BIOC 432- Exam 3 Guided Questions

What are the general rules of genetic codes?

1) The sequence of bases in a codon must follow the direction of translation (Codons are read from 5' to 3') 2) The code is non-over-lapping (adjacent trinucleotides: one nucleotide can be only part of one codon not two different codons) 3) The code is read in a fixed reading frame (starts from a start codon and reads by 3s until the end; a genetic code can be read in three different reading frames depending on which base one begins with)

What is Posttranslational modification of proteins? (Lecture 15)

Can drive transport, reversible or irreversible. Some types include: -enzymatic removal of formyl group from first residue, or removal of Met and sometimes additional residues -Removal of signal sequences or other regions -Removing sequence to activate an enzyme -Proteolysis, disulfide bond formation -Attachment of a functional group or macromolecule to the fully synthesized protein

What is chromatin condensation to form heterochromatin?

Chromatin is genomic DNA that has condensed using protein-DNA complexes. The condensation of DNA can dramatically recuse the size of DNA. Heterochromatin is the most condensed where transcription is inactive or being actively inhibited or repressed.

What is the second clue in protein synthesis?

Crick's adaptor hypothesis. A small nucleic acid could serve as an adaptor between RNA and protein synthesis if it could bind RNA and an amino acid. One end of the adaptor would bind to a specific amino acid and the other end would bind to a specific sequence in the mRNA.

How do chromosomes work in humans?

Each cell should contain 23 pairs of chromosomes (46 total). Females should have two X chromosomes and males should have an X and a Y chromosome, one chromosome inherited from the mother and one from the father.

What are the techniques to examine protein and DNA interaction?

Electrophoresis: molecule size, smaller are lower on the gel, mobility shift when testing protein of interest and DNA Fragments of DNA using autoradiogram there were be a blank spot where the protein is interaction with that region of DNA ChIP Seq

What are codon-anticodon interaction and orientation in ribosome?

Every codon has a corresponding anticodon (tRNA). There are more codons than tRNAs and so some must bind to more than 1 codon. A codon in mRNA is orientated 5' to 3'.

Why most of DNA binding motifs of transcription factors bind to the major groove of DNA

For 2 main reasons. 1) There is more room for proteins to access the sides of the bases. 2) The pattern of H-bond donors and acceptors on the bases are more distinct on the major groove of DNA than on the minor groove.

What is the DNA binding motif helix-loop-helix?

Found in eukaryotes. Contain a loop region between the DNA binding alpha helix and the dimerization alpha helix.

What is the DNA binding motif leucine zipper?

Found in eukaryotic cells. contains a Leu every 7th position in the region of protein required for dimerization.

What is transfer RNA (tRNA) function?

Functions as an adaptor molecule, is the driving force for protein synthesis.

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Start of short answer material

What is Nirenberg-Leder experiment?

The assignment of triplet codons to specific amino acids based on retention of radioactive aminoacylated tRNA molecules on nitrocellulose filter that binds to proteins. If the anticodon and codon were not complementary then the radioactive aminoacyl tRNA passed through the filter.

What is nonspecific interaction?

The phosphate backbone of the DNA interactions with the protein

What is DNA binding motif?

There are four main types: helix-turn-helix, zinc finger motif, leucine zipper, and helix-loop-helix. The motifs are found in transcription factor proteins.

What are the general rules of protein synthesis?

There are three main clues for protein synthesis. 1.Proteins synthesized at ribosomes 2.tRNA acts as an "adapter" to translate mRNA into protein 3.Amino acids activated for synthesis by attachment to tRNA via aminoacyl-tRNA synthetases

What is the exp to decipher the first codon and others?

20 different test tube reactions Spike each with a different radioactive amino acid (one at a time) Add the polyU RNA Recover the proteins by acid precipitation, the one with radioactivity in the protein pellet is the one with the code. phe was first from poly-U.

What is definition of open reading frame?

A portion of a DNA molecule that, when translated to amino acids, has no stop codons.

What is the role of three sites (E, P, A) of ribosome in protein synthesis?

