Biochem Old Stuff Flashcards
Aliphatic amino acids
VIAL
Valine, isoleucine, alanine, leucine
Basic amino acids
Positively charged at pH7
HAL
Beer lambert law
A=ElC
Amino acids w polar side chains
Hydrophilic
Serine, Threonine, Tyrosine = can be phosphorylated
Asparagine, Glutamine
Acidic amino acids
Negatively charged at pH7
Aspartic acid
Glutamic acid
Sulfur amino acids
Cysteine and Methionine
Henderson-Hasselbalch Equation
pH = pKa + log A/HA
Peptide bind is formed between
An acid group (carboxyl) and amino group
Alpha-helix
Usually begins with proline
H-bond between every 4 amino acids
Steps of DNA cloning
Isolate DNA Purify and fragment Insert into a vector Insert vector into bacterial host cell = transformation Replication bacteria for multiple copies
Features of a bacterial vector
Ori
Ab resistant gene
Recognition sites (RE cleavage)
Insertion site for transfene
Requirements for DNA sequencing by Sanger Method
Template - ssDNA of unknown sequence
Lacked DNA primers and polymerase enzyme
dNTPs
ddNTPs - chain terminators
Histone proteins include
H1,H2A,H2B,H3,H4
Nucleosome = all except H1
Tails - chromatin remodeling
1.5 wraps of DNA around each core
Histone modifications
Acetylation (HAT = opens and HDAC)
Methylation
Ubiquination
Phosphorylation
Gene locations
Chromosome number 7
Arm (p or q)
Position
Telomeric repeat
5’-TTAGGG-3’
Autosomal dominant
Equally male and female
Heterozygous
Verticals inheritance
Ex: polydactylism - incomplete penetrance, variable expressivity (variation in strength)
Autosomal recessive
Homozygote
Equal in male and female
Often skips generations
Ex. Phenylketonuria PKU - cannot metabolize phenylalanine, low protein diet
X-linked dominant
Females twicely affected
Usually heterozygote
Ex: Rett Syndrome - mutated MECP2 gene
X-linked Recessive
Males more affected
Ex: Hemophilia A
Leigh Syndrome
Mitochondrial Inherited Disorder
From mother to all offspring, male and female equally
4 causes of genetic mutations
Ionizing radiation - X-rays, gamma rays
Non-ionizing - UV
Chemicals - alkylating agents
Biological agents - viruses
Base-pair Substitutions (Point Mutations)
1) Transversion Purine –> pyrimidine
2) Transition pyrimidine –> pyrimidine
3) Missense (amino acid change)
4) Nonsense (STOP codon)
5) Silent mutation (no aa change)
Insertion/Deletion mutations
Frame shift mutation
Ex: Huntingtons disease
Fragile X Syndrome
Splice site mutation
Exon exclusion
Intron inclusion
Alt 3’ site
Alt 5’ site
Chronic granulomatous disease
Philadelphia Chromosome
Gene 9 and 22 fused
Proliferation of WBC
Robertsonian chromosome abnormality
2 Short arms are lost and the long arms fuse
Only occurs amongst two acrocentric chromosomes (13,14,15,21,22)
Phenotypically normal
DNA Repair - excision mechanisms (3)
(Cut,copy,paste)
Base-excision
-cleavage of glycosidic bond, no damage done to helix
Nucleotide-excision
-damage caused helix distortion, cleavage of phosphodiester bonds
Mismatch repair
-methylation
Isoenzyme
Same reaction but different properties
Factors affecting enzymes
Temp
pH (pepsin - 2.5 trypsin - 6)
Ionic strength
Cofactor availability
Ternary Complex consists of
eIF2, GTP, Initiating AA, methionyl-tRNAmet
De-Novo Pathway for Purines forms _____,
IMP; IMP to GMP via IMP dehydrogenase uses 1 ATP
IMP to AMP via Asp and GTP, releases fumerate
Bases involved in purine salvage pathway
Adenosine + PRPP via APRT —> AMP
Guanine + PRPP via HGPRT —> GMP
