosomy X
  3. Oncogenic Aneuploidy
113
Q

How does Oncogenic Aneuploidy occur?

A

During mitosis or meiosis, partial crossing over occurs during metaphase.

114
Q

DNA Replication in Eukaryotic Cells:

  1. Binding of __a__ proteins
  2. Binding of DNA __b__
  3. Loading of DNA __b__ onto DNA strand
  4. DNA __b__ unwinds the DNA double strand
  5. RNA __c__ synthesis enables DNA __d__ to start first DNA chain
  6. Formation of __e__
A 
a - initiator
b - helicase
c - primer
d - polymerase
e- replication forks
115
Q

Proteins Involved in DNA Replication:
FUNCTION - deoxynucleotide polymerization
FUNCTION - ATP-driven processive unwinding of DNA
NAME - Topoisomerases
NAME - DNA Primase
FUNCTION - prevents premature reannealing of dsDNA
FUNCTION - seals the single strand nick between the nascent chain and Okazaki fragments on lagging strand

A

Proteins Involved in DNA Replication:
NAME - DNA Polymerase
NAME - Helicases
FUNCTION - relieves torsional strain that results from helicase-induced unwinding
FUNCTION - intiates synthesis of RNA primers
NAME - Single-Strand Binding Proteins (SSBs)
NAME - DNA Ligase

116
Q

What are the three types of DNA damage?

A
  1. Natural (Replication)
  2. Spontaneous / Endogenous
  3. Exogenous
117
Q

What are the three examples of Endogenous DNA damage?

A

Deamination, Oxidation, Methylation

118
Q

What are the three examples of Exogenous DNA damage?

A

UV Radiation, Ionizing Radiation, Drugs and Environmental Exposure

119
Q

mRNA

120
Q

tRNA

A

transfer; links mRNA to amino acid

121
Q

rRNA

A

machinery for translation

122
Q

miRNA

A

inhibit / modulate translation

123
Q

snRNA

A

intron removal

124
Q

IncRNA

A

regulate mRNA and gene transcription via RNA Pol II

125
Q

Are exons or introns expressed?

126
Q

Which group of drugs inhibits RNA synthesis by targeting RNA Polymerase?

A

Rifamycin Group (antimycobacterials)

127
Q

What must occur during Initiation?
_RNA must associate with _RNA
Location: ____ codon (____)

A

mRNA must associate with rRNA

Location: “start” codon (Met)

128
Q

What must occur during Elongation?
_RNA is read in sets of three nucleic acids (____)
Growing chain in _-site
Amino acid added in _-site and shifted ____

A

mRNA is read in sets of three nucleic acids (codon)
Growing chain in P-site
Amino acid added in A-site and shifted down

129
Q

When does chain elongation stop in Termination?

A

when tRNA associating lacks an amino acids

130
Q

What type of genetic disease is Duchenne Muscular Dystrophy?
How often does it occur?
How is it caused?

A

X-linked
1 in 5,000 male births
caused by missense mutation in the dystrophin gene (dystrophin is an essential protein that maintains muscle fiber integrity)

501: Foundations I (2 decks)

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