MCB BASED ON PACKET

What protein examples transport or carry substances?

Hemoglobin and albumin.

What protein examples act as hormones or chemical signals?

Insulin and thyroxine.

Which proteins defend against pathogens?

Immunoglobulins.

What storage role does albumin have in embryonic organisms?

It serves as a stored food source.

What do chaperone proteins do?

They help other proteins fold correctly.

What is the role of protein families?

They consist of similar yet distinct proteins that can perform related functions.

What defines primary protein structure?

The amino-acid chain or sequence.

What defines secondary protein structure?

Local folding of the polypeptide chain through hydrogen bonds, including alpha helices, beta strands or sheets, and turns.

What defines quaternary protein structure?

Interaction among multiple peptide chains or subunits.

What is an isoenzyme or isoform?

An alternative protein structure that catalyzes the same reaction with different efficiencies.

How can reversible covalent modifications regulate enzymes?

Adding or removing functional groups can activate or inactivate enzymes.

What is irreversible proteolytic activation?

A protein is cut apart to become fully active.

What is heteroallostery?

An effector or inhibitor binds at an allosteric site and changes substrate binding at the active site.

What is homoallostery or cooperativity?

Binding of one substrate changes the binding efficiency of subsequent substrate molecules.

What would happen if the locations of Ran GAP and GEF were reversed?

Their functional distribution would reverse in the nucleus.

What would happen if Ran GAP were missing?

There would be no efficient way to cleave the phosphate.

What is a genome?

A collection of chromosomes.

When are chromosomes readily visible under a microscope?

During mitosis, when they are highly compacted.

What chromosome content is expected in a diploid cell?

Two chromosome sets, or diploid content.

How can chromosome regions be distinguished cytologically?

Orcein can stain heterochromatin C-bands, while other stains can reveal all heterochromatin regions or both G-bands and Q-bands in euchromatin regions.

What can spectral karyotyping reveal?

It paints chromosomes different colors and can reveal cancer-cell translocations, deletions, and aneuploidy.

Why is supercoiling alone sufficient for some genomes but not eukaryotic genomes?

Small circular genomes in prokaryotes and some viruses can be compacted by supercoiling, but large linear eukaryotic genomes require DNA wrapping around histones to form nucleosomes.

What is genetic redundancy?

The presence of multiple copies of genes, chromosomes, and repetitive DNA motifs.

Why do cells carry many copies of rRNA genes?

They need many ribosomes, so multiple rRNA gene copies allow faster rRNA production.

What evolutionary process also creates genetic redundancy?

Gene duplication.

Where is satellite DNA commonly found?

In long tandem repeats, often in heterochromatin at centromeres, telomeres, and other noncoding regions.

How is repetitive DNA classified?

Highly repetitive satellite DNA versus middle-repetitive tandem repeats and interspersed retrotransposons.

How are tandem-repeat copy numbers distributed?

Copy number varies among individuals, and repeats are dispersed randomly throughout the genome.

What diseases are associated with trinucleotide-repeat expansion?

Huntington disease and fragile X syndrome.

What fraction of the human genome is predicted to consist of transposable elements?

About 45%.

What are transposons thought to be derived from?

Relics of past virus integrations that retained the ability to move.

How can transposon insertion affect genes?

Insertion is nonrandom and can create new genes, RNA, or inserted protein-coding and regulatory regions.

What is global duplication by repetitive elements?

Addition of repetitive elements that enables deletions, inversions, and translocations of large chromosome portions.

How can local repeated elements affect DNA replication?

They can cause polymerase slipping.

Which base replaces thymine in RNA?

Uracil.

What structural feature did antiparallel base pairing create?

An antiparallel double helix of consistent width.

What did Griffith's transformation experiment show?

Dead virulent smooth bacteria transferred genetic information to living rough bacteria, transforming them and killing the mouse.

What happened when Griffith injected dead virulent smooth bacteria alone?

The mouse lived.

What happened when dead virulent smooth bacteria were mixed with living rough bacteria?

The mouse died, and smooth bacteria were recovered.

What did Avery, MacLeod, and McCarty test?

They treated dead smooth bacteria with protease, ribonuclease, or deoxyribonuclease before testing transformation.

How did Hershey and Chase distinguish DNA from protein?

They labeled phage protein with radioactive sulfur and phage DNA with radioactive phosphorus.

What did the Hershey-Chase experiment conclude?

The phosphorus-labeled DNA entered bacteria, so DNA is the genetic material.

What are examples of macromolecular machines?

Ribosomes, nuclear pores, nucleoli, centrosomes, and stress granules.

What are examples of membrane-enclosed compartments?

Endoplasmic reticulum, mitochondria, transport vesicles, and lysosomes.

What is the fluid-mosaic model of the cell membrane?

A flexible mixture of lipids, proteins, and carbohydrates organized around a phospholipid bilayer.

Where are membrane carbohydrates presented?

They decorate lipids and proteins only on the extracellular surface, not the cytosolic surface.

What sequence of events is proposed in the endosymbiotic model?

An anaerobic archaeon formed a nucleus and primitive nuclear membrane, an engulfed aerobic bacterium became a mitochondrion, and an engulfed photosynthetic bacterium became a chloroplast.

