Exam 2 - IB 204 UIUC 2026

Definitions/iclicker questions pulled from slides in class

What is developmental genetics

investigates how a single cell becomes multicellular

What approaches can geneticists use to understand developement?

• comparative genomics

• model organisms

What is a gene?

• a sequence of nucleic acids (DNA or RNA) that contains information necessary to specify a biological trait

• often code for protein sequences

• includes the regulatory sequences necessary to control expression

What components make up a gene and how are they organized?

Which are found in exons?

• coding sequences

• untranslated regions utrs

How many RNA polymerases do prokaryotes have?

one

What is the prokaryotic RNA made of?

5 subunits + sigma factor = holoenzyme complex

How many RNA polymerases do Eukaryotes have?

3 (plants have 5)

What are the eukaryotic RNA polymerases made of?

12 subunits depending on the Pol

What does RNA polymerase II transcribe?

protein coding genes

cis-elements

the words that make up the language of the genetic code, made of short sequences of DNA or RNA

trans-factors

the interpreters of the genetic code, protein or RNA molecules that recognized and bind to cis-elements to enact a particular function

What kind of factor is a general transcription factor?

trans-factor

What are general transcription? factors?

• They bind to the core promoter region of genes

• Involved in positioning RNA polymerase to transcribe a gene

• Some have additional role roles in initiating transcription

TBP

recognizes the TATA-box and recruits other general transcription factors to the TSS

TFIIB

recruits RNA in a polymerase to the transcriptional start site TSS.

TATA box

DNA sequence found upstream of TSS to position RNA Pol II

TFIIH

Multi protein complex that has a helicase and kinase activity

Pre-initiation complex

inactive complex

What are considered cis-elements?

• TATA box

• Start codon

• BRE element

What is true during eukaryotic transcription?

ATP hydrolysis by TFIH leads to the formation of the open complex by melting dsDNA

What is necessary for cellular machinery to recognize the end of a gene?

the poly A signal PAS, cIS-element defining the end of a gene

What would you predict to be the impact of a mutation in the PAS of a gene?

the 3’UTR would be significantly longer

What are the pros of the fruit flies?

• Short life cycle equals quick results

• Small equals cheap to maintain and large scale experiments

• Simple genetics

• Easy to genetically modify because it can make targeted disruptions to test gene function

• Similar genetics to humans

Limitations of fruit flies

some findings may not be applicable to other species

Maternal effect genes

expressed by the mother before fertilization and work to establish the basic head to tail body plan of the embryo(defect will cause loss of an anterior posterior identity)

Gap genes

involved in defining embryo segments, deletion of which causes loss of adjacent body segments resembling a gap in body plan

Pair rule genes

involved in generating embryos segments deletion of which causes loss of alternating segments

Segment polarity genes

hope to find the interior and posterior polarities with each embryonic segment(defect will convert segment of smooth cuticle into denticles)

Example of maternal effect genes

bicoid

example of gap genes

kruppel

example of pair-rule genes

eve stripe

example of segmentation genes

wingless

Hox genes

homeotic transitions

What are the advantages of multicellularity?

it allows specialization of functions, allowing organisms to conduct more complex tasks, which can assist with survival

What factors distinguish different cell types

The genes expressed in each cell type this results in different proteins being present or absent, providing the cell with different characteristics

How does a single cell become a multicellular organism?

• First stages of development following fertilization zygote is transcription silent

• Maternal transcripts and proteins initiate development, relying on translational regulation

Morphogen

a signal that determines cell patterning by forming a concentration gradient by diffusion or transport and influences cell development in dose dependent matter

Auxin

a small molecule, which is most concentrated at developing root tips and impacts, developmental, gene expression in plants

Retinoic acid

small molecule which synthesis in the middle of region of the embryo where it has higher concentration then in posterior regions bins and activates, receptors, triggering, developmental gene expression

Bicoid

special type of maternal mRNA that is tethered to the anterior

Characteristics of a morphogen

1. Form concentration gradient

2. Diffuse

3. Dose dependent activity

50S LSU

has peptidyl transfer

E site

is the point where tRNA's exit the ribosome

P site

Location where the initiator tRNA binds

A site

is the point where tRNA's enter the ribosome

30S SSU

ribosome component which binds mRNA's

Shine-dalgarno sequence

nucleotide sequence on mRNA that correctly position ribosome at the start codon

What types of mechanisms are involved in translational regulation by bicoid?

• Protein-nucleic acid interactions

• Protein- protein interactions

• Presents or absence of proteins

Types of regulