Genetics 2 Flashcards by Denisse Tiangco

5’ methylguanosine CAP
3’ polyadenylic TAIL

Determines amino acid sequence

Massive

mRNA

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Smallest RNA
Cloverleaf form

Brings amino acid

Tiny

Adaptor molecule

tRNA

transfer RNA

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35% ribosomes
65% RNA
Molecular scaffold

Catalyzes peptide bond formation

Contains 30s and 50s subunit

Rampant

rRNA

ribosomal RNA

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Synthesis of mRNA from DNA

Only one DNA strand transcribed
Proceeds 5’ -> 3’ direction

Consists of initiation, elongation and termination

Promoter regions identified as start of transcription

DNA strands rejoin after RNA transcription

RNA transcription

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Post transcriptional processing
(capping, tailing, splicing of mRNA)

Inhibited by Rifampicin, alpha aminitin and intercalators

RNA transcription

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Protein synthesis
rRNA, tRNA, mRNA

Initiation and start codons

Elongation of polypeptide chain: amino to carboxyl end

Termination and stop codons

Translation

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Inhibited by streptomycin
tetracycline
erythromycin
puromycin
chloramphenicol

Translation

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Transport of mRNA into cytosol
Initiation
Elongation
Termination

Translation

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Actinomycin D
Daunomycin
Rifamycin
Ofloxacin

inhibit

Replication

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Actinomycin D
Daunomycin
Rifamycin

inhibit

Transcription

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Tetracycline
Streptomycin
Erythromycin
Chloramphenicol
Puromycin

Inhibit

Translation

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ribosomal binding site in the mRNA, generally located upstream of the start codon AUG

Helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon

Core DNA sequence 5’ TATAAT-
3

Shine-Dalgarno Sequence

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sequence TATAAT of six nucleotides (thymine-adenine-thymine) etc. that is an essential part of a promoter site on DNA for transcription to occur in bacteria

Involved in the initial recognition of the promoter by RNA polymerase

Pribnow-Schaller box

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exists only in prokaryotes

eukaryotic equivalent of the Shine-Dalgarno sequence is called the

Kozak sequence

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A DNA sequence (cis-regulatory element) found in the promoter region of genes in eukaryotes

Goldberg-Hogness box

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Small piece of DNA that inserts itself into another place in the genome

Jumping Genes

Transposons

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Chromatin consists of very long double-stranded DNA molecules and a nearly equal mass of rather small basic proteins

histones

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Unpaired change in nucleotide sequence in DNA

Base substitution - transition and transversion produces insertion, deletion, frameshift

Could be silent, missense or nonsense

Could be spontaneous or induced

Mutation

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Transition and transversion produces insertion, deletion, frameshift

Base substitution

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Point mutations:

Silent mutation
Missense
Non-sense mutation

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No change in the amino acid

Silent mutation

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A different amino acid

Missense

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Stop codon is specified

Non-sense mutation

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If the deletion or insertion is not a multiple of three -> resulting to a markedly changed protein

Frameshift mutation

Insertions and deletions

ex: Colorectal cancer (microsatellite instability)
Crohn’s
Cystic fibrosis

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An agent that damages DNA bringing about structural changes (mutation)

Mutagen

Base substitutions: C - T C - A

Transition Transversion

Amino acid substitution | Altered protein structure and function

Missense Mutation

formation of stop codons | premature terminations

Non sense mutations

Amino acid substitution | No change in protein function

Silent mutation

Substitution of valine for glutamic acid at position-6 of each b-chain

Missense mutation | Sickle Cell Anemia

``` Tautomeric base mispairs Simple misalignment of repeated bases Palindromic misalignment Metabolism of quasipalindromes Insertional mutagenesis (jumping genes or transposons) ```

Spontaneous mutation

Ionizing radiation | Ultraviolet radiation

Radiation mutagenesis

Induced mutation

Radiation mutagenesis | Chemical mutagenesis

Strand breaks (single and double) Oxidation of sugar moiety Rupture of hydrogen bonds Deamination/dehydroxylation

Direct effects

Add alkyl group to nitrogen or oxygen atoms in the bases N - nitrosamines Aflatoxins Ethylene dibromide Amino acid hydrosylates

Alkyating agents

Mechanisms of DNA repair

Excision repair Photoreactivation Recombinational repair

Protective Mechanisms Enzymatic

``` Photolyase * Superoxide dismutase * Catalase * Glutathione peroxidase * Glutathione transferase Desulfitase Demethylase Copy-editing enzyme ```

