BioChem Flashcards
1
Q
Tuberous Sclerosis
What kind of inheritance?
Manifestations?
A
Autosomal Dominant w/ incomplete penetrance
Harmatomas of CNS and Retina, Adenoma Sebaceum (cutaneous angiofibroma), Mitral Reg, Ash-Leaf Spots on skin, Cardiac Rhabdomyomas, Mental Retardation, Renal Angiomyolipomas and Renal Cysts, Seizures, Increased incidence of astrocytomas
2
Q
Histones? Charge Amino Acids What do they form? What ties it together?
A
Positively charged
Lysine and Arginine
Octamer tied together by H1
3
Q
DNA methylation Which Nucleotides When in cell cycle? Function What organisms
A
C and A
Template strand is methylated during DNA replication which allows mismatch repair enzymes to distinguish between old and new strands
Prokaryotes
4
Q
What does Histone Methylation do?
A
Inactivates DNA
5
Q
What does Histone Acetylation do?
A
Relaxes DNA coiling allowing for transcription
6
Q
Purines
Names
Rings
What is it made from?
A
“PURe As Gold”
Adenine, Guanine
2 rings
Glycine, Aspartate, Glutamine
7
Q
Pyrimidines
Names
A
“CUT the PY”
Cytosine, Uracil, Thymine
8
Q
Molecular group on Guanine
A
Ketone
9
Q
Molecular group on Thymine
A
MeTHYl
10
Q
How is Uracil made?
A
Cytosine gets Deaminated
11
Q
RNA Nucleotides?
A
G-C, A-U
12
Q
DNA Nucleotides
A
G-C, A-T
13
Q
Which nucleotide bond is strongest
A
G-C has 3 hydrogen bonds
14
Q
How is DNA melting point affected
A
↑ GC content –> ↑ melting temperature
15
Q
Nucleoside
A
Base + Ribose
16
Q
Nucleotide
A
Base + Ribose + Phosphate linked by 3’5’ phosphodiester bond
17
Q
What makes up Pyrimidines
A
Aspartate and Carbamoyl Phosphate
18
Q
Basic schematic of de novo purine synthesis
A
Start with sugar + phosphate (PRPP)
Then add base
19
Q
Basic schematic of de novo pyrimidine synthesis
A
Make temporary base (orotic acid)
Add sugar + phosphate (PRPP)
Modify base
20
Q
Purine synthesis pathway
A
Ribose 5-P –> PRPP ->->-> IMP –> AMP and GMP
21
Q
Inhibition of de novo purine synthesis
A
6-mercaptopurine blocks de novo purine synthesis
22
Q
Production of deoxyribonucleotides
A
Ribonucleotide reductase converts ribonucleotides into deoxyribonucleotides
23
Q
CTP synthesis
A
Ribose 5-P –> PRPP
PRPP + Orotic Acid –> UMP –> UDP –> CTP
24
Q
dTMP synthesis
A
Ribose 5-P –> PRPP
PRPP + Orotic Acid –> UMP –> UDP –> [Ribonucleotide reductase] –> dUDP –> dUMP –> [Thymidylate Synthase] –> dTMP
25
What pathways is Carbamoyl Phosphate involved with?
de novo pyrimidine synthesis and urea cycle
26
Ornithine transcarbamoylase deficiency
What is it?
Findings
OTC is a key enzyme in the urea cycle
Deficiency leads to accumulation of carbamoyl phosphate which is then converted into orotic acid
↑ Orotic acid with hyperammonemia
27
What inhibits Ribonucleotide reductase
Hydroxy Urea
28
What inhibits Thymidylate Synthase?
5-Fluorouracil
29
What inhibits human Dihydrofolate reductase
| Net result?
Methotrexate
| ↓ dTMP
30
What inhibits bacterial Dihydrofolate reductase
| Net result?
Trimethoprim
| ↓ dTMP
31
THF and dTMP synthesis
THF --> N5N10 methylene THF --> [Thymidylate Synthase] --> DHF --> [Dihydrofolate reductase] --> THF
32
```
Orotic Aciduria
What is it?
