Flashcards in BioChem Deck (149):
What kind of inheritance?
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
What do they form?
What ties it together?
Lysine and Arginine
Octamer tied together by H1
When in cell cycle?
C and A
Template strand is methylated during DNA replication which allows mismatch repair enzymes to distinguish between old and new strands
What does Histone Methylation do?
What does Histone Acetylation do?
Relaxes DNA coiling allowing for transcription
What is it made from?
"PURe As Gold"
Glycine, Aspartate, Glutamine
"CUT the PY"
Cytosine, Uracil, Thymine
Molecular group on Guanine
Molecular group on Thymine
How is Uracil made?
Cytosine gets Deaminated
Which nucleotide bond is strongest
G-C has 3 hydrogen bonds
How is DNA melting point affected
↑ GC content --> ↑ melting temperature
Base + Ribose
Base + Ribose + Phosphate linked by 3'5' phosphodiester bond
What makes up Pyrimidines
Aspartate and Carbamoyl Phosphate
Basic schematic of de novo purine synthesis
Start with sugar + phosphate (PRPP)
Then add base
Basic schematic of de novo pyrimidine synthesis
Make temporary base (orotic acid)
Add sugar + phosphate (PRPP)
Purine synthesis pathway
Ribose 5-P --> PRPP ->->-> IMP --> AMP and GMP
Inhibition of de novo purine synthesis
6-mercaptopurine blocks de novo purine synthesis
Production of deoxyribonucleotides
Ribonucleotide reductase converts ribonucleotides into deoxyribonucleotides
Ribose 5-P --> PRPP
PRPP + Orotic Acid --> UMP --> UDP --> CTP
Ribose 5-P --> PRPP
PRPP + Orotic Acid --> UMP --> UDP --> [Ribonucleotide reductase] --> dUDP --> dUMP --> [Thymidylate Synthase] --> dTMP
What pathways is Carbamoyl Phosphate involved with?
de novo pyrimidine synthesis and urea cycle
Ornithine transcarbamoylase deficiency
What is it?
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
What inhibits Ribonucleotide reductase
What inhibits Thymidylate Synthase?
What inhibits human Dihydrofolate reductase
What inhibits bacterial Dihydrofolate reductase
THF and dTMP synthesis
THF --> N5N10 methylene THF --> [Thymidylate Synthase] --> DHF --> [Dihydrofolate reductase] --> THF
What is it?
Where is the defect?
Inability to convert orotic acid to UMP
de novo pyrimidine synthesis pathway
↑ orotic acid in urine, Megaloblastic anemia (does not improve with B12 or folic acid), Failure to thrive, No hyperammonemia
Oral uridine administration
Adenine salvage pathway
Adenine + PRPP --> [APRT] --> AMP
AMP can become Nucleic acids, Adenosine, or IMP
Fate of Adenosine in salvage pathway
Adenosine can become AMP or Adenosine deaminase (ADA) can turn it into Inosine
Fate of IMP in purine salvage pathway
Hypoxanthine + PRPP --> [HGPRT] --> IMP
IMP can become inosine, AMP, or GMP
Fate of Inosine in Purine salvage pathway
Adenosine --> Inosine
Inosine --> Hypoxanthine
Fate of Hypoxanthine in Purine salvage pathway
Hypoxanthine can become IMP, Inosine, or Xanthine
Fate of Guanine in Purine salvage pathway
Guanine +PRPP --> [HGPRT] --> GMP
Guanine --> Guanosine
Guanine --> Xanthine
Fate of Guanosine in Purine salvage pathway
GMP --> Guanosine
Guanine ↔ Guanosine
Fate of GMP in Purine salvage pathway
GMP can be come Nucleic Acids, IMP or Guanosine
Adenosine Deaminase Deficiency
What does it lead to
Excess ATP and dATP leads to an imbalance in nucleotide pool via feedback inhibition of ribonucleotide reductase thus preventing DNA synthesis thus ↓ Lymphocyte count
1st disease to be treated by experimental human gene therapy
"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
Genetic Code Features
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
Same AA usually at 3rd position of condon (tRNA wobble)
Changed AA to a similar AA
Early stop codon
Misreading of all downstream nucleotides resulting in truncated, nonfunctional protein
What inhibits it
Creates a nick in the helix to relieve supercoil created during replication
Fluoroquinolones inhibit prokaryotic topoisomerase II
DNA pol III
Direction of synthesis
5' --> 3'
Proofreads 3' to 5'
DNA pol I
Functions with directions
Degrades RNA primer and replaces it with DNA
Synthesis 5' --> 3'
Proofreading 3' --> 5'
Exonuclease 5' --> 3'
Catalyzes the formation of phosphodiesterase bonds within strand of dsDNA. Joins Okazaki fragments
Adds DNA to 3' end of chromosome to avoid loss of genetic material with every duplication
Nucleotide Excision repair
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
Base Excision repair
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
Newly synthesized strand is recognized, mismatched nucleotides are removed and gap is filled and resealed
Mutated in Hereditary NonPolyposis Colorectal Cancer (HNPCC)
Nonhomologous end joining
Brings together 2 ends of DNA fragments to repair double stranded breaks
No requirement for homology
Mutated in ataxia telangiectasia
Direction of DNA and RNA synthesis?
