Biochemistry Review

Flashcards about molecular biology, genetics, cell biology, and principles of metabolism.

Why does DNA exist in chromatin form?

DNA exists in the condensed, chromatin form to fit into the nucleus. Histones help condense DNA.

What are the key differences between heterochromatin and euchromatin?

Heterochromatin is condensed, appears darker, and is transcriptionally inactive while euchromatin is less condensed, appears lighter, and is transcriptionally active.

How do DNA methylation and histone acetylation affect gene transcription?

DNA methylation represses gene transcription, while histone acetylation increases gene transcription.

What is the difference between a nucleoside and a nucleotide?

Nucleoside = base + (deoxy)ribose. Nucleotide = base + (deoxy)ribose + phosphate linked by 3′-5′ phosphodiester bond.

Which amino acids are necessary for purine synthesis?

Glycine, Aspartate, Glutamine

How does Leflunomide affect pyrimidine synthesis?

Leflunomide inhibits dihydroorotate dehydrogenase in pyrimidine synthesis.

How do 6-Mercaptopurine, azathioprine, mycophenolate, and ribavirin affect purine synthesis?

6-Mercaptopurine (6-MP) and its prodrug azathioprine inhibit de novo purine synthesis. Mycophenolate and ribavirin inhibit inosine monophosphate dehydrogenase.

How do Hydroxyurea, Methotrexate, trimethoprim and pyrimethamine affect nucleotide synthesis?

Hydroxyurea inhibits ribonucleotide reductase. Methotrexate, trimethoprim, and pyrimethamine inhibit dihydrofolate reductase.

How does adenosine deaminase (ADA) deficiency lead to severe combined immune deficiency (SCID)?

ADA deficiency leads to increased dATP, decreased ribonucleotide reductase activity, decreased DNA precursors, and decreased lymphocytes, causing SCID.

How does the absence of HGPRT in Lesch-Nyhan syndrome lead to its characteristic symptoms?

Absent HGPRT leads to decreased GMP and IMP, increased purine synthesis, and excess uric acid production, leading to intellectual disability, self-mutilation, aggression, hyperuricemia, gout, and dystonia.

What are the key features of the genetic code?

Unambiguous, degenerate/redundant, commaless/nonoverlapping, and universal.

What are the key enzymes and proteins involved in DNA replication?

Origin of replication, Helicase, Single-stranded binding proteins, DNA topoisomerases, Primase, DNA polymerase III, DNA polymerase I, DNA ligase, and Telomerase.

Compare the mechanisms of Nonhomologous end joining and Homologous recombination.

Nonhomologous end joining brings together 2 ends of DNA fragments to repair double-stranded breaks where Homology is not required. Homologous recombination requires 2 homologous DNA duplexes to restores duplexes accurately without loss of nucleotides.

What are the key differences between nucleotide excision repair, base excision repair, and mismatch repair?

Nucleotide excision repair repairs bulky helix-distorting lesions (e.g., pyrimidine dimers) and is defective in xeroderma pigmentosum. Base excision repair removes altered bases. Mismatch repair corrects mismatched nucleotides and is defective in Lynch syndrome

What is the degree of change from least to most in DNA mutations?

Silent << missense < nonsense < frameshift

How does the lac operon respond to changes in glucose and lactose levels?

Low glucose leads to increased cAMP, activation of CAP, and increased transcription. High lactose unbinds the repressor protein, increasing transcription.

What are the functions of promoters, enhancers, and silencers in gene expression?

Promoter: Site where RNA polymerase II and transcription factors bind. Enhancer: DNA locus where activators bind, increasing gene expression. Silencer: DNA locus where repressors bind, decreasing gene expression.

What are the key steps in RNA processing in eukaryotes, and where do they occur?

Capping of 5′ end, polyadenylation of 3′ end, and splicing out of introns. These processes occur in the nucleus.

What are the roles of RNA polymerase I, II, and III in eukaryotes?

RNA polymerase I makes rRNA in the nucleolus. RNA polymerase II makes mRNA, miRNA, and snRNA. RNA polymerase III makes 5S rRNA and tRNA.

Compare the roles for exons and introns.

