Gene Regulation Part 1

Question 1

Chromatin is a combination of

Answer 1

DNA and protein (histones)

Question 2

Histones are

Answer 2

any group of basic proteins found in chromatin

Question 3

Define nucleosome

Answer 3

a structural unit of a eukaryotic chromosome

Question 4

What is a eukaryotic chromosome?

Answer 4

A length of DNA coiled around a core histone

Question 5

How are genes regulated?

Answer 5

Chromatin structure and the control of transcription factors (MAIN WAYS) but also mRNA processing, and control of translation

Question 6

Chromosome structure goes what to what

Answer 6

DNA double helix, to supercoiling around histones, which make nucleosomes, which make up chromatin the spaghetti noodles to make up a chromosome

Question 7

General transcription factors are also known as

Answer 7

basal transcription factors

Question 8

What are basal transcription factors?

Answer 8

A class of protein transcription factors that bind to specific sites (promoters) on DNA to activate transcription of genetic information from DNA to mRNA

Question 9

How does chromatin structure affect transcription?….and thus how genes are regulated

Answer 9

DNA packing (the shape of the DNA) can alter the level of transcription because when DNA is is tightly wound into nucleosomes it is not available for transcription. (LITERALLY you can’t go through transcription because it’s all wound up)

Question 10

How can chromatin structure be altered in order to undergo transcription?

Answer 10

There are remodeling proteins that can change the DNA packing in specific areas to remove nucleosomes, in order for transcription factors to bind and allow transcription take place.

Question 11

Define epigenetics

Answer 11

Changes in gene sequence or phenotype that don’t involve changes to the DNA sequence. These are also defined as heritable changes in gene activity and expression that occur without alteration in DNA sequence

Question 12

Euchromatin

Answer 12

Regions with highly transcriptional activity who are loosely packed

Question 13

Heterochromatin

Answer 13

Regions with low or no transcriptional activity who are tightly, densely packed

Question 14

Difference between chromatin and a nucleosome go

Answer 14

Chromatin is the whole spaghetti structure to make up a chromosome. A nucleosome is one singular thing of the pictures you always used to draw. The coiled DNA with four histones

Question 15

What is a cytosine?

Answer 15

The letter C. LITERALLY.IT’S THE LETTER C

Question 16

What is methylation?

Answer 16

DNA methylation is an epigenetic mechanism used by cells to control gene expression. A number of mechanisms exist to control gene expression in eukaryotes, but DNA methylation is a commonly used epigenetic signaling tool that can fix genes in the “off” position

Question 17

what does acetylated mean?

Answer 17

Adding an acetyl group

Question 18

how can genes be switched on and off?

Answer 18

It depends on how tightly packed they are but this happens through methylation, which makes euchromatin or heterochromatin

Question 19

What are the three different types of motifs you need to know for this test?

Answer 19

helix loop helix(HLH), helix turn helix(HTH), and zinc finger

Question 20

What is the TATA box?

Answer 20

A DNA sequence that indicates where a genetic sequence can be read and decoded. It is a type of promoter sequence, which specifies to other molecules where transcription begins.

Question 21

What is transcription?

Answer 21

The process by which an RNA molecule is produced from a DNA sequence

Question 22

Affinity

Answer 22

the pull towards something

Question 23

What are the three different types of protein domains that can interact with DNA?

Answer 23

HLH, HTH, and zinc finger

Question 24

Difference between motif and domain

Answer 24

A domain can function by itself. It is independently stable. If a motif has a biological function, it can be called a domain. ex. zinc-finger motifs are also related to DNA , are also related to DNA binding, so they are also called zinc-finger domains. This means motifs are structural characteristics and domains are functional regions of a protein.

Question 25

How do transcription factors search for specific binding sequences?

Answer 25

They slide along the DNA segment, ON THE INTERIOR OF THE HELIX, until it finds its specific binding sites

Question 26

How can transcription factors become dislodged from the DNA strand when searching for specific binding sequences? And how do they overcome this?

Answer 26

It can encounter other proteins that are in the way, compacted sections of DNA, or movement of the DNA itself.
Scientists suggest the TF make short hops to bypass other proteins and compacted sections of DNA.

Question 27

Transcription factors are?

Answer 27

DNA binding proteins that control transcription

Question 28

What are three examples of transcription factors?

Answer 28

Basal, activator, repressor

Question 29

the same transcription factor can influence ______ genes

Answer 29

many

Question 30

What do transcription factors modulate transcription?

Answer 30

These regulatory proteins modulate transcription by determining when, where, and how much transcription occurs in a particular type of cell

Question 31

Why is gene expression regulated?

Answer 31

So genes can be turned on and off at the appropriate time. This occurs during development, when responding to the environment, maintaining homeostasis,

Question 32

How does the cell know it needs to maintain homeostasis?

Answer 32

Through cellular signaling

Question 33

Cellular signaling

Answer 33

Cellular communication process that governs basic activities of cells and coordinates all cells in action

Question 34

What are two common types of cellular signaling?

Answer 34

The kinase cascade and second messenger pathway

Question 35

what is a kinase cascade?

Answer 35

A kinase enzyme that modifies other proteins by chemically adding phosphate groups to them (phosphorylation). This, (phosphorylation), usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins

Question 36

Second messenger pathway

Answer 36

Molecules that relay information received at the receptors on the cell surface-such as the arrival of protein hormones, or growth hormones-to target molecules in the nucleus and/or cytosol

Question 37

Cytosol

Answer 37

an aqueous component of the cytoplasm of the cell

Question 38

Short term processes of cellular signaling

Answer 38

Cellular movement, etc.

Question 39

What are the long term effects of cellular signaling

Answer 39

The activation of transcription factors
Which in turn causes movement of TFs from cytoplasm to the nucleolus (where it can act),
and phosphorylation on the transcription factor itself to initiate dimerization. It does this to become active and thus DNA binding can occur because it IS active

Question 40

Dimerization

Answer 40

two transcription factors coming together so it can act