Cell Biology Exam 2

What are genomes composed of?

DNA

What does DNA code for?

Genes, regulatory sequences, nucleosome binding sites, origins of replication, centromeres, telomeres, junk, and more

What determines the morphology, biochemistry, and function of a cell?

Differences in gene expression and protein activity

True or False: Most cells have different genomes

False, they are all the same

Can the genome from a differentiated cell be reprogrammed? Why or why not?

Yes, reprogrammed to express genes necessary to make the entire organism (cloning)

The experiment by taking a nucleus and extracting it to later inject it into an empty egg where factors will make the correct genes to be expressed is an example of what?

The reprogramming of the genome from a differentiated cell

What regulates gene expression?

Transcription factors and regulatory proteins which control RNA polymerase activity

Packaging of the DNA

What is responsible for the switching from one cell state to another?

Combinations of key regulatory proteins

What is a promoter?

DNA sequence where transcription factors and RNA polymerase bind to initiate transcription

Where are promoters located?

Adjacent to and “upstream” of the gene it controls

Is this a prokaryote or eukaryote? How do you know?

This is a eukaryote, this is because prokaryotes do not have introns but this gene does

Where does regulation of gene expression and protein activity occur?

It occurs at a number of steps

Name the first step of gene expression regulation and protein activity

Transcriptional control

Name the second step of gene expression regulation and protein activity

RNA processing control

Name the third step of gene expression regulation and protein activity

RNA transport control

Name the fourth step of gene expression regulation and protein activity

Translation control

Name the fifth step of gene expression regulation and protein activity

Protein activity control

How is gene expression controlled in eukaryotes?

Transcription factors, general and specific

How is gene expression controlled in prokaryotes?

Promoter access

What do regulatory proteins bind to for transcription factors?

Promoters of genes

What are promoters?

DNA sequences that have the correct chemical properties to bind to transcription factors

How do transcription factors regulate transcription?

By regulating RNA polymerase

What do transcription factors do in eukaryotes?

Form large protein complexes containing enhancer and repressor proteins

What are certain amino acids in a transcription factor’s DNA binding domain perfectly positioned to?

Hydrogen bond with certain nucleotides in the promoter DNA

What is a consensus sequence?

Nucleotides most commonly found at a given location within the promoter.

What are consensus sequences responsible for?

Binding to the transcription activator

What do transcription factor alpha helices interact with?

Specific nucleotides in the DNA

What do zinc fingers contain?

Zinc ions that hold the structure together

What does a leucine zipper contain?

Leucine amino acids to hold the structure together

True or False: Leucine amino acids are polar

False, nonpolar

Is it enhancers or promoters that are bi-directional?

Enhancers

How do regulatory transcription factors target specific genes?

By reading short patches of DNA sequences called enhancers

Where do enhancers act?

100-1000s of bp upstream or downstream from transcription start

Are enhancers modular or just one per start site?

Modular

Define modular

Mix and match, able to move to new genes

Are enhancers or promoters unidirectional?

Promoters

Where do promoters act?

At transcription start

Are promoters modular or just one per start site?

One per transcription start site

What is transcription governed by?

Proteins bound to DNA regulatory sequences

Where are regulatory sequences located?

Upstream of transcription initiation site

What do regulatory proteins do?

They can turn on or off genes by regulating RNA polymerase

Where do regulatory sequences bind?

To specific DNA sequences

Define combinatorial control

Effect of many regulatory proteins on transcription

What are master regulators of a number of genes in a given process?

Transcription factors

What are enhancers?

Proteins that help activate transcription

What are repressors?

Proteins that repress transcription

What is both a combination hormone receptor and transcription factor?

The glucocorticoid receptor

How is the glucocorticoid receptor induced?

By stress

What is the transcription factor Antennapedia responsible for?

Turning on a number of genes involved in antenna formation

What does flower organ formation involve?

Three transcription factors A, B, and C

What are flower organ formation dependent on?

The activity of a unique combination of these transcription factors

True or False: Organ A in flowers blocks organ B

False, it blocks organ C

How does organ A block organ C in flowers?

Turning on expression of a repressor protein that represses transcription of C

True or False: DNA packaging regulates transcription

True

DNA must be (BLANK) for eukaryote transcription factors to have access to DNA

Unpackaged

Why are histones covalently modified?

Because it loosens their grip on DNA

Why would chromatin be remodeled to express genes?

To expose DNA

What is histone acetylation?

Covalent modification that results in weaker DNA-histone interactions and enhanced gene expression

What happens when lysine residues get acetylated?

The positive charges get removed which reduces affinity between histones and DNA which is easier for RNA to access genes to carry out transcription

What can enhance gene expression?

Histone acetylation

What represses gene expression?

Histone deacetylatione

How can histone complexes be repositioned along chromosomal DNA?

By using energy from ATP hydrolysis

Why is spreading nucleosomes apart good?

It exposes more DNA allowing for gene transcription as well as DNA replication

True or False: In prokaryotes, multiple promoters govern multiple genes

False, one promoter governs multiple genes

List three things that the operon consists of

Set of genes under control of one promoter

One large mRNA is produced

Multiple proteins translated

Where are sequences in the operon?

Upstream of transcription start site

Define promoter in operons

Sequence that initiates transcription

What do operators do in operons

Allows polymerase access to promoter

What do repressors do in proteins?

Blocks transcription

What do activators do in proteins?

Initiates transcription

What do tryptophan levels modulate?

Repressor binding to operator

What do activator proteins do?

They trigger transcription

Why do cells regulate gene expression?

So as to not waste energy making proteins and metabolites that are not needed

Where is the lac operons activator DNA binding site?

Near the promoter

What does the lac operon interact with?

With RNA polymerase to initiate transcription

True or False: Bacteria prefer glucose

True

What is Triton X-100

Weak non-ionizing detergent

Define osmosis

Movement of water from low concentration to high

Why is water able to do osmosis?

Because it has a charge

True or False: Only prokaryotes have a plasma membrane

False, all cells are surrounded by a plasma membrane

What do plasma membrane define?

The boundary of the cell membrane

What does the plasma membrane separate?

The internal aqueous contents from the environment of the cell

What are cell membranes composed of?

Lipids and proteins

What is the major component of cellular membranes?

Phospholipids

What are phospholipids composed of?

Polar head group and nonpolar tail groups

True or False: Phospholipids are amphipathic

True

Define amphipathic

Having both hydrophobic and hydrophilic parts

Which fatty acid is solid at toom temperature?

Saturated fatty acid

Is it saturated or unsaturated fatty acids that are all single bonds in fatty acid carbon chains?

Saturated fatty acids

Is it saturated or unsaturated fatty acids that have some double bonds in fatty acid carbon chains?

Unsaturated fatty acids

When a double bond forms a kink in the fatty acid, what results?

Lipids not packing as tightly

Why can’t protons cross membrane?

Due to being small and also because they’re positively charged

True or False: Cholesterol is NOT amphipathic

False, it is

What do phospholipids spontaneously form?

Lipid bilayers with the nonpolar tails on the inside and polar head groups on the outside

How are lipid bilayers most stable?

As spheres

What are the four functions of membranes?

Compartmentalization

Control substance flow in and out of compartment

Serve to localize and organize cell function

Detection and transmission of extracellular signals

In flowers, when only transcription factors B and C are expressed, what organs will they have?

Only carpels and stamens

What is the most common type of phospholipid?

Phosphatidylcholine

What do membranes compartmentalize?

Plasma membrane and organelles

What do cell membranes act as?

Selective barriers that exclude harmful substances and can allow for the buildup and sequestration of molecules