Learn: UW BIOL 200 EXAM 3 | Quizlet

Describe several ways a bacterial cell can control the rate of transcription at a specific operon or the amount of specific protein that's active

-transcriptional control: regulation of genes by changing the rate at which genes are transcribed to produce mRNA

-both negative and positive control

*negative: binding of regulatory protein to DNA represses transcription

*positive: binding of regulatory protein to DNA promotes transcription

*both impact RNA polymerase's ability to bind to promoter

-translational control: regulation of gene expression by various mechanisms that alter the lifespan of mRNA or the efficiency of translation

-post-translational control: regulation of gene expression by modification of proteins (addition of phosphate group or sugar residues)

constitutively active

Genes that are always being expressed

inducible genes

Genes that can be turned on and off

Operon

a region of bacterial DNA that codes for a series of functionally related genes and is transcribed from a single promoter into one mRNA

Predict which genes are on/off in lac operon under various conditions and explain how this state relates to bacterial fitness

-Global gene regulation occurs when a group of genes is turned into a regulon which allows for a group of genes to be regulated by the same regulatory molecule

-these regulons can be regulated with positive or negative control and allows bacterial cells to respond to changes in their environment such as temperature, a loss of nutrients, shift to new environment, or extensive DNA damage

Compare contrast bacterial vs eukaryotic gene regulation

-both can be regulated at transcriptional, translational, and post-translational levels

-eukaryotes also have chromatin remodeling and RNA processing

-chromatin remodeling: the process by which the structure of chromatin is changed to inhibit or activate transcription

*interaction between DNA and histones must be altered for RNA polymerase to be able to bind

*DNase works to cut DNA and can only do so when it's not tightly wrapped by proteins

*chromatin is altered through DNA methylation

-RNA processing: the changes that a primary RNA transcript undergoes to become a mature RNA molecule (Ex: 5' cap and 3' Poly A tail, remove introns, etc)

Compare contrast location of bacterial and eukaryotic DNA regulatory sequences

-transcription and translation are separated by the nucleus in eukaryotes whereas in prokaryotes simultaneous transcription and translation can occur in the cytosol

Explain how chromatin structure can impact eukaryotic gene expression

-chromatin is made up of DNA, Histone proteins, and non Histone proteins in repeating units called nucleosomes

-in order for DNA to be transcribed, chromatin must uncoil or be open for RNA polymerase to bind and transcribe

-acetylation at Histone proteins occurs with HAT enzyme causing uncoiling of chromatin, creating euchre matin and an increase in transcription

-HDAC enzyme can reverse this and condense chromatin creating heterochromatin and decreasing transcription

-this is a form of transcriptional gene regulation in eukaryotes

Explain how one gene can code for more than one mRNA

One gene can code for more than one mRNA through alternative splicing. Alternative splicing is when a pre-mRNA is spliced one out of two or many ways. If it is spliced differently it will produce a different mature mRNA and a different protein. It depends on which exons are kept and which aren't. These different combinations lead to different phenotypes from the same gene.

Given a gene, predict possible alternatively spliced forms of mRNA

Given a scenario, propose a hypothesis for how a cell's environment could lead to expression of a subset of genes

-our environment impacts how our genes are expressed

-certain genes are optimally active under certain conditions such as temperature, pH, etc.

-if our environment is altered in a way that causes a subset of genes to be optimally active, those genes will now be expressed even though there was no change in DNA

Explain what GFP is and why we study it

Interpret data from reporter gene assay

Transcription repressor

A protein that binds to a specific regulatory region of DNA to prevent transcription of an adjacent gene.

Transcription activator

A protein that binds to a specific regulatory region of DNA to permit transcription of an adjacent gene.

Transcription factor

A regulatory protein that binds to DNA and affects transcription of specific genes.

Operator

short DNA region, adjacent to the promoter of a prokaryotic operon, that binds repressor proteins responsible for controlling the rate of transcription of the operon

CAP, cAMP

-CAP: catabolite activator protein

-in the presence of cAMP, binds to CAP site on operon to activate transcription

-high glucose leads to low cAMP leading to no CAP binding leading to less transcription of lac operon

LacZ (beta-galactosidase)

Catalyzes lactose Breakdown to Glucose + Galactose

LacL (repressor)

binding turns off lac operon expression

Nucleosome

Repeating units in chromatin that are made up of base pairs of double helix DNA that's wrapped around a core of 8 histones

LacY (permease)

transports lactose into the cell

Histone

protein molecule around which DNA is tightly coiled in chromatin

-H2A, H2B, H3, H4

Condensed/decondensed chromatin

-condensed: tightly coiled, HDAC, decrease in transcription

-decondensed: uncoiled, HAT, increases transcription

Histone acetyl transferase (HAT)

An enzyme that adds acetyl groups to histone, facilitating unpacking and RNA transcription.