Pathway involved?
Where is the defect?
Genetics
Findings
Treatment
```
```
Inability to convert orotic acid to UMP
de novo pyrimidine synthesis pathway
UMP synthase
Autosomal Recessive
↑ orotic acid in urine, Megaloblastic anemia (does not improve with B12 or folic acid), Failure to thrive, No hyperammonemia
Oral uridine administration
```
33
Adenine salvage pathway
Adenine + PRPP --> [APRT] --> AMP
| AMP can become Nucleic acids, Adenosine, or IMP
34
Fate of Adenosine in salvage pathway
Adenosine can become AMP or Adenosine deaminase (ADA) can turn it into Inosine
35
Fate of IMP in purine salvage pathway
Hypoxanthine + PRPP --> [HGPRT] --> IMP
| IMP can become inosine, AMP, or GMP
36
Fate of Inosine in Purine salvage pathway
Adenosine --> Inosine
| Inosine --> Hypoxanthine
37
Fate of Hypoxanthine in Purine salvage pathway
Hypoxanthine can become IMP, Inosine, or Xanthine
38
Fate of Guanine in Purine salvage pathway
Guanine +PRPP --> [HGPRT] --> GMP
Guanine --> Guanosine
Guanine --> Xanthine
39
Fate of Guanosine in Purine salvage pathway
GMP --> Guanosine
| Guanine ↔ Guanosine
40
Fate of GMP in Purine salvage pathway
GMP can be come Nucleic Acids, IMP or Guanosine
41
```
Adenosine Deaminase Deficiency
PathoPhys
Genetics
What does it lead to
Treatment
```
Excess ATP and dATP leads to an imbalance in nucleotide pool via feedback inhibition of ribonucleotide reductase thus preventing DNA synthesis thus ↓ Lymphocyte count
Autosomal recessive
SCID
1st disease to be treated by experimental human gene therapy
42
```
Lesch-Nyhan Syndrome
Deficiency
Metabolic result
Genetics
Findings
```
"He's Got Purine Recovery Trouble"
HGPRT mutation which converts hypxanthine into IMP and Guanine into GMP
Excessive uric acid production and de novo purine synthesis
X linked recessive
Retardation, Self-Mutilation, Aggression, Hyperuricemia, Gout, Choreoathetosis
43
```
Genetic Code Features
Unambiguous
Degenerate
Commaless
Universal
```
Each codon = 1 AA
Most AA are coded by multiple codons except for Methionine (AUG) and Tryptophan (UGG)
Nonoverlapping: fixed starting point at a continuous sequence of bases except in some viruses
Conserved throughout evolution except in human mitochondria
44
Silent mutation
Same AA usually at 3rd position of condon (tRNA wobble)
45
Missense mutation
Changed AA to a similar AA
46
Nonsense mutation
Early stop codon
47
Frameshift
Misreading of all downstream nucleotides resulting in truncated, nonfunctional protein
48
DNA topoisomerases
Function
What inhibits it
Creates a nick in the helix to relieve supercoil created during replication
Fluoroquinolones inhibit prokaryotic topoisomerase II
49
DNA pol III
What organisms?
Direction of synthesis
Other functions?
Prokaryotic only
5' --> 3'
Proofreads 3' to 5'
50
DNA pol I
What organisms
Function
Functions with directions
```
Prokaryotic only
Degrades RNA primer and replaces it with DNA
Synthesis 5' --> 3'
Proofreading 3' --> 5'
Exonuclease 5' --> 3'
```
51
DNA ligase
Catalyzes the formation of phosphodiesterase bonds within strand of dsDNA. Joins Okazaki fragments
52
Telomerase
Adds DNA to 3' end of chromosome to avoid loss of genetic material with every duplication
53
Nucleotide Excision repair
Process
What kind of lesions does it repair
Disease involving this pathway
Specific endonucleases release the oligonucleotide-containing damaged bases. Then DNA pol and Ligase fill and reseal the gap
Repairs bulky helix distorting lesions
Xeroderma pigmentosum: Prevents repair of pyrimidine dimers because of UV light
54
Base Excision repair
Process
What kind of lesions does it repair?