Protective Mechanisms Compounds with protective groups

``` Acetyl CoA Glutathione Water Amino acids Vitamins and minerals ```

Removal of errors | Proof reading of DNA polymerase due to 3’ —> 5’ exonuclease activity

DNA repair

Diseases associated with defects in DNA repair

XP | Hereditary retinoblastoma

DNA is repaired rather than degraded very efficient High priority process for maintaining cellular function

DNA repair

DNA repair in these cells to preserve species

germ cells

DNA repair in these cells to avoid uncontrolled cell growth and disease (cancer)

somatic cells

Recognition and removal of altered portion of DNA by repair nucleases “Filling in” of gaps by DNA polymerase Sealing of nicks by ligase

Fundamental steps in DNA repair

A composite DNA made up of a DNA fragment ligated with another DNA

Recombinant DNA

Sequence-specific endonucleases Cut doubled stranded DNA at specific sites Recognize palindromic regions

Restriction enzymes

Cleave DNA at palindromic sites Derived from bacteria Produce DNA fragments of manageable size

Restriction enzymes

A test to identify the chromosomal location of an affected gene Flourescence in situ hybridization to a chromosome region with a deletion or mutated gene is a powerful new tool in genetic diagnosis

FISH | Fluoresence in-situ hybridization

Amplifies very tiny pieces of DNA Repeated cycles of denaturation, annealing, polymerization of primers (20-30x) Uses heat-stable DNA polymerase (Taq POL) DNA primers and dNTPs Used in forensic medicine

Polymerase Chain Reactions (PCR)

A method to amplify small quantities of DNA or RNA This powerful tool is helpful in genetic research and diagnosis. It also has been valuable in the rapid diagnosis of infectious diseases such as herpes simplex virus and tuberculosis

Polymerase Chain Reaction

An inherited difference in the pattern of restriction enzyme digestion

Restriction fragment length Polymorphism RFLP

A plasmid into which the DNA sequences from bacteriophage lambda that are necessary for the packaging of DNA

Cosmid

Enzyme responsible for unwinding DNA

helicase

Both parental strands serve template Strand seprated by helicase Requires DNA Polymerase III and I Semi-conservative process

DNA replication

unwinding of DNA and primer formation

Initiation

Formation of daughter DNA strands

Elongation

Removal of mismatched bases

Proof-reading

DNA Replication

Initiation Elongation Termination

origin/Region of replication studied from E. coli

Oric

begins at a single origin of replication called oric Unwinding and formation of Primers

Initiation

Are short RNA oligonucleotides which provide 3’-OH for initiation of DNA synthesis

Primers

3’ OH

Primer terminus

Drug that inhibits RNA polymerase used in traveller’s diarrhea

Rifaximin | Rifampin

Extends the primers

DNA Polymerase III

Removes the primers for ligase to ligate Okazaki fragments

DNA Polymerase I

RNA transcription begins at

promoter region

Inhibited by rifampicin, a- aminitin and intercalators

RNA transcription

Three bases in DNA code for one amino acid. The DNA code is copied to produce Determines amino acid sequence

mRNA

Translation involves Not found in other steps

Transport of mRNA into cytosol

OH 3’ end is where 5’ end is where

amino acid is attached phosophate is attached

Parts of tRNA

``` Oh 3’ end (acceptor arm) Phosphorylated 5’ end Dihydrouridine loop T loop Anticodon loop ```

Responsible for insertional mutagenesis Small piece of DNA that inserts itself into another place in the genome

Jumping Genes | Transposons

Microlesion

Frameshift Base substitution 1) transition 2) transversion

Macrolesion

Deletion Duplication Rearrangement

A mutation that is produced by treatment with a physical or chemical agent that affects the deoxyribonucleic acid molecules of a living organism Chemical or physical

Induced mutations

A region of DNA nucleotide sequence is identical with an inverted sequence

Palindrome

DNA repair enzymes for the damage of UV light

Photolyases

Damaged base is cut out and replaced with DNA

NER Nucleotide excision repair | Base repair

Responsible of pyrimidine dimers formed from UV radiation

Nucleotide Excition Repair | NER

Results from faulty nucleotide excision repair NER

Xeroderma pigmentosum

Mutation to Zn-Cu superoxide dismutase

ALS

``` 55/M Dysphagia Dysarthria Weakness of ALL Ext Progressive weight loss Severe muscle wasting Tongue fasciculations Spasticity Atrophy Bilateral babinski ``` Zn-Cu Superoxide dismutase 1

ALS | Lou Gehrig’s Disease

Microscopic inclusion bodies in spinal cord of ALS

Bunina bodies

Drug of Choice that improves survival of ALS

Riluzole

Riluzole blocks

Glutamate