Exons contain coding genetic information whereas Introns do not code for protein and stay in the nucleus.

What are the key structural features of tRNA?

All tRNAs have CCA at the 3′ end, where the amino acid is covalently bound. The T-arm contains the TΨC sequence for tRNA-ribosome binding. The D-arm contains dihydrouridine residues for aminoacyl-tRNA synthetase recognition.

What enzyme is responsible for the accuracy of amino acid selection during translation?

Aminoacyl-tRNA synthetase (uses ATP). It matches an amino acid to the tRNA by scrutinizing the amino acid before and after it binds to tRNA.

What is involved in translation initiation

Eukaryotic initiation factors (eIFs), Shine-Dalgarno sequence (prokaryotes).

Describe Going APE in translation

A site = incoming Aminoacyl-tRNA. P site = accommodates growing Peptide. E site = holds Empty tRNA as it Exits.

Posttranslational modifications to proteins can include what?

Removal of N- or C-terminal propeptides, covalent alterations, and chaperone protein.

What are the key regulatory molecules of the cell cycle?

Cyclin-dependent kinases (CDKs), cyclins, and tumor suppressors.

What are the cell types?

Permanent, Stable, and Labile.

What is the function of the rough endoplasmic reticulum (RER)?

Site of synthesis of secretory (exported) proteins and of N-linked oligosaccharide addition to proteins. Rich in mucus-secreting goblet cells and antibody-secreting plasma cells. Proteins within organelles are formed here.

What is the function of the smooth endoplasmic reticulum (SER)?

Site of steroid synthesis and detoxification of drugs and poisons. Rich in hepatocytes and steroid hormone–producing cells.

Describe the function of COPI, COPII, and Clathrin.

COPI: Golgi --> Golgi (retrograde); cis-Golgi --> ER. COPII: ER --> cis-Golgi (anterograde). Clathrin: trans-Golgi --> lysosomes; plasma membrane --> endosomes.

What is I-cell disease?

Inherited lysosomal storage disorder due to defect in N-acetylglucosaminyl-1-phosphotransferase. Results in coarse facial features, gingival hyperplasia, corneal clouding, restricted joint movements, claw hand deformities, kyphoscoliosis, and increased plasma levels of lysosomal enzymes.

What are the key functions of the peroxisome?

β-oxidation of very-long-chain fatty acids (VLCFA), α-oxidation of branched-chain fatty acids, catabolism of amino acids and ethanol, and synthesis of bile acids and plasmalogens.

What are the Peroxisomal Diseases?

Zellweger syndrome, Refsum disease, and Adrenoleukodystrophy.

What are the key functions of microfilaments, intermediate filaments, and microtubules in the cytoskeleton?

Microfilaments: Muscle contraction, cytokinesis. Intermediate filaments: Maintain cell structure. Microtubules: Movement, cell division.

list Drugs that act on microtubules

Microtubules get constructed very terribly: Mebendazole, Griseofulvin, Colchicine, Vinca alkaloids, and Taxanes.

Describe Cilia Structure

Motile cilia consist of 9 doublet + 2 singlet arrangement of microtubules. Nonmotile (primary) cilia work as chemical signal sensors.

Primary ciliary dyskinesia results in what?

Autosomal recessive dynein arm defect leads to immotile cilia, causing situs inversus recurrent infections and infertility.

What happens in the Sodium-potassium pump?

For each ATP consumed, 2 K+ go in to the cell and 3 Na+ go out of the cell.

Describe the different Collagen Types

Myofibroblasts are responsible for secretion and wound contraction. Type I: Bone, Skin, Tendon. Type II: Cartilage. Type III: Reticulin. Type IV: Basement membrane.

What is Osteogenesis imperfecta?

Genetic bone disorder caused by a variety of gene defects (most commonly COL1A1 and COL1A2 ( most common form is autosomal dominant with decreased production of otherwise normal type I collagen

What is Ehlers-Danlos syndrome?

Faulty collagen synthesis causing hyperextensible skin, hypermobile joints, and tendency to bleed.

What is Menkes disease?

