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501: Foundations I > Exam I > Flashcards

Exam I Flashcards

(130 cards)

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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
Acidic Amino Acids (Negatively-Charged) (2 total)
Aspartic Acid, Glutamic Acid
26
Isoelectric Point: pH value at which a molecule carries no ____
electrical charge
27
Isoelectric Point Equation When it is an acidic amino acid, use ____. When it is a basic amino acid, use ____.
pI = (pKaC + pKaN) /2 acidic: pI = (pKaC + pKaR) /2 basic: pI = (pKaR + pKaN) /2
28
Essential Amino Acids (PVT TIM HALL)
Phenylalanine, Valine, Threonine Tryptophan, Isoleucine, Methionine Histidine, Arginine, Leucine, Lysine
29
What is the Kreb's Cycle?
The biosynthesis of non-nutritionally essential amino acids used to generate energy through oxidation of Acetyl-CoA
30
Peptide: a chain of ____ linked via ____
amino acid residues, amide bonds
31
Free amino acids can move from ____ to the brain, gut, kidney (produces ____), or the liver (produces ____ and ____).
muscle, NH3, urea, glucose
32
What is the Urea Cycle?
A process which converts toxic ammonia into urea by use of amino acids and a series of enzymes
33
Protein Synthesis: | DNA --1--> mRNA --2--> Proteins --> Post-Translational Modifications
1. Transcription (occurs in Nucleus) | 2. Translation (occurs in Cytosol)
34
Steps of Translation (3 total)
1. Initiation 2. Elongation 3. Termination
35
Primary Structure
amino acid sequence
36
Secondary Structure
folding of segments of polypeptides into geometrically ordered units (alpha-helix or beta-sheets); governed by hydrogen bonds
37
Tertiary Structure
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
38
Quaternary Structure
the number and types of polypeptide units of oligomeric proteins and their spatial arrangements
39
Post-Translational Modifications of Proteins | 1. Proteolysis
PRODUCT: protein cleavage INVOLVED ENZYME: proteases PURPOSE: protein maturation
40
Post-Translational Modifications of Proteins | 2. Acetylation Deacetylation
PRODUCT: acetyl N-terminal, acetyl side chain of Lys residues INVOLVED ENZYME: acetylase PURPOSE: change charge binding; histone and gene regulation
41
Post-Translational Modifications of Proteins 3. Phosphorylation Dephosphorylation
``` PRODUCT: Ser-OH --> Ser-OP3 Thr-OH --> Thr-OP3 Tyr-OH --> Tyr-OP3 INVOLVED ENZYME: kinase phosphatase PURPOSE: change charge; cell signaling ```
42
Post-Translational Modifications of Proteins | 4. Lipid Attachment
PRODUCT: farnesylation INVOLVED ENZYME: lipid transferase PURPOSE: anchor proteins to membrane for regulation
43
Post-Translational Modifications of Proteins | 5. Glycosylation
PRODUCT: addition of carbohydrates to Asn, Ser, Thr INVOLVED ENZYME: glycosyl transferase PURPOSE: glycoproteins; protection of cell surface
44
In what ways does glycosylation affect a protein? (6 total)
Affects solubility, stability, cellular localization, trafficking and clearance, immunogenicity, and self-recognition
45
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?
1. Structural Proteins (Fibrous) 2. Actin and Myosins 3. Collagens, Fibronectin, Laminin, Proteoglycans
46
What classification of proteins contains enzymes, receptors for signal transduction, antibodies, transcription factors, chaperons, carrier proteins, and growth factors?
Functional Proteins (Globular)
47
What is the function of myoglobin?
Stores oxygen in muscle
48
What is the function of hemoglobin?
Stores and transports oxygen in blood
49
Cytochrom C: heme-containing ____ localized in the ____ inner membrane and is involved in production of ____ via the ____ (oxidative phosphorylation)
protein, mitochondria, ATP, electron transport chain
50
Metabolic Disorders | 1. Type I Diabetes
CAUSE / DEFICIENCY IN: insulin because immune system attacks insulin producing cell TREATMENT: insulin
51
Metabolic Disorders | 2. Type II Diabetes Mellitus
CAUSE / DEFICIENCY IN: either low insulin or insulin resistance TREATMENT: insulin, diet, glucose-lowering medicine
52
Metabolic Disorders | 3. Urea Cycle Disorder
CAUSE / DEFICIENCY IN: N-acetyl glutamate synthase; carbamoyl phosphate synthase, ornithine transcarbamylase; argininsuccinate synthase TREATMENT: give the down stream metabolite
53
Metabolic Disorders | 4. Phenylketonuria
CAUSE / DEFICIENCY IN: phenylalanine hydroxylase | TREATMENT: diet, enzyme substitutes
54
Metabolic Disorders | 5. Gaucher's Disease
CAUSE / DEFICIENCY IN: beta-glucoereberosidase | TREATMENT: enzyme replacement therapy
55
Metabolic Disorders | 6. Lactose Intolerance
CAUSE / DEFICIENCY IN: lactase | TREATMENT: diet, enzyme substitutes
56
Dimerizing Receptors: lead to downstream ____ of ____-binding proteins and regulation of gene expression
phosphorylation of DNA
57
What are the two pathways of protein degradation?