5' --> 3'
5' end of dNTP
In which direction is mRNA read?
5' --> 3'
Direction of Protein Synthesis
N to C
Most abundant type of RNA
Ways to remember types of RNA?
"Rampant, Massive, Tiny"
Eukaryotic start codon
"AUG inAUGurates protein synthesis"
AUG (rarely GUG) which codes for Methionine
Prokaryotic start codon
AUG which codes for formylmethionine
mRNA stop codons
UGA: U Go Away
UAA: U Are Away
UAG: U Are Gone
TATAAT and CAAT
Start of transcription numbering
Eukaryotic RNA pol
I, II, III
Numbered in order that they are used in protein synthesis
II: mRNA - can open DNA at promoter site
No proofreading function but can initate chains
Prokaryotic RNA pol
1 RNA pol (multisubunit complex) makes all 3 kinds of RNA
What inhibits RNA pol II
What does it lead to
α-amanitin (from mushroom)
Hepatotoxicity if ingested
RNA processing in eukaryotes
What is initial transcript called?
What is it called if destined for transcription?
Where does processing occur?
Heterogenous nuclear RNA
Processing occurs in the nucleus
RNA processing in eukaryotes
Capping on 5' end with 7-methylguanosine
Polyadenylation an 3' end
Splicing out of introns
What is required for RNA to be transported out of the nucleus
Only processed RNA can be transported out of the nucleus
What enzyme does it?
Does not require a template
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
Disease involving snRNPs
Lupus: autoAbs to spliceosomal snRNPs
What is on end?
Which end binds AAs
On 3' end is 5' CCA 3' along with a high percentage of chemically modified bases
3' is bound to AA
Scrutinizes AA before and after it binds tRNA
If incorrect, bond is hydrolyzed
AA-tRNA bond has energy for formation of peptide bond
Bind 30S subunit and prevents attachment of aminoacyl tRNA to A site
40S and 60S
30S and 50S
Protein synthesis initiation
Activated by GTP hydrolysis
Initiation Factors help assemble 40S ribsomal subunit with the initiator tRNA and are then released
Protein synthesis Elongation
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
Protein synthesis Termination
Stop codon recognized by release factors and complete protein is released from ribosome
Bind 30S and inhibit formation of initiation complex and cause misreading of mRNA
Binds 50S and inhibits peptidyl transferase
Bind 50S and prevent release of uncharged tRNA after it has donated its AA
Process of Proteasomal degradation
Attachment of Ubiquitin tags them for breakdown
Stages of cell cycle
G1 --> [Rb, p53] --> S --> G2 --> Mitosis
G1, S, and G2
Stages of mitosis
Prophase, Metaphase, Anaphase, Telophase
Regulation of Cell Cycle
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
p53 and Hypophosphorylated Rb
Normally inhibit G1 to S progression
Permanent cell type
What do they form
Remain in G0
Regenerate from stem cells
Neurons, Skeletal muscle, Cardiac muscle, RBCs
Stable cell types
Enter G1 from G0 when stimulated
Hepatocytes and Lymphocytes
Never go to G0. Divide rapidly with a short G1
Bone marrow, Gut epithelium, Skin, Hair follicles, Germ cells
Rough Endoplasmic Reticulum
What kind of proteins are synthesized here?