X-linked recessive connective tissue disease caused by impaired copper absorption and transport due to defective Menkes protein ATP7A, causing defective collagen cross-linking.

What is Marfan syndrome?

Defective fibrillin-1, a glycoprotein that forms a sheath around elastin and sequesters TGF-β.

What is Homocystinuria?

Cystathionine synthase deficiency leading to homocysteine buildup. Presentation similar to Marfan syndrome.

What is a Polymerase chain reaction?

Molecular biology lab procedure used to amplify a desired fragment of DNA.

What is CRISPR/Cas9?

Genome editing tool derived from bacteria that consists of a guide RNA (gRNA) , which is complementary to a target DNA sequence, and an endonuclease (Cas9), which makes a single- or double-strand break at the target site

Describe SNoW DRoP:

Southern = DNA, Northern = RNA, Western = Protein

What is Flow cytometry?

Laboratory technique to assess size, granularity, and protein expression (immunophenotype) of individual cells in a sample; Antibodies are then tagged with a unique fluorescent dye. Sample is analyzed one cell at a time by focusing a laser on the cell and measuring light scatter and intensity of fluorescence

What is Enzyme-linked immunosorbent assay or ELISA?

Immunologic test used to detect the presence of either a specific antigen or antibody in a patient’s blood sample. Detection involves the use of an antibody linked to an enzyme.

What is Fluorescence in situ hybridization?

Fluorescent DNA or RNA probe binds to specific gene or other site of interest on chromosomes.

What is RNA interference?

Process whereby small non-coding RNA molecules target mRNAs to inhibit gene expression.

What is Codominance?

Both alleles contribute to the phenotype of the heterozygote.

What is Variable expressivity?

Patients with the same genotype have varying phenotypes.

What is Incomplete penetrance?

Not all individuals with a disease show the disease.

What is Pleiotropy?

One gene contributes to multiple phenotypic effects.

What is Anticipation?

Increased severity or earlier onset of disease in succeeding generations.

What is Epistasis?

The allele of one gene affects the phenotypic expression of alleles in another gene.

What is Linkage disequilibrium?

Measured in a population, not in a family, and often varies in different populations; Tendency for certain alleles to occur in close proximity on the same chromosome more or less often than expected by chance.

What is Mosaicism?

Presence of genetically distinct cell lines in the same individual.

What is Locus heterogeneity?

Mutations at different loci result in the same disease.

What is Allelic heterogeneity?

Different mutations in the same locus result in the same disease.

What is Heteroplasmy?

Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrially inherited disease.

What is Uniparental disomy?

Offspring receives 2 copies of a chromosome from 1 parent and no copies from the other parent.

What is the Bottleneck effect?

Fitness equal across alleles --> natural disaster that removes certain alleles by chance --> new allelic frequency (by chance, not naturally selected)

What is Natural selection?

Alleles that increase species fitness are more likely to be passed down to offspring and vice versa.

What is Genetic drift?

A dramatic shift in allelic frequency that occurs by change (not by natural selection).

What does Hardy-Weinberg Law state?

P + q = 1, and p2 + 2pq + q2 = 1.

What are the signs and symptoms of Prader-Willi syndrome

Hyperphagia, obesity, intellectual disability, hypogonadism, hypotonia.

What are the signs and symptoms of Angelman syndrome?

Hand-flapping, Ataxia, severe Intellectual disability, inappropriate Laughter, Seizures.

What is Autosomal dominant inheritance?

Often due to defects in structural genes. Many generations, both males and females are affected.

What is Autosomal recessive inheritance?

Often due to enzyme deficiencies. Usually seen in only 1 generation. Commonly more severe than dominant disorders; patients often present in childhood.

What is X-linked recessive inheritance?

Sons of heterozygous mothers have a 50% chance of being affected. No male-to-male transmission. Skips generations.

What is X-linked dominant inheritance

Transmitted through both parents. Children of affected mothers each have a 50% chance of being affected. 100% of daughters and 0% of sons of affected fathers will be affected.

What is Mitochondrial inheritance?

Transmitted only through the mother. All offspring of affected females may show signs of disease. Variable expression in a population or even within a family due to heteroplasmy.