Histone deacetylase (HDAC)

The enzymatic activity that removes an acetyl group from a histone tail, which promotes the repression of gene transcription (condenses chromatin)

Enhancer

A DNA segment containing multiple control elements that can recognize certain transcription factors that stimulate the transcription of nearby genes.

Regulatory sequence

Any segment of DNA that is involved in controlling transcription of a specific gene by binding certain proteins. (Ex: promoter, operator)

TATA binding protein (TBP)

A general transcription factor that binds to the TATA box and assists in attracting other general transcription factors and RNA polymerase II to eukaryotic promoters.

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

Gene expression

The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs.

Exon

expressed sequence of DNA; codes for a protein

Intron

A noncoding, intervening sequence within a eukaryotic gene that is removed after transcription

Alternative splicing

Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins. Increases the diversity of proteins.

Epigenetic

the study of environmental influences on gene expression that occur without a DNA change

Reporter gene assay

An assay to determine the location of enhancer elements in Eukaryotic cells. The assay involves cloning a series of 5' or 3' promoter deletions upstream of a reporter gene and transfecting this cloned product into cells to see how it expresses.

Post translational modification

Regulation of gene expression by modification of proteins often through the addition of a phosphate group or sugar residues

Describe how the chemical properties of a signal affect localization of the receptor for that signal

Examine signaling pathways (GPCR, RTK, and new signaling pathways), stepwise, identifying components, interactions, and structural/functional changes

GPCR:

G protein coupled receptor signaling pathway

1) extracellular signal binds to transmembrane receptor in plasma membrane

2)G protein is intracellular, inactive, and tethered via lipids that were added posttranslationally

3) receptor undergoes conformational change allowing the receptor to interact with the G protein causing causing the G protein to undergo a conformational change and exchange GDP to GTP

RTK:

Predict how alteration of signal molecules, signal transduction proteins, and second messengers will impact a signal transduction pathway

Explain how cyclin/CDKs regulate the cell cycle and explain how cell cycle checkpoints are an example of signal integration

There are two main checkpoints which regulate the cell cycle, one before DNA replication and one before mitosis. CDKs (cyclic dependent kinases) are responsible for phosphorylation of suppressor molecules such as Rb but only work in the presence of cyclin. When these molecules are phosphorylation they are deactivated and cell continues with DNA replication and/or mitosis. Cdk is always present but its default form is inactive. It is only activated when bound to cyclin.

Predict how mutations in cell cycle genes could influence cell cycle progression

Mutations

Describe the process of DNA replication, including description of necessary factors and their functions

Predict how interrupting a part of the replication machinery could affect DNA synthesis

Understand the purpose of PCR

Design primers to amplify a given DNA region using PCR

Predict the result of varying different parameters in a PCR reaction

Signal

Receptor

Signal transduction

GPCR

G protein

Second messenger

A small, nonprotein, water-soluble molecule or ion, such as calcium ion or cyclic AMP, that relays a signal to a cell's interior in response to a signal received by a signal receptor protein

RTK

Phosphotyrosine

Ras

Cyclin

Cyclin-dependent kinase (Cdk)

M-phase promoting factor (MPF)

Cell-cycle checkpoints

Interphase

G1, S, G2, M, G0 phases

Feedback inhibition

Ubiquitin

Proteasome

Social signal

Ligase

Topoisomerase

Primase

DNA polymerase I

DNA polymerase III

Helicase

Single-stranded binding protein

Origin of DNA replication

Polymerase chain reaction

Primer

PCR cycle

Taq polymerase

Primer annealing

Denaturation

Extension

Explain the principles of development and how they would or would not be observed in a developmental process

Explain the process by which uniform group of cells adopts different fates during development

Compare and contrast totipotency, pluripotency, and differentiation

Predict effect of altering expression of bicoid or hunchback in fly development

Predict the effect of altering concentration and/or affinity on molecular interactions

Interpret the results of a FISH experiment

Apply "find it", "lose it", "move it" strategy to interpret data

Explain the function of the Organizer

Explain how a cell "knows" its position within an organism

Predict and/or interpret results of transplantation experiments

Critique the appropriateness of different model systems to address a particular question in biology (e.g., how is the body plan established?)

Explain how transcription factor interactions can lead to turning on/off different sets of genes

Cell proliferation

Programmed cell death (apoptosis)

Totipotent

Multipotent

Determined

Differentiated

Cell differentiation