cell and molec exam 1 flashcards set 2

What bond holds amino acids together?

A peptide bond

Histone proteins bind DNA very tightly. What are the likely chemical properties of the amino acid side chains on their DNA-interacting surface — non-polar, negatively charged, or positively charged? Why?

Positively charged. DNA's sugar-phosphate backbone is negatively charged, so histones need positively charged (basic) side chains — like lysine and arginine — to electrostatically attract and bind that negatively charged backbone.

A Mars organism can be genetically transformed like bacteria. Researchers ran an Avery/MacLeod/McCarty-style experiment using DNase, RNase, Protease, and Lipase in different combinations:

Mix	DNase	RNase	Protease	Lipase	Transformation?
A	+	+	−	+	No
B	+	−	+	−	Yes
C	−	+	+	+	No
D	+	−	−	+	Yes

Whats transforming the molecule and why?

RNA. Look at what's consistent: RNase is present in BOTH failed mixes (A and C) and absent in BOTH successful mixes (B and D) — that's a perfect correlation. DNase, Protease, and Lipase are all present in at least one successful mix each, so their presence/absence doesn't track with the outcome. Only destroying RNA blocks transformation every time, so RNA must be the genetic material for this organism.

DNA origins of replication are 30% Adenine. What percent is Cytosine? Show your work.

By Chargaff's rules, %A = %T, so %T = 30%. A+T = 60%. The remaining 40% is split evenly between G and C (since %G=%C), so %C = 20%.

Why would a higher %A (and therefore %T) at an origin of replication matter for DNA replication initiation?

A-T base pairs have only 2 hydrogen bonds (vs. 3 for G-C), so A/T-rich regions require less energy to pull apart. This makes it easier for the strands to separate/melt open at the origin — which is exactly what needs to happen first for replication to begin.

What molecule is primarily responsible for organizing mitotic chromosomes into highly compacted structures — heterochromatin, condensin, histones, or monopolin?

A: Condensin (histones package DNA into nucleosomes generally, but condensin is specifically responsible for the higher-order looping/compaction seen in mitotic chromosomes).

Which of the following require telomeres — eukaryotic linear chromosomes, prokaryotic circular chromosomes, eukaryotic plasmids, prokaryotic plasmids? (Choose all correct)

Only eukaryotic linear chromosomes. Telomeres protect the ENDS of linear DNA — circular DNA (prokaryotic chromosomes, and plasmids of either origin, which are circular) has no ends to protect, so it doesn't need telomeres.

Name one additional feature (besides an origin of replication) required for eukaryotic chromosome maintenance, and its role.

Telomeres — protect chromosome ends from degradation/fusion and solve the "end-replication problem" so the chromosome doesn't shrink with every division. Centromere — required for kinetochore assembly and spindle microtubule attachment, ensuring correct chromosome segregation during cell division.

What's needed for transcription to initiate — template DNA, RNA polymerase, ribonucleotide triphosphates, and/or termination factors? (Choose all correct)

Template DNA, RNA polymerase, and ribonucleotide triphosphates (NTPs). Termination factors act at the END of transcription, not at initiation.

Given a consensus sigma-32 promoter sequence and two real gene promoters, how do you determine which gene is more strongly bound/expressed?

Count the number of base mismatches between each gene's promoter and the consensus sequence (at both the -35 and -10 regions). Fewer mismatches = closer match to consensus = tighter sigma factor binding = more likely to be highly expressed. (Worked example: Consensus -35 CCCTTGAA/-10 CCCGATNT vs. Gene 1 CCGTTGAT/CCGGATTT [3 total mismatches] vs. Gene 2 CGGTTAAT/CCAAATTT [6 total mismatches] → Gene 1 is the closer match, so Gene 1 is more likely bound more tightly/expressed more highly.)

What protein does a sigma factor recruit to the promoter to begin transcription?

RNA polymerase (the sigma factor is a subunit that helps direct/recruit the RNA polymerase core enzyme to a specific promoter sequence).

Gene 1 is regulated by HilD (activator, active under low oxygen) and Lrp (repressor, active when leucine — a co-repressor — is present). In which condition does transcription occur: (1) low oxygen + high leucine, or (2) low oxygen + low leucine? Why?

