Gene Expression II

Eve

gene responsible for defining the body plan for fruit flies

lacZ

encodes beta-galactosidase

beta-galactosidase

breaks down lactose

• can break down X-gal into a dark blue compound

repressors; activators

each regulatory element has its own sequence to recruit:

• a set of _______

• a set of _______

activators

Within stripe 2 of the regulatory DNA segment in eukaryotes, only what is recruited?

Combinational control

can also generate different cell types

transcription regulators

different combinations can generate many distinct cell types during development

new

after cell division, a cell may begin expressing a ______ transcript regulator, creating a new regulatory combination

Eight (A-H)

How many different cell types can be produced using only three transcription regulators?

regulators

Each cell type (A-H) expresses a unique set of genes based on its specific combination of ____________.

Red blood cells, epidermal (skin) cells, and gut epithelial cells.

What are three examples of specialized cells that are terminally differentiated and cannot divide?

by proliferating precursor cells

If a specialized cell like a red blood cell cannot divide, how is it replaced?

precursor cells

arise from a small population of self-reviewing stem cells

Stem cells

undifferentiated and can divide for long periods (often the organism’s lifetime)

specialized cells

most cannot divide and are terminally differentiated

T

T or F?

after division, a stem cell daughter can either remain a stem cell or begin a pathway toward terminal differentiation through precursor-cell

bone marrow

Stem cells change/differentiate where?

Differentiated cells

can be grown in culture and reprogrammed

• from adult mouse or human tissues

transcription regulators

Forced expression can reverse the differentiated state of what?

key regulators

Oct4, Sox2, and Klf4 are all considered

ES-like

Key regulators reprogram cells into an embryonic stem-like state called

iPS

can be used to make almost any cell type imaginable

positive

Cell memory is primarily driven by ______ feedback.

cell memory

used for proliferating cells to maintain their identity

• must remember what transcription factors they must keep as they divide

• cells remember what they have + don’t have then pass it on to the next generation

DNA methylation

addition of methyl groups to DNA

• generally associated with transcriptional repression

compact

The addition of methyl groups to DNA promotes a more ______ chromatin structure

gene expression

A more compact chromatin structure limits what?

histone methylation

lead to chromatin compaction and reduced transcription

Covalent histone modifications

regulate gene activity by altering DNA packaging (chromatin structure)

• also for inheriting gene expression patterns

histones

During DNA replication, each daughter strand receives half of the parental modified ______, preserving gene expression patterns.

epigenetic inheritance

DNA sequence is NOT changed during positive feedback—methylation or histone modifications

initiation

Translation requires what complex?

ribosome binding site

By folding into additional structures, RNA can either prevent or allow the ribosome to bind to its __________________.

mRNA

The ribosome binding site is a special sequence on the ______ where the ribosome makes contact.

hides

When RNA folds into an additional structure, it _____ the ribosome binding site, preventing the ribosome from binding.

exposed

When RNA does not fold (or folds differently), the ribosome binding site is ______, allowing the ribosome to bind and start translation.

microRNAs (miRNAs)

tiny RNA molecules that:

• control gene expression by base-pairing with specific mRNAs and reducing both their stability and their translation into protein

RISC (RNA-induced silencing complex)

• involved in miRNA maturation

• responsible for mRNA degradation

RNA interference (RNAi)

is triggered by long, double-stranded RNA (dsRNA).

Viruses; Transposable elements

dsRNAs can come from:

Dicer

enzyme in the cytosol that cuts long dsRNA into short fragments

small interfering RNAs (siRNAs)

Dicer enzyme cuts long dsRNA into short fragments called what?

siRNA

RISC uses what as a guide to target complementary RNA?

complementary RNA

RISC targets which RNA?

RISC

siRNAs are loaded into _____ proteins.

silencing

When RISC targets complementary RNA using the siRNA guide, the result is __________ or degradation of the target RNA.

miRNAs

RISC uses the same complex for siRNAs as it does for __________.

silencingl; degradation

RISC uses the siRNA as a guide to find complementary RNA, resulting in the _____ or ______ of the target RNA.

RNA-inducing transcriptional silencing (RITS)

an alternative protein complex, besides RISC, that siRNAs can be loaded into

RITS pathway

Attracts chromatin-modifying enzymes to silence the expression of complementary genes (transcriptional silencing).

viral infections

The RITS pathway is useful for combating transposon elements and _____________.

Telomerase

has lncRNA that is the template for DNA replication, but also binds the enzyme (protein) that performs the activity.

• also is a protein-RNA complex

lncRNA

can serve as scaffolds that bring together proteins that function in the same cell processes

CRISPR

a tool used in gene editing; a defense system bacteria & archaea have against viruses

Spacers

• correspond to sequences of viral DNA from a previous infection

• used as templates for future infections

Cas (CRISPR-associated) proteins

Proteins associated with the CRISPR system

CRISPR regions

constant DNA sequences separated by variable sequences known as spacers

PAM (protospacer adjacent motifs)

Cas proteins recognize sequences on viral DNA known as ______.

DNA

The CRISPR-Cas9 system recognizes ______ but works as RNA.

PAM

Cas proteins cleave the region next to the _______ (protospacer).

protospacer

gets incorporated in the genome and becomes a spacer

Cas9

If spacer is matching with viral DNA of phage, _____ will activate and destroy the foreign DNA.

CRISPR

Step 1: short viral DNA sequence is integrated into CRISPR locus

Step 2: RNA is transcribed from CRISPR locus, processed, and bound to Cas protein

Step 3: small crRNA in complex with Cas seeks out and destroys viral sequences