Specific glycosylases recognize and remove damaged bases. Apurinic/Apyrimidinic endonucleases cut DNA at both sites. Empty sugar is removed. Gap is filled in and resealed
Important in reapir of spontaneous/toxic deamination
55
Mismatch Repair
Process
Disease
Newly synthesized strand is recognized, mismatched nucleotides are removed and gap is filled and resealed
Mutated in Hereditary NonPolyposis Colorectal Cancer (HNPCC)
56
Nonhomologous end joining
Process
Requirements
Disease
Brings together 2 ends of DNA fragments to repair double stranded breaks
No requirement for homology
Mutated in ataxia telangiectasia
57
Direction of DNA and RNA synthesis?
| Energy source?
5' --> 3'
| 5' end of dNTP
58
In which direction is mRNA read?
5' --> 3'
59
Direction of Protein Synthesis
N to C
60
Most abundant type of RNA
rRNA
61
Ways to remember types of RNA?
"Rampant, Massive, Tiny"
62
Eukaryotic start codon
"AUG inAUGurates protein synthesis"
| AUG (rarely GUG) which codes for Methionine
63
Prokaryotic start codon
AUG which codes for formylmethionine
64
mRNA stop codons
UGA: U Go Away
UAA: U Are Away
UAG: U Are Gone
65
Promoter code
TATA Box
| TATAAT and CAAT
66
Start of transcription numbering
+1
67
Termination signal
AATAAA
68
Eukaryotic RNA pol
I, II, III
Functions
Numbered in order that they are used in protein synthesis
I: rRNA
II: mRNA - can open DNA at promoter site
III: tRNA
No proofreading function but can initate chains
69
Prokaryotic RNA pol
1 RNA pol (multisubunit complex) makes all 3 kinds of RNA
70
What inhibits RNA pol II
| What does it lead to
α-amanitin (from mushroom)
| Hepatotoxicity if ingested
71
RNA processing in eukaryotes
What is initial transcript called?
What is it called if destined for transcription?
Where does processing occur?
Heterogenous nuclear RNA
pre-mRNA
Processing occurs in the nucleus
72
RNA processing in eukaryotes
Capping on 5' end with 7-methylguanosine
Polyadenylation an 3' end
Splicing out of introns
73
What is required for RNA to be transported out of the nucleus
Only processed RNA can be transported out of the nucleus
74
Polyadenylation
What enzyme does it?
Template?
Signal
Poly-A polymerase
Does not require a template
AAUAAA
75
Steps of Splicing pre-mRNA
```
Primary transcript combines with snRNPs (small nuclear ribonucleoproteins) and other proteins to form a spliceosome
Lariat shaped (looped) intermediate is generated
Lariat is released to remove intron precisely and join 2 exons
```
76
Disease involving snRNPs
Lupus: autoAbs to spliceosomal snRNPs
77
```
tRNA
Length
Secondary structure
What is on end?
