Genetic biochemistry

DNA Replication Transcription

RNA

Protein
Translation

DNA double helix Nucleosome, histones

Solenoid structure

chromosome

Replication: semiconservative

The replication
Enzymes: - DNA-dependent DNA polymerase I (repair), II (not clear), III (polymerase) - Topoisomerase (helicase) unwinding, girase a pos. -> neg. supercoil - Primase synthesis of RNA primer - Ligase binds DNA fragments Four deoxyribonucleoside triphosphates (dATP, dGTP, dCTP, dTTP)

Replication steps: Initiation

A dnaA protein is bound to the oriC region, which is detached, helicase (dnaC protein) -> replication fork, primosome SSB protein stabilizes the single strand DNA Girase decreases the tension of the strand induced by the helicase Primase enhances the synthesis of the RNA primer

Replication steps: elongation

Polymerase III catalyzes the binding of dNTP-s to the 3OH group of the ribose in the RNA primer, PPi is released Pairs: A =T, CG, polymerase III controls it The new strand is synthesized in 5 > 3 direction Leading strand (continuous synthesis), lagging strand forms loops (Okazaki fragments) The many RNA primers are decomposed by an enzyme complex (DNA polymerase I) having RNAse and exonuclease activity The gaps are filled by the polymerase I, the fragments are linked together by ligase

Replication: termination
Replication is bidirectional, it has multiple origins In case of the circular bacterial DNA the process ends when the two bifurcations meet on the opposite side compared to the ori region Special proteins signal the end of the replication, stopping the helicase activity

Repair
Mutations are caused by UV light, dithymines are formed > xeroderma pigmentosum, it can lead to skin cancer; germicid lamps are used NH2 group deamination: C -> U (preservatives) Substitution, insertion, deletion Mutations have regularly negative effect, sometimes give advantages or can be silent Ames test: to evaluate the mutagenic effect Salmonella typhimurium His requirement

Transcription

Transcription: steps
One DNA strand is transcripted DNS-dependent RNA polymerase -> RNA synthesis, U instead of T. In case of the coli bacteria the core of the enzyme 2, and subunits are also bound to it ( is important in the initiation) Preinitiation: The enzyme is bound to the promoter region of the DNA (5TATAAT3, 5TTGACA3), unwinds the DNA segment, the first nucleotide (purin) binds to the subunit

Transcription steps
Initiation: the synthesis of the RNA molecule starts at the 5 end, PPi is released, the polymerase is detached from the promotor region Elongation: the DNA unwinds, transcription bubble is formed (20 basepair), the polymerase inhibits double strand DNA formation Termination: the factor protein recognizes the stop region on the template DNA (or hairpin sequence), the polymerase is detached from the DNA, dissociates

Replication, transcription - differences

Ribonucleotides are necessary U instead of T No primer required Only some DNA segments are transcripted, while during replication the entire genom is duplicated Many mistakes are made, no efficient repair

RNA processing
Exons: aminoacid codifying sequences Introns: non-coding regions (cleaved out) Exons linked together Adding or removing polynucleotide segments mRNA, rRNA, tRNA formation, final function can be fulfilled

Reverse transcription
RNA viruses (ex. HIV) The genom is RNA, it is transcripted to DNA (reverse transcriptase is necessary) RNA is decomposed from the RNA-DNA hybrid, replaced by a DNA strand The viral DNA is inserted in the DNA of the host cell, can be transcripted, might be dormant Genes of retroviruses: gag (virus core), pol (protease, integrase, reverse transcriptase), env (envelope), mutations are frequent

Translation: aminoacid activation

The genetic code

first letter 5 end
U
U C

Second letter

third letter 3 end

A G

Phe Phe Leu Leu

C

Ser Ser Ser Ser

Pro Pro Pro Pro

Tyr Tyr STOP STOP

His His Gln Gln

Cys Cys STOP Trp

Arg Arg Arg Arg

U C A G U C A G

Leu Leu Leu Leu

Ile Ile Ile Met

Val Val Val Val

Thr Thr Thr Thr

Ala Ala Ala Ala

Asn Asn Lys Lys

Asp Asp Glu Glu

Ser Ser Arg Arg

Gly Gly Gly Gly

U C A G
U C A G

The genetic code

Universal No spaces Collinear No interference One meaning Redundant

Posttranslational modifications
The first aa is cleaved out (Met, fMet) Amino-, carboxy terminal end cleaved out Collagene OH-ation (Lys, Pro) Glikoproteins: carbohydrates are attached Tyr sidechains + I2 thyreoglobuline Hormone activation: prohormones Formation of disulfide briges

Mechanism of transcription regulation

structure genes

transcription mRNA translation repressor protein -galactosidase permease transacetylase

mRNA

Inhibiting drugs
Doxorubicin inhibit DNA (used in the treatment of leukemia) Amanitin, phalloidin inhibits RNA elongation Difteria toxin, puromycin, tetracyclin, chloramfenicol, streptomycin inhibit protein synthesis

Biochemistry of digestion and nutrition

Digestion
Oral cavity: mucins in saliva, lysosim, absorption of drugs, digestive enzymes Stomach: gastric juice, cell types Pancreas: zymogenes, active enzymes Liver: bile Small intestine: final digestion, absorption, APUD Colon: water retention, K+, HCO3-

Caries in infants
The resistance of the dental tissues to acids influences the occurrence of the caries. Mineralization of the teeth in the fetus begins in the second trimester of the pregnancy, thus it is influenced by the state of health of the mother, her diet and lifestyle Severe chronic diseases, metabolic disorders like gestational toxicosis, endocrine pathology influence the unborn child, leading to multiple, painful caries. Prematurity, trauma at birth, chronic disease of the infant have a bad influence Caries are rare in infant that have been breastfed

The parietal cell

Treatment of ulcer
Antiacids: Al(OH)3, CaCO3 Secretion inhibitor: - receptor blockers (antiAck, antihistamine) - antienzyme drugs (carboanhydrase inhibitors, protompump inhibitors) Mucosa protecters: - PG E derivatives - bismuth derivatives Antibacterial: against Helicobacter pylori Surgical treatment: resection of the stomach, vagotomia

Nutrition
Carbohydrates: give instant energy, the best are those that are absorbed slowly Lipids: high energetic value, saturated/unsaturated fatty acids - source Proteins: are necessary for the growth process, renewing the tissues. The complete proteins are from animal sources. High intake is in pregnant and breastfeeding women Vitamins, fibres, bioactive substances, water

Feeding the infant

Breastfeeding 4-6 months Artificial: milk formulas Mixed: mothers milk + formula Not under 1 year: avoid fruits with tiny seeds, albumen, fish, peas, beans, apricot, cherry, cucumber, corn, pork Under 6 months avoid gluten After 6 months Fe: liver, meat, egg yolk