A-site: binds aminoacyl-tRNAs (except initiator tRNA = fMet-tRNAfMet binds to P site). P-site: binds initiator tRNA and peptidyl-tRNA (growing chain). E-site: binds deacylated tRNA (exit site)

What is the third clue in protein synthesis?

Activation of amino acids. For activation the amino acids are attached to heat soluble RNA (tRNA).

Many gene regulatory proteins bind to multiple sites on the genome. How does affinity play a role?

Affinity of the protein for the DNA differ from one site to another. Protein levels determine what sites will be bound by a protein. High levels of protein will bind to a DNA site with weak affinity.

What are stem cells? (why are they important)

After an egg is fertilized, the first few cell divisions make a ball of totipotent cells. They have the potential to differentiate into various different tissues.

What is the role of EF-Tu and EF-G in elongation?

Aminoacyl-tRNA binds first to EF-Tu complex. EF-G is translocase and bound to GTP.

What is Single Nucleotide Polymorphisms(SNP)?

Can be used to make a molecular fingerprint of an individual, usually by one mutation and a single nucleotide change.

What is peptide formation mechanism?

Peptide bond formation is catalyzed by the elongation step where ribosomes move along the mRNA matching tRNAs to each codon during protein synthesis. Polypeptide synthesis composes of the initiation, elongation, termination, and ribosome recycling steps. Important factors are ribosomes, mRNA, tRNA, translation factors, and ribosome recycling factors.

What is the difference in the amino acid for the first codon between prokaryotes and eukaryotes?

Prokaryotic cells have the start codon code for N-formyl-methionine that is carried by the initiator tRNA. Eukaryotic cells have the start codon code for methionine and is also carried by the initiator tRNA.

What happens during protein DNA interactions?

Protein binds nonspecifically to DNA (mostly through the backbone phosphates), and slides up and down the DNA until a specific binding site is encountered.

What is the first clue in protein synthesis?

Proteins are synthesized on ribosomes. Ribosomes organize the interactions between codons and anticodons in aminoacyl-tRNAs. Ribosomes catalyze the formation of peptide bonds between adjacent amino acid residues. RNA does the catalysis of peptide bond formation.

What is targeting of protein to nucleus?

Proteins synthesized on free ribosomes and directed to sub cellular locations based on targeting sequences. Location of the sequence varies within the protein targeted for nucleus. Nature of the sequence is multiple different kinds; a common motif includes a short segment rich in Lys and Arg residues.

What is SOS regulon?

Regulates a set of genes involved in response to DNA damage or inhibition of replication. Activated by DNA damage, controlled by negative regulator (LexA repressor)

What is the general procedure of protein synthesis?

There are five stages of protein synthesis. 1) The tRNAs are aminoacylated. 2) Translation initiation occurs when an mRNA and an aminoacylated tRNA are bound to the ribosome. 3) In elongation, the ribosome moves along the mRNA, matching tRNAs to each codon and catalyzing peptide bond formation. 4) Translation is terminated at a stop codon, and the ribosomal subunits are released and recycled for another round of protein synthesis. 5) Following synthesis, the protein must fold into its active conformation and ribosome components are recycled.

What are chromosomes?

These are located inside the nucleus of animal and plant cells during mitosis. Chromosomes are made of protein and a single DNA molecule. They are passed from parents to offspring. The DNA in the chromosomes carry specific instructions to make the organism unique.

What is the mechanism of acetylation of histone lysine residues at histone tails?

This process is a chromatin modifying process and is post-translational histone modification. Acetylated by histone acetyltransferases (HAT) to neutralize positive charges or make a negative charge to loosen histone binding to DNA. Added to the N-terminal tails. Acetyl groups are removed by histone deacetylases (HDAC)

What is Genome-Wide Association Study (GWAS)?

An examination of genome-wide set of genetic variants in different individuals for variants associated with disease traits, such as hypertension, obesity, or hyperlipidemia. Many GWAS-implicated SNPs are in noncoding sequences.

How do mutations in the bacterial genome affect the function of the lac operon? (basic lac operon information will be provided)

Can cause the lac operon to not respond effectively causing it to be stuck inactive or active.