Condition 2 (low oxygen + low leucine). In both conditions HilD is active (low oxygen), but in condition 1 the high leucine level activates the Lrp repressor, which binds the operator and blocks RNA polymerase — repressor binding generally overrides/blocks activator help. In condition 2, leucine is low, so Lrp stays inactive and can't block anything, letting active HilD help RNA polymerase transcribe the gene freely.

If a mutation prevents the Lac repressor from binding the operator, what happens to transcription?

Transcription is always ON, regardless of lactose levels — nothing can block RNA polymerase anymore.

Predict protein levels for a true target gene of the let-7 miRNA in a let-7-deletion cell line.

Protein levels increase. miRNAs normally repress translation and/or promote degradation of their target mRNAs via RISC; without let-7, that repression is lost, so more protein gets made

Fluoride addition dramatically increases expression of a reporter gene fused to the eriC 5' UTR sequence. What kind of regulator is this, and how does it work?

A riboswitch — an RNA element (usually in the 5' UTR) that directly binds a small molecule (here, fluoride ions) without needing any protein regulator. Ligand binding changes the RNA's secondary structure, which switches gene expression on (in this case, by relieving a block on transcription/translation of the downstream eriC gene).

The amino acid tyrosine is what type — positively charged, negatively charged, polar, or non-polar?

Polar (it has a hydroxyl [-OH] group on its side chain, giving it polarity without a full charge).

Why is an insertion/deletion of exactly 3 base pairs less harmful to protein function than an insertion/deletion of 1 base pair? (Real question, from rifampicin/RpoB resistance mutations)

The genetic code is read in triplet codons. A 3-bp indel adds or removes exactly one whole codon (one amino acid) without shifting how the rest of the sequence is grouped into codons — everything downstream stays in the correct reading frame. A 1-bp indel shifts the reading frame for every codon downstream of the mutation, completely scrambling the amino acid sequence from that point on (and often creating a premature stop codon) — this is a frameshift mutation.

What is a silent mutation, and what feature of tRNAs makes silent mutations possible?

A silent mutation changes a DNA/codon nucleotide but does NOT change the amino acid produced. This is possible because the genetic code is degenerate (multiple codons can specify the same amino acid), which works because of wobble base pairing — some tRNAs can recognize more than one codon due to flexible pairing at the third ("wobble") position of the codon-anticodon interaction.

At the ribosome's A site, what are the two mechanisms that ensure the correct amino acid is added to the growing chain?

(1) Aminoacyl-tRNA synthetase specificity — each synthetase recognizes one specific amino acid AND its one matching tRNA, and covalently attaches them together, so the right amino acid gets loaded onto the right tRNA in the first place. (2) Codon-anticodon base pairing — the charged tRNA's anticodon must correctly base-pair with the mRNA codon sitting in the A site; only a tRNA with a matching anticodon (and thus the correct amino acid) can stably bind there.

After a new aminoacyl-tRNA is accepted into the A site, what's the next step of elongation?

Peptide bond formation between the new amino acid (A site) and the growing chain (P site), followed by translocation — the ribosome shifts one codon down the mRNA, moving the A-site tRNA to the P site and the old P-site tRNA to the E site (where it's released).

Where does peptide bond formation occur, and what actually catalyzes the reaction?

It occurs at the interface of the large ribosomal subunit (the "peptidyl transferase center"), between the A and P sites. It's catalyzed by rRNA (ribosomal RNA), not a protein — which is why the ribosome is called a ribozyme.

What are two structural differences between prokaryotic and eukaryotic ribosomes that antibiotics can exploit?

1) Ribosome size: prokaryotes = 70S, eukaryotes = 80S. (2) Ribosome composition/subunits: prokaryotic 70S = 30S small + 50S large subunit; eukaryotic 80S = 40S small + 60S large subunit — the different rRNA and protein composition of each gives antibiotics selective targets on bacterial ribosomes without harming human ones.

Why is it important to have antibiotic classes that target different sites within the ribosome (rather than just one)?

Different antibiotics can block different specific steps of translation (e.g., tRNA binding, peptide bond formation, ribosome movement along the mRNA). Having multiple distinct targets matters because bacteria can evolve resistance to any single antibiotic through mutation — having several different targets available gives more backup options to still stop bacterial growth even after resistance develops to one drug.