Site of synthesis of secretory (exported) proteins
N linked oligosaccharide addition to many proteins
RER in neurons
Synthesizes ChAT (choline acetyltransferase) to make ACh and peptide NTs
What do free ribosomes produce
Cytosolic and organellar proteins
Which kind of cells are rich in RER?
Mucus-secreting goblet cells of SI and Ab secreting plasma cells
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
Modifications that take place in Golgi?
Modifies N-oligosaccharides on Asparagine
Adds O-oligosaccharides on Serine and Threonine
What directs proteins to lysosomes
Mannose-6-Phosphate added in lysosomes
I cell disease
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
Vesicle trafficking proteins
COPI: Retrograde (Golgi --> Golgi, Golgi --> ER)
COPII: Anterograde (Golgi --> Golgi, ER --> Golgi)
Clathrin: trans-Golgi --> lysosomes, Plasma membrane --> Endosomes (receptor mediated endocytosis)
Membrane enclosed organelle involved in catabolism of very long fatty acids and AA
Barrel shaped protein complex that degrades damaged or unnecessary proteins tagged for destruction by ubiquitin
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
Molecular motor proteins
Dynein: retrograde in MTs (+ --> -)
Kinesin: anterograde in MTs (- --> +)
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)
Where is the mutation?
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
9+2 arrangement of MTs. 9 doublets of MTs + 2 individual MT in middle
Dynein links peripheral 9 doublets
Associated with what developmental defect
Immotile cilia due to dynein arm defect
Male infertility, ↓ female fertility, Bronchiectasis, Recurrent sinusitis
Associated with sinus inversus
Actin and Myosin functions
Microvilli, Muscle contraction, Cytokinesis, Adherens junctions
Intermediate filament names and stains
Vimentin: Connective tissue
Cytokeratin: Epithelial cells
Glial Fibrillary Acid Protein (GFAP): NeuroGlia
Plasma Membrane composition
Cholesterol, Phospholipids, Sphingolipids, Glycolipids, and Proteins
When is Na/K APTase phosphorylated
When open to extracellular side
Inhibits Na/K ATPase by binding to K site
Digoxin and Digitoxin
Inhibits Na/K ATPase leading indirectly to increased Ca --> increased contractility
Most abundant protein in the human body
Type I collagen
Where is it present?
Most common collagen (90%)
Bone, Skin, Tendon, Dentin, Fascia, Cornea, Late Wound Repair
Defective in Osteogenesis Imperfecta
Where is type II collagen
Cartilage (including hyaline, Vitreous body, Nucleus pulposus
Type III collagen
Where is it present
Reticulin - skin, blood vessels, uterus, fetal tissue, granulation tissue
Ehlers-Danlos (vascular type)
Type IV collagen
Where is it present
Basement membrane (basal lamina)
"Be (So Totally) Cool, Read Books"
I: Bone, Skin, Tendon
IV: Basement Membrane
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)
Type of collagen
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)
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)
Type of collagen involved?
# of types
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
Can be AD or AR
Joint dislocation, berry aneurysm, organ rupture
Type of collagen involved
Variety of genetic defects but most commonly X linked recessive
Progressive hereditary nephritis, deafness, and ocular disturbances
What is it? Where is it?
What is it made of?
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)
What causes wrinkles of aging?
Reduced collagen and elastin production
DNA electrophoresed, transfered to filter, denatured, labeled with probe
Southern - DNA
Northern - RNA
Western - Protein
Identifies DNA-Binding Proteins using labeled oligonucleotide probes
Nucleic acid sequences arranged on a grid and samples hybridize to the chip
Can detect SNPs
Enzyme-Linked Immunosorbent Assay
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
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)
What is it?
What tissue can it be gotten from?
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
Where is it?
Binds complimentary mRNA to initiate translation - Shine Delgarno Sequence
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
Septic Shock Acidosis
What kind of acidosis
Lactic Acidosis with an Anion Gap
Tissue Hypoxia --> Anaerobic Respiration and impairment of OxPhos
How does TNF alpha affect glucose uptake
TNF --> Serine phosphorylation which decreases the activity of the Insulin RTK
Floppy baby with jaundice, enlarged tongue, hypotonia, umbilical hernia, hoarse cry, constipation...
What do they have
What are they at risk for?
Congenital heart defects
How does Radiation kill tumor cells?
dsDNA breaks and free radicals