Which end binds AAs
```
75-90 NTs
Cloverleaf form
On 3' end is 5' CCA 3' along with a high percentage of chemically modified bases
3' is bound to AA
78
tRNA Charging
Enzyme
Proofreading
Energy
Aminoacyl-tRNA synthetase
Scrutinizes AA before and after it binds tRNA
If incorrect, bond is hydrolyzed
AA-tRNA bond has energy for formation of peptide bond
79
Tetracyclines
Bind 30S subunit and prevents attachment of aminoacyl tRNA to A site
80
Eukaryote Ribosomes
Even #s
| 40S and 60S
81
PrOkaryote Ribosomes
Odd #s
| 30S and 50S
82
Protein synthesis initiation
Activated by GTP hydrolysis
| Initiation Factors help assemble 40S ribsomal subunit with the initiator tRNA and are then released
83
Protein synthesis Elongation
"Going APE"
1. Aminoacyl-tRNA binds A site (except initiator methionine)
2. rRNA catalyzes peptide bond formation transferring polypeptide into A site
3. Peptidyl tRNA moved into P site and empty tRNA moves to E site
84
Protein synthesis Termination
Stop codon recognized by release factors and complete protein is released from ribosome
85
Aminoglycosides
Bind 30S and inhibit formation of initiation complex and cause misreading of mRNA
86
Chloramphenicol
Binds 50S and inhibits peptidyl transferase
87
Macrolides
Bind 50S and prevent release of uncharged tRNA after it has donated its AA
88
Process of Proteasomal degradation
Attachment of Ubiquitin tags them for breakdown
89
Stages of cell cycle
G1 --> [Rb, p53] --> S --> G2 --> Mitosis
90
Interphase
G1, S, and G2
91
Stages of mitosis
Prophase, Metaphase, Anaphase, Telophase
92
Regulation of Cell Cycle
CDKs
Cylcins
Cyclin-CDK complexes
CDKs are constitutively present and inactive
Cyclins are regulatory and are produced in a phase specific manner
Cyclin-CKD complexes activate and the inactivate for cell cycle to progress
93
Tumor Suppressors
Names
Function
p53 and Hypophosphorylated Rb
| Normally inhibit G1 to S progression
94
Permanent cell type
Phase
What do they form
Examples
Remain in G0
Regenerate from stem cells
Neurons, Skeletal muscle, Cardiac muscle, RBCs
95
Stable cell types
Name
Phase
Examples
Quiescent
Enter G1 from G0 when stimulated
Hepatocytes and Lymphocytes
96
Labile cells
Phase
Examples
Never go to G0. Divide rapidly with a short G1
| Bone marrow, Gut epithelium, Skin, Hair follicles, Germ cells
97
Rough Endoplasmic Reticulum
What kind of proteins are synthesized here?
Protein modifications
Site of synthesis of secretory (exported) proteins
| N linked oligosaccharide addition to many proteins
98
Nissl Bodies
```
RER in neurons
Synthesizes ChAT (choline acetyltransferase) to make ACh and peptide NTs
```
99
What do free ribosomes produce
Cytosolic and organellar proteins
100
Which kind of cells are rich in RER?
Mucus-secreting goblet cells of SI and Ab secreting plasma cells
101
Smooth Endoplasmic Reticulum
What is synthesized here?
Which cells are rich in it?
Site of steroid synthesis and detoxification of drugs and poisons
Liver hepatocytes and steroid hormone-producing cells of adrenal cortex are rich in SER
102
Modifications that take place in Golgi?
Modifies N-oligosaccharides on Asparagine
| Adds O-oligosaccharides on Serine and Threonine
103
What directs proteins to lysosomes
Mannose-6-Phosphate added in lysosomes
104
I cell disease
Genetics
PathoPhys
Presentation
Inherited lysosomal storage disorder
Failure of addition of mannose-6-phosphate in golgi means enzyme are directed outside of cell instead of lysosomes
Coarse facial hair, Clouded corneas, Restricted joint movement, High plasma levels of lysosomal enzymes. Often fatal in childhood
105
Vesicle trafficking proteins
COPI
COPII
Clathrin
COPI: Retrograde (Golgi --> Golgi, Golgi --> ER)
COPII: Anterograde (Golgi --> Golgi, ER --> Golgi)
Clathrin: trans-Golgi --> lysosomes, Plasma membrane --> Endosomes (receptor mediated endocytosis)
106
Peroxisomes
Membrane enclosed organelle involved in catabolism of very long fatty acids and AA
107
Proteasomes
Barrel shaped protein complex that degrades damaged or unnecessary proteins tagged for destruction by ubiquitin
108
```
Microtubules
Composition
What is each dimer bound to?
What cellular structures does it make up? What functions are they involved with?
How does it grow and collapse?