What is the Golgi apparatus structurally?

Stacks or discs of plasma-membrane-like cisternae.

What does the Golgi apparatus do?

It modifies proteins and lipids and serves as a trafficking center.

What structural feature enables lysosomal function?

Lysosomes contain digestive enzymes that function at low pH.

What do lysosomes degrade?

Organelles and biomolecules.

What is the principal function of chloroplasts?

Photosynthesis.

What is the nucleolus composed of?

rRNAs, ribosomal proteins, and regulatory or modifying proteins and RNAs.

What does the nucleolus do?

It makes ribosomal subunits and is the largest biomolecular condensate.

What are ribosomes made of?

Ribosomal RNAs and ribosomal proteins arranged into two subunits.

What do ribosomes do?

Protein synthesis or translation.

How does euchromatin permit transcription-factor access?

It loops out from compact regions, exposing DNA to protein factors.

What is a lampbrush chromosome?

A special polytene chromosome with extended loops.

What is a Barr body?

An inactivated, heterochromatic X chromosome.

What do histone locus bodies assemble?

Histones.

What is the basic nucleosome structure?

A histone octamer wrapped by about 147 base pairs of DNA.

What interactions hold the nucleosome together?

Attraction between positively charged arginine and lysine residues and the negatively charged sugar-phosphate backbone of DNA.

Why are histone tails important?

They are primary sites of modification.

What is chromatin remodeling?

Regulation of interconversion between euchromatin and heterochromatin, which can spread in wave-like fashion.

What stops heterochromatin spreading?

A barrier or insulator DNA sequence that acts like an impassable wall.

What can reverse a chromatin state?

Rewriting histone marks can reverse the tide of chromatin remodeling.

What does epigenetics study?

Heritable gene-expression changes caused by external factors without corresponding changes to the DNA sequence.

What diseases can result from altered DNA methylation?

Imprinting disorders, cancer, and altered expression of cytosolic factors.

How can methylation contribute to cancer?

Hypermethylation can turn off tumor-suppressor genes such as BRCA1 and APC, while hypomethylation can destabilize chromosomes.

What are examples of cytosolic factors with maternal effects?

The oocyte or egg cytosol contains many proteins such as transcription factors and noncoding RNAs such as modifiers and regulators.

Which histone proteins receive acetylation and related esters?

H2A and H2B.

Which histones can be phosphorylated, ubiquitinated, sumoylated, O-GlcNAcylated, or ADP-ribosylated?

All histones.

What are histone-mark readers?

Proteins that recognize combinations of histone marks and interpret their meaning.

How does acetylation usually affect chromatin?

It activates transcription and promotes euchromatin by destabilizing histone-DNA interactions.

What does it mean that the genetic code is nonoverlapping?

Each mRNA nucleotide normally belongs to only one codon in a translation event, although overlapping genes can share DNA space.

What does it mean that the genetic code is universal?

Almost all life uses the same code.

Why are DNA replication polymerases called DNA-dependent DNA polymerases?

DNA is both the template and the product.

Why are transcription polymerases called DNA-dependent RNA polymerases?

DNA is the template and RNA is the product.

Which factor is recruited first during promoter recognition?

TFIID.

What does TBP do at the TATA box?

The TATA-binding protein recognizes the TATA box and distorts the DNA helix.

What else does TFIID bind besides the TATA box?

The initiator element and downstream promoter element.

What does TFIID recognize overall?

The TATA box and other DNA sequences near the transcription start site.

What helicase function does TFIIH provide?

It unwinds DNA at the transcription start point.

What is an enhancer?

A DNA binding site for an activator protein that can recruit the transcription machinery.

What marks the end of transcription initiation?

Actions of TFIIH.

Which DNA strand serves as the RNA template?

Only one strand of the DNA duplex.

In what direction does RNA grow?

5-prime to 3-prime.

What is promoter-proximal pausing?

RNA polymerase II pauses after transcribing about 20-60 nucleotides.

Why does promoter-proximal pausing occur?

It provides time to resolve heterochromatin and check the work completed so far.

Which factor induces promoter-proximal pausing?

Negative elongation factor, NELF.

Which factor works with NELF to maintain pausing?

DSIF, the DRB-sensitivity-inducing factor.

What is SPT4 related to?

The Ty retrotransposon family in yeast.

What does ELF1 do in some cells?

It helps SPT4-like factors and is important in immune cells and in bypassing unstable trinucleotide repeats.

What broad role does DSIF have beyond pausing?

It helps transcribe through nucleosomes.

What does FACT do during elongation?

It removes histones and facilitates chromatin transcription.

What does NAP1 recycle?

H2A/H2B histone dimers.

Why are topoisomerases needed during transcription?

Superhelical stress occurs in front of RNA polymerase, and topoisomerases maintain DNA coiling tension.

What else does PARP1 ADP-ribosylate?

Many other chromatin-associated proteins, coordinating binding and removal of elongation factors.

How does RNA elongation fidelity compare with other processes?

Probably moderate: temporary RNA mistakes are less harmful than permanent ones, fidelity is higher than DNA repair and reverse transcription, but lower than DNA replication and varies by gene.

What enables prokaryotic transcription termination?

Rho protein or RNA secondary structure such as a hairpin.