ATP-Independent and ATP + Ubiquitin Dependent
58
Describe ATP-dependent protein degradation.
requires ATP, ubiquitin, and ubiquitinating enzymes
59
Describe ATP-independent protein degradation.
specific to blood circulating proteins; first they are deglycosylated then degraded by lysosomes in liver cells
60
``` Lipid Class Fatty Acids (FA) ```
produce energy, synthesis of triglycerides and phospholipids
61
Lipid Class | Triglycerides (TG)
lipid storage (unused calories)
62
Lipid Class | Phospholipids
cell membranes, cell signaling
63
Lipid Class | Cholesterol
cell membranes, steroids, vitamin D, and bile acid synthesis
64
Lipid Class | Bile Acids
solubilize dietary fat and oil and help with their intestinal absorption
65
Lipid Class | Eicosanoids
signaling, regulation of inflammation
66
Lipid Class | Sphingolipids
cell signaling; cell membrane stabilization; protection against harmful chemicals
67
What are fatty acids? They occur in the body mainly as ____, and are present in natural fats, and contain an ____ number of carbons
esters, even
68
What are Omega 3 Fatty Acids and what is their function?
essential polyunsaturated fatty acids, | decrease inflammation and glucose in the body
69
Triglycerides: storage form of ____ in ____
fatty acids, tissues
70
What is Hypertriglyceridemia?
high levels of T.G. that could lead to complications such as heart attacks, diseases, strokes, obesity, and metabolic syndromes
71
Classes of Phospholipids (4 total)
Choline, Ethanolamine, Serine, Inositol
72
Platelet Activating Factors (PAF): functions as a mediator of ____, acute ____ reactions, and _____ shock
hypersensitivity, inflammatory, anaphylactic
73
Fatty Acid Synthesis: completed via ____ involving ____ and requires ____
elongation, acyl-CoA, ATP
74
Fatty Acid Beta-Oxidation (Degradation): occurs in the ____ for fatty acids less than ____ carbons
mitochondria, 18
75
Functions of Cholesterol (4 total)
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
What can Cholesterol be metabolized into? (3 total)
Steroid Hormones, Vitamin D, and Bile Acids
77
What is Hypercholesterolemia? | And why are Statins prescribed to treat it?
Hypercholesterolemia is high levels of circulating cholesterol. Statins inhibit the first step in cholesterol synthesis.
78
What are Eicosanoids? Give three examples.
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
Monosaccharides (Formula)
CnH2nOn
80
``` Classifications of Monosaccharides KETOSES (NUMBER OF CARBONS) 1. Dihydroxyacetone (3) 2. Erythrulose (4) 3. Ribulose (5) 4. Fructose (6) 5. Sedoheptulose (7) ```
``` ALDOSES Glycerose (3) Erythrose (4) Ribose (5) Glucose (6) ------------ (7) ```
81
Aldoses (Functional Group)
Terminal CHO
82
Ketoses (Functional Group)
C=O
83
Sugars exist in the ____ - form in the body.
D
84
alpha-conformation
substituent on carbon-1 is in the opposite direction of the substituent on carbon-6
85
beta-conformation
substituent on carbon-1 is in the same direction of the substituent on carbon-6
86
Glycosidic Linkages 1. Starch 2. Cellulose 3. Glycogen
1. alpha-(1->4) glycosidic linkage 2. beta-(1->4) glycosidic linkage 3. alpha-(1->6) glycosidic linkage
87
What is Glycogenesis? (2 words) | How much ATP does it utilize?
Glycogen Synthesis | 1 ATP
88
``` Cellular Respiration 1 Acetyl-CoA = ____ 1 NADH = ____ 1 FADH2 = ____ 1 molecule of glucose produces ____ molecules of ____ ```
1 ATP, 3 NADH, 1 FADH2 2.5 ATP 1.5 ATP two, pyruvate
89
"N-Linked" Glycan
Asn -any amino acid (except Pro)- Ser/Thr
90
"O-Linked" Glycan
linkage between the monosaccharide N-Acetylgalactosamine and the side chain of a serine or threonine
91
The extracellular side of the plasma membrane is composed of ____, ____, and ____.