```
α and β subunits
Each dimer has 2 GTPs bound to it
Flagella, Cilia, Mitotic spindles, Centrioles
Slow Axonal Transport and Cell Movement
Grows slowly, collapses quickly
Involved in slow axoplasmic transport in neurons
109
Molecular motor proteins
Dynein: retrograde in MTs (+ --> -)
Kinesin: anterograde in MTs (- --> +)
110
Drugs that act on MTs
Mebendazole/Thiabendazole: antihelminthic (prevents polymerization)
Griseofulvin: antifungal (prevents polymerization)
Vincristine/Vinblastine: anticancer (prevents polymerization)
Paclitaxel: anti-breast cancer (Stabilizes MTs)
Colchicine: antigout (prevents polymerization)
111
Chediak-Higashi Syndrome
Where is the mutation?
PathoPhys
Presentation
Mutation in lysosomal trafficking regulator gene (LYST)
LYST required for MT dependent sorting of endosomal proteins into late multivesicular endosomes
Recurrent pyogenic infections, Partial albinism, Peripheral neuropathy
112
Cilia
Structure
Motor proteins
Disease
9+2 arrangement of MTs. 9 doublets of MTs + 2 individual MT in middle
Dynein links peripheral 9 doublets
Kartagener's Syndrome
113
Kartagener's Syndrome
PathoPhys
Presentation
Associated with what developmental defect
Immotile cilia due to dynein arm defect
Male infertility, ↓ female fertility, Bronchiectasis, Recurrent sinusitis
Associated with sinus inversus
114
Actin and Myosin functions
Microvilli, Muscle contraction, Cytokinesis, Adherens junctions
115
Intermediate filament names and stains
```
Vimentin: Connective tissue
Desmin: Muscle
Cytokeratin: Epithelial cells
Glial Fibrillary Acid Protein (GFAP): NeuroGlia
Neurofilaments: Neurons
```
116
Plasma Membrane composition
Cholesterol, Phospholipids, Sphingolipids, Glycolipids, and Proteins
117
When is Na/K APTase phosphorylated
When open to extracellular side
118
Ouabain
Inhibits Na/K ATPase by binding to K site
119
Cardiac Glycosides
Names
MoA
Digoxin and Digitoxin
| Inhibits Na/K ATPase leading indirectly to increased Ca --> increased contractility
120
Most abundant protein in the human body
Collagen
121
Type I collagen
Frequency
Where is it present?
Disease
Most common collagen (90%)
Bone, Skin, Tendon, Dentin, Fascia, Cornea, Late Wound Repair
Defective in Osteogenesis Imperfecta
122
Where is type II collagen
Cartilage (including hyaline, Vitreous body, Nucleus pulposus
123
Type III collagen
Where is it present
Disease
Reticulin - skin, blood vessels, uterus, fetal tissue, granulation tissue
Ehlers-Danlos (vascular type)
124
Type IV collagen
Where is it present
Disease
```
Basement membrane (basal lamina)
Alport Syndrome
```
125
Collagen mnemonic
```
"Be (So Totally) Cool, Read Books"
I: Bone, Skin, Tendon
II: Cartilage
III: Reticulin
IV: Basement Membrane
```
126
Collagen synthesis inside the fibroblasts
1. RER: translation of α chains (preprocollagen)
2. ER: Hydroxylation of specific proline and lysine residues (requires VitC)
3. ER: Glycosylation of pro-α-chain hydroxylysine residues
4. Formation of procollagen via hydrogen and disulfide bonds (triple helix of 3 α chains)
5. Exocytosis
127
```
Osteogenesis imperfecta
Type of collagen
PathoPhys
Genetics
Presentation
```
```
Type I collagen defect
Problem forming triple helix of collagen α chains
Genetic bone disorder caused by a variety of gene defects but most common form is Autosomal Dominant
Brittle bones (multiple fractures with minimal trauma), Blue sclerae (translucent connective tissue over choroidal veins), Hearing loss (abnormal middle ear bones), Dental imperfections (lack of dentin)
```
128
Collagen synthesis outside of fibroblasts
1. Cleavage of disulfide rich terminal regions of procollagen forming insoluble tropocollagen
2. Reinforcement of many staggered tropocollagen molecules by covalent lysine-hydroxylysine cross linkage (by Cu2+ containing lysyl oxidase)
129
```
Ehlers-Danlos
Type of collagen involved?