What are the differences between euchromatin and heterochromatin? (Lecture 16)

Heterochromatin contains histone H3 modified by methylation of lysine 9 and 27. (inactive/condense) Euchromatin tails are more extensively acetylated in euchromatin. Euchromatin contains contains histone H3 extensively acetylated on lysine 9, 27 and other H3 lysines. Euchromatin also contains H3 that are modified by methylation of lysine 4, and phosphorylation of serine 10. (active/open)

What is the mechanism by which puromycin inhibits protein synthesis?

Inhibits protein synthesis in both eukaryotes and prokaryotes. Puromycin is a peptidyl acceptor that terminates translation. The amino group of puromycin attacks the carbonyl carbon of the polypeptide at the P site. Then puromycin binds at the A site. when a peptide bond is formed the polypeptide transfers to the puromycin molecule inhibiting the addition of other amino acids since it is released from the ribosome.

What is the Trp operon?

Is in E. coli containing gene regulatory region and coding sequences for five enzymes in the tryptophan biosynthetic pathway.

What is the DNA binding motif helix-turn-helix?

Lambda, Lac and Trp repressors. 20 amino acids long, contains 2 alpha-helices connected by a short turn. The second helix is called the recognition helix and has direct contacts with major grooves.

Compare the trp repressor and attenuation in trp operon regulation.

Regulation by the trp repressor and attenuation are both mechanisms for reducing expression of the trp operon when levels of tryptophan are high. However, trp repressor blocks initiation of transcription and attenuation prevents completion of transcription.

What are the other related materials to protein degradation?

Some common mechanisms: ER-associated degradation (ERAD), Mitochondria-associated degradation (MAD), and autophagy.

Briefly how the Trp repressor controls the Trp operon.

The Trp operon has a repressor that binds to DNA in the presence of tryptophan. Trp repressor is a homodimer. When Tryptophan is abundant, it binds to repressor, causes it to bind to the operator, and slows expression of genes for Trp synthesis. It has helix-turn-helix motifs that interact with DNA via the major groove

What are the different types of stem cell differentiation?

Totipotent cells: the ability to differentiate into any tissue type or to complete an organism. Pluripotent cells: the ability to differentiate into the three germ cell layers and many types of tissues. They cannot make a complete organism. Multipotent stem cells: can self-renew by dividing, present in specific tissues. Usually adult stem cells. I.E. hematopoietic stem cell. Unipotent cells: The ability to differentiate into one type of cell or tissue. I.E. a liver stem cell.

Briefly how attenuation controls the Trp operon.

Transcriptional termination by RNA polymerase is favored when tryptophan levels are high because there is abundance of charged Trp-tRNA causes the ribosome to quickly synthesize the leader region allowing the termination structure by the 3-4 region hairpin to form and transcription of the trp operon ends. Transcriptional elongation by RNA polymerase is favored when tryptophan levels are low because the ribosome stalls at Trp condons because Trp-tRNA is limiting resulting in slow synthesis of the leader. This stalling prevents region 1 from pairing with region 2 forming the non-terminator structure by the 2-3 region hairpin preventing formation of 3-4 hairpin and transcription of the trp operon continues.

What is Protein DNA interaction?

Two types of noncovalent interactions. nonspecific interaction and specific interaction. Protein alpha helices bind in the major groove of DNA, specific amino acids in proteins make contact with nucleotide bases.

What is specific interaction?

Typically hydrogen bonds between the base pairs and amino acid side chains. Arg, Lys, Gln and Asn are found to make contact with nucleotide bases.

What is protein degradation by ubiquitin system?

Ubiquitin is highly conserved by all eukaryotes. Ubiquinated proteins are cleaved by the 26S proteasome complex. Proteins are linked to ubiquitin by three enzymes; Activating enzyme E1, Conjugating enzyme E2, and Ligating enzyme E3.

What is the DNA binding motif zinc finger motif?

Usually found in eukaryotes, Zif268 transcription factor contains three zinc finger motifs in tandem. 30 amino acids long, 1 Zn atom coordinated with 2 Cys and 2 His residues, the alpha helix of the zinc finger motif binds to major groove of DNA helix.