Glycolipids, Glycoproteins, and Carbohydrates
92
The intracellular side of the plasma membrane is composed of ____, ____, and ____.
Cholesterol, Proteins, and Phospholipids
93
Increased membrane fluidity can be associated with a) saturated fatty acids or b) unsaturated fatty acids?
b
94
Only CO2, N2, O2, and ____-soluble molecules can pass through the cell membrane.
lipid
95
How do other molecules move through the cell membrane? 1. Large molecules bind to ____. 2. Glucose binds to ____. 3. Ions are transported via ____.
1. receptors 2. ping-pong receptors 3. pumps or ion channels
96
What is the permeability coefficient?
a measure of the ability of a molecule to diffuse across permeability membrane
97
Membrane Transport of Small Molecules __1.__ (along gradient) __2.__ (against gradient) __1a.__ __1b.__
1. Passive Transport 1a. Simple Diffusion 1b. Facilitated Diffusion 2. Active Transport
98
Types of Transporters (3 total)
Uniport, Symport, Antiport
99
Define ion channels. Are they always open? (What type are open?) What affects their permeability?
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
``` ATP-Driven Active Transporters: P-Type - signifies ____ F-Type - signifies ____ V-Type - signifies ____ ABC-Type - signifies ____ ```
P-Type - signifies phosphorylation F-Type - signifies energy coupling factors V-Type - signifies vacuolar ABC-Type - signifies ATP-binding cassette transporter
101
What are two types of Endocytosis?
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
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
Special Transport Features 1. Lipid Rafts 2. Caveolae 3. Gap Junctions
103
____ 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
Mutations 1. Achondroplasia 2. Familial Hypercholesterolemia 3. Cystic Fibrosis
104
Purine or Pyrimidine + Sugar = ____
Nucleosides (Ribonucleic Acid or Deoxyribonucleic Acid)
105
Purine or Pyrimidine + Sugar + Phosphates = ____
Nucleotides (i.e. Oligonucleotides (DNA, mRNA, miRNA, tRNA), energy (ATP, GTP), if cyclic then messengers (cAMP, cGMP)
106
Purine or Pyrimidine + Vitamins = ____
Coenzymes
107
Purine Bases
Adenine, Guanine
108
Pyrimidine Bases
Cytosine, Uracil, Thymine
109
List three differences between DNA and RNA.
1. Thymine vs. Uracil 2. 2'-deoxyribose vs. ribose 3. double-stranded vs. single-stranded
110
How many sets of DNA do humans have? | How many chromosomes do humans have?
23 sets of DNA (diploid) | 46 chromosomes
111
What direction does DNA Replication occur in?
5' -> 3' direction
112
Three Major Defects in DNA: 1. ____ hint: Down Syndrome 2. ____ 3. ____ hint: Cancer
1. Triosomy 21 2. Monosomy X 3. Oncogenic Aneuploidy
113
How does Oncogenic Aneuploidy occur?
During mitosis or meiosis, partial crossing over occurs during metaphase.
114
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 - initiator b - helicase c - primer d - polymerase e- replication forks ```
115
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
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
What are the three types of DNA damage?
1. Natural (Replication) 2. Spontaneous / Endogenous 3. Exogenous
117
What are the three examples of Endogenous DNA damage?
Deamination, Oxidation, Methylation
118
What are the three examples of Exogenous DNA damage?
UV Radiation, Ionizing Radiation, Drugs and Environmental Exposure
119
mRNA
messenger
120
tRNA
transfer; links mRNA to amino acid
121
rRNA
machinery for translation
122
miRNA
inhibit / modulate translation
123
snRNA
intron removal
124
IncRNA
regulate mRNA and gene transcription via RNA Pol II
125
Are exons or introns expressed?
exons
126
Which group of drugs inhibits RNA synthesis by targeting RNA Polymerase?
Rifamycin Group (antimycobacterials)
127
What must occur during Initiation? _RNA must associate with _RNA Location: ____ codon (____)
mRNA must associate with rRNA | Location: "start" codon (Met)
128
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 ____
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
When does chain elongation stop in Termination?
when tRNA associating lacks an amino acids
130
What type of genetic disease is Duchenne Muscular Dystrophy? How often does it occur? How is it caused?
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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