PathoPhys
Presentation
# of types
Inheritance
Associations
Don't confuse w/
```
Type III or V defect
Problems with cross linking by Cu2+ containing lysyl oxidase
Hyperextensible skin, Easy bleeding and bruising, Hypermobile joints
6 types
Can be AD or AR
Joint dislocation, berry aneurysm, organ rupture
Marfan's
130
VitC deficiency
Scurvy
131
Alport Syndrome
Type of collagen involved
Inheritance
Presentation
Type IV
Variety of genetic defects but most commonly X linked recessive
Progressive hereditary nephritis, deafness, and ocular disturbances
132
```
Elastin
What is it? Where is it?
What is it made of?
Scaffolding?
Where does cross-linking take place?
What does cross-linking accomplish?
What breaks it down?
```
Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect verbetrae --> relaxed and stretched conformations)
Rich in proline and glycine (nonhydroxylated forms)
Tropoelastin with fibrillin scaffolding
Cross-linking takes place extracellularly and gives elastin its elastic properties
Broken down by elastase (which is normally inhibited by α1 antitrypsin)
133
What causes wrinkles of aging?
Reduced collagen and elastin production
134
Southern Blot
DNA electrophoresed, transfered to filter, denatured, labeled with probe
135
Blots mnemonic
SNoW DRoP
Southern - DNA
Northern - RNA
Western - Protein
136
Northern Blot
RNA used
137
Western Blot
Protein used
138
Southwestern Blot
Identifies DNA-Binding Proteins using labeled oligonucleotide probes
139
Microarrays
Nucleic acid sequences arranged on a grid and samples hybridize to the chip
Can detect SNPs
140
Enzyme-Linked Immunosorbent Assay
Indirect
Direct
Indirect: Test antigen to see if specific Ab is in pt's blood. Secondary Ab coupled to a color generating enzyme is added to detect 1st Ab
Direct: Test Ab coupled to a color generating enzyme to see if a specific antigen is present in pt's blood
141
Fluorescence in situ Hybridization (FISH)
Fluorescent DNA or RNA probes bind to specific gene sites on chromosomes.
Used for specific localization of genes and direct visualization of anomalies at molecular level (when deletion is too small to be karyotyped)
142
Karyotyping
What is it?
What tissue can it be gotten from?
Uses
Metaphase chromosomes are stained, ordered, and numbered according to morphology, size, arm-length ratio and banding pattern
Blood, Bone marrow, Amniotic fluid, Placental tissue
Used to diagnose chromosomal imbalances
143
16S ribosome
Where is it?
Function
30S ribosome
| Binds complimentary mRNA to initiate translation - Shine Delgarno Sequence
144
Lac Operon when Glucose is added
Glucose --/ AC, leading to a decrease in cAMP
| When glucose is not present, cAMP is high and cAMP-CAP complex promotes transcription
145
Septic Shock Acidosis
What kind of acidosis
Impairment
Lactic Acidosis with an Anion Gap
| Tissue Hypoxia --> Anaerobic Respiration and impairment of OxPhos
146
How does TNF alpha affect glucose uptake
TNF --> Serine phosphorylation which decreases the activity of the Insulin RTK
147
Floppy baby with jaundice, enlarged tongue, hypotonia, umbilical hernia, hoarse cry, constipation...
What do they have
What are they at risk for?
Hypothyroidism
| Congenital heart defects
148
How does Radiation kill tumor cells?
dsDNA breaks and free radicals
149
Rasburicase
Mechanism
Use
Metabolizes Uric Acid into Allantoin which is more soluble
| Tumor Lysis Syndrome