Hypoxanthine + PRPP via HGPRT —> IMP
Partial deficiency in enzyme HGPRT results in
High Hypoxanthine and Guanine = converted to Uric acid
PRPP = goes to de novo pathway
Absolute deficiency of HGPRT
Lesch-Nyhan Syndrome
Symptoms: gout, mental retardation, self destruction, nephropathy
Purine catabolism
Forms Uric acid
Products can be used for de novo pathway
AMP deaminase
Adenosine deaminase
Conversion of AMP to ATP
AMP -> ADP via adenylate kinase
ADP -> ATP
Conversion of GMP to GTP
GMP -> GDP via guanylate kinase
Control steps for IMP synthesis during purine synthesis
1) PRPP formation inhibited by ADP, GDP
2) Addition of first N inhibited by AMP,ADP,ATP.GMP,GDP, GTP and stimulated by PRPP
Mycophenolic acid
Inhibits IMP dehydrogenase during GTP formation from IMP to prevent cell proliferation (immunosuppressant in kidney transplants)
Pathway for UMP synthesis for pyrimidines
Glutamine attaches
Asp added, ring closure
Decarboxylation forming UMP
Ring adds to PRPP (committed step)
Conversion of UTP to CTP in pyrimidine synthesis
Via amide group from glutamine , uses 2ATP
Control steps of Pyrimidine synthesis
1) glutamine and bicarbonate combination inhibited by UDP and UTP, activated by ATP, PRPP
2) UMP formation inhibited by UMP
Ribonucleotide reductase
Reduces NTPs into dNTPs during dNTP formation.
Tetramer with 2 heterodimers
RNR1 = allosteric control sites, ATP = activates dATP = Inactivates
RNR2 = active site where NDP converted to dNDPs
Drug interactions in dTMP synthesis
5-Fluorouracil = thymidylate synthase inhibitor (cancer chemotherapy)
Methotrexate = dihydrofolate reductase inhibitor
Trimethoprim = Antibiotic, binds to bacterial dihydrofolate reductase better than mammalian enzyme
Purine catabolism disorders
SCID = adenosine deaminase mutations, selectively kills lymphocytes
Myoadenylate deaminase deficiency = cannot provide fumerate via conversion of AMP to IMP. Easily fatigued and muscle cramps
Gout = insoluble Uric acid crystals = treated by allopurinol (Hypoxanthine analog), Inactivates Xanthippe oxidase
Purine synthesis differences from pyrimidines
Utilizes Glycine, GTP, formate and forms Uric acid, where pyrimidine synthesis does not
Pyrimidine forms malonyl CoA
Important monosaccharides
Glucose
Fructose
Galactose
Glycosidic bond includes
Bond between OH of anomeric C and another reactive group (usually OH of another sugar)
Reducing OH
Non Reducing OH
Reducing = OH is free and not involved in a glycosidic bond
Important disaccharides
Sucrose (glucose-fructose)
Lactose (glucose-galactose)
Maltose (glucose-glucose)
Glucose polymers linked:
Branched every:
Alpha-(1,4)
Alpha-(1,6)
Chondroitin 4 and 6 Sulfates
GAG - the most abundant one
N-acetylgalactosamine and glucuronic acid
In cartilage, aorta, tendons, ligaments
Keratan Sulfates
N-acetylglucosamine and galactose (no uronic acid)
Connective tissue
Hyaluronic acid
N-acetylglucosamine and glucuronic acid
Synovial fluid of joints
Dermatan sulfate
N-acetylgalactosamine
Skin, blood vessels, heart valves, CT
Heparin and Heparan Sulfate
Glucosamine and glucuronic/iduronic acid
Anticoagulant
Arsenate
Replaces phosphate in step from GAP to 1,3 BPG resulting in no ATP formation
Fluoroacetate
Binds CoA and is converted to Fluoroacetate via citrate synthase and competitively inhibits aconitas
Causes of diabetes type 1
Absolute deficiency of insulin Genetic Environmental Viruses Drugs and chemicals