List the Incidence of Autosomal trisomies

Down (21) , Edwards (18) , Patau (13)

What are the Findings of Down syndrome (trisomy 21)?

intellectual disability, flat facies, prominent epicanthal folds, single palmar crease, incurved 5th finger, gap between 1st 2toes, duodenal atresia

What are the Findings of Edwards syndrome (trisomy 18)?

Prominent occiput, Rocker-bottom feet, Intellectual disability, Nondisjunction, Clenched fists with overlapping fingers, Clenched fists with overlapping fingers

What are the Findings of Patau syndrome (trisomy 13)?

severe intellectual disability, rocker- bottom feet, microphthalmia, microcephaly, cleft lip/palate, holoprosencephaly, polydactyly, cutis aplasia

What are the Findings of Cri-du-chat syndrome?

microcephaly, moderate to severe intellectual disability, high-pitched crying, epicanthal folds, cardiac abnormalities (VSD).

What are the Findings of Williams syndrome?

distinctive elfin facies, intellectual disability, hypercalcemia, well-developed verbal skills, extreme friendliness with strangers, supravalvular aortic stenosis.

What happens with Essential fatty acids

Linoleic acid (omega-6) is metabolized to arachidonic acid. Linolenic acid (omega-3) and its metabolites have cardioprotective and antihyperlipidemic effects.

Are A, D, E,K water or fat soluble vitamins?

Fat soluble

Are B1 (thiamine: TPP) B2 (riboflavin: FAD, FMN) B3 (niacin: NAD+) B5 (pantothenic acid: CoA) B6 (pyridoxine: PLP) B7 (biotin) B9 (folate) B12 (cobalamin) C (ascorbic acid) water or fat soluble?

Water soluble

What are the Findings of Vitamin A deficiency?

Night blindness (nyctalopia), dry, scaly skin (xerosis cutis), dry eyes (xerophthalmia)

what results from Wernicke encephalopathy?

Acute, reversible, life-threatening neurologic condition: Confusion, Ophthalmoplegia/ Nystagmus, Ataxia

Wernicke-Korsakoff syndrome leads to…

Damage to medial dorsal nucleus of thalamus, mammillary bodies.

What are the Findings of Vitamin B2 deficiency?

Cheilosis (inflammation of lips, scaling and fissures at the corners of the mouth), “magenta” tongue, corneal vascularization

What are the Findings of Vitamin B3 deficiency?

diarrhea, dementia (also hallucinations), dermatitis

What are the Findings of Vitamin B5 deficiency?

Dermatitis, enteritis, alopecia, adrenal insufficiency may lead to burning sensation of feet

What are the Findings of Vitamin B6 deficiency?

Convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemia

What are the Findings of Vitamin B7 deficiency?

Relatively rare: Dermatitis, enteritis, alopecia.

What are the Findings of Vitamin B9 deficiency?

Macrocytic, megaloblastic anemia; hypersegmented PMNs; glossitis; no neurologic symptoms

What are the Findings of Vitamin B12 deficiency?

Macrocytic, megaloblastic anemia; hypersegmented PMNs; paresthesias and subacute combined degeneration

What are the Findings of Vitamin C deficiency?

swollen gums, easy bruising, petechiae, hemarthrosis, anemia, poor wound healing, perifollicular and subperiosteal hemorrhages, “corkscrew” hair

What are the Findings of Vitamin D deficiency?

Rickets in children (deformity, such as genu varum “bowlegs” ), osteomalacia in adults (bone pain and muscle weakness), hypocalcemictetany

What are the Findings of Vitamin E deficiency?

Hemolytic anemia, acanthocytosis, muscle weakness, demyelination of posterior columns and spinocerebellar tract

What are the Findings of Vitamin K deficiency

Neonatal hemorrhage with PT and aPTT but normal bleeding time

What are the Findings of Zinc deficiency

Delayed wound healing, suppressed immunity, male hypogonadism, -->adult hair, dysgeusia, anosmia

What is Kwashiorkor?

Protein malnutrition resulting in skin lesions, edema due to --> plasma oncotic pressure, liver malfunction

What is Marasmus?

Deficient in calories but no nutrients are entirely absent