BIO 3170 Final

Which amino acid is usually excluded from alpha helices as they cannot participate in hydrogen bonding?

What kind of interaction holds together protein secondary structure?

R groups project ___ from the surface of the alpha helix and determine the chemical nature of the helix

How many residues make up a beta turn?

A coiled-coil motif is composed of two alpha helices wound around each other. The seam is stabilized by interactions between heptad ___ and ___ hydrophobic side chains at regular intervals along each strand.

The zinc-finger motif is present in many DNA-binding proteins that help regulate what?

The zinc-finger motif is a 25-residue motif with two invariant __ residues and two invariant __ residues

What type of interaction helps to stabilize tertiary protein structure?

What is the hydrophobic effect? (in relation to tertiary protein structure)

Match the ways to visualize proteins

The transcription initiation complex is an example of what type of structure?

How to enzymes accelerate rates of cellular reactions?

Trypsin is a serine protease whose substrate-binding pocket contains a catalytic site which is composed of which three amino acids?

Why is protein degradation necessary?

Polyubiquitinylation targets proteins for proteasomal degradation. Put its steps in order

Put the steps of proteolysis in order

Match the enzyme to its type of activity

Transcriptional control is like a switch that can be turned on and off

Match the type of organism to the mode of gene regulation

The lac operon encodes 3 enzymes required for the __ of lactose. The trp operon encodes 5 enzymes required for the __ of tryptophan.

To initiate transcription, E. coli RNA polymerase must associate with a sigma factor, most commonly sigma __ (number).

The lac repressor binds to the __ of the lac operon when not bound to lactose.

When lactose is absent, transcription of the lac operon is __.

E. Coli synthesized cAMP in response to low glucose levels. cAMP binds to a transcriptional activator protein and binds to the __ of the lac operon when complexed with cAMP.

Match the scenario to the outcome on lac operon expression

The lac repressor always binds to the main operator and one of the two secondary operators.

The lac operon's default state is __, the trp operon's default state is __.

Enhancers are always found in direct proximity to the gene they regulate.

What is the advantage to dimerization?

Glucorticoid receptor promotes transcription of target genes when glucorticoid hormones binds to the __ activation domain

What are the four major classes of activation (transactivation) domains?

What structural motif of DNA binding domains interacts with the major groove of the target DNA?

Associate the binding domain to the mode of binding.

What is the most common DNA-binding motif?

CREB (cyclic AMP response element-binding protein) is activated by what?

Combinatorial transcription regulation involved interaction of structurally unrelated transcription factors bound to closely spaced binding sites in DNA.

Which proteins make up the enhanceosome complex of the beta-interferon enhancer?

The ligand-receptor complex functions as a transcription activator.

Match the functional region of the nuclear receptor to its function.

Put the steps of hormone-dependent gene activation in order.

Response elements contain inverted repeats separated by how many base pairs?

For class I receptors, the hormone interacts with the receptor in the __, while for class II receptors it interacts in the __.

Match the heterodimeric nuclear receptor with its function.

In heterodimeric nuclear receptors, which subunit defines the hormone response and direct repeat binding sites?

How is beta-catenin tagged for degradation in the absence of Wnt?

How does the UAS/GAL4 overexpression system work?

Match the type of gene expression "logic circuit" to its name

What are the five master transcription factors (Yamanaka factors) that regulate embryonic stem cell pluripotency?

You are able to induce the dedifferentitation of fibroblast cells back into pluripotent stem cells by inserting Yamanaka factors.

Name some medical uses of patient-specific iPS cells

Morphogen gradients help establish what in growing organisms? (multiple answers are correct)

A cut planaria worm is able to regenerate a head and tail in the proper spots due to gradients of which protein?

Veratrum californicum makes cyclopamine, which inhibits __ synthesis, which is needed (Post-Translational Modification) for Hedgehog production and reception.

Dividing nuclei are given information of their position along the axis in flies by the ratio of which two proteins?

In Drosophila, axis determination genes that activate gap genes come from the mother.

Match the genes involved in Drosophila axis anterior-posterior formation to their function

In Drosophila embryo, the bicoid protein is most concentration at the __ end.

What would happen if you were to inject bicoid mRNA to the middle of a growing drosophila embryo?

MicroRNAs hybridize with which region of the target mRNA?

Match the type of inhibiting RNA to its functions

Associate the proteins involved in miRNA biogenesis/processing with their function

MiRNAs can be used as disease biomarkers

What is the name of the miRNA found in food fed to bee larvae which induces worker development?

In bees, miR162a was shown to __ gene expression levels of the cell-signalling pathway regulator TOR

In bees, what is the main factor that determines formation of worker bees vs. Queen bees?

During early embryogenesis, DNA is heavily methylated

De novo methylation is mediated by methyltransferase DNMT_, and maintained by DNMT_ following DNA replication.

When methylation affects CpG islands, methyl-binding proteins trigger a silencing cascade that involved the deacetylation and methylation of histone __.

How does DNA methylation affect gene expression?

DNA methylation is heritable

Which protein ensures methylation patterns are faithfully replicated by scanning DNA and depositing methyl groups on newly synthesized DNA, opposite methyl groups on the old strand?

Match the type of epigenetic inheritance to its definition

What is the histone code?

The histone code is influenced by environmental factors

Induction of a gene by a transcription factor can still occur if the target DNA is condensed.

What kind of protein works in the opposite manner as a pioneer transcription factor?

Histone tails are generally much more extensively __ in euchromatin than in heterochromatin.

This protein contributes to heterochromatin condensation by binding to histone H3 N-terminal tails trimethylated at lysine 9

Match the domains/proteins associated with histone deacetylation and hyperacetylation with their function

Restriction sites are typically __, and yield fragments with either blunt or sticky ends.

Plasmids replicate jointly with the cell's chromosomal DNA

Plasmid vectors contain three basic components. What are they?

How can you differentiate between cells that have successfully taken up your fusion plasmid vs. Cells whose plasmids have re-ligated? (alpha-complementation)

What are the three major steps of PCR amplification?

Put the steps of the CRISPR defensive pathway in order

What does CRISPR stand for?

Cas9 cleaves target DNA at __ location(s).

What are the two ways the cell repairs target-gene inactivation by the CRISPR-Cas9 system?

What is the difference between subfunctionalization and neofunctionalization?

Explain how RNA could have evolved from individual nucleotides.

The last universal common ancestor (LUCA) was likely: (check all that apply)

MRNA sequences cannot be modified after transcription.

How are octopi with the same genome able to live in arctic waters as well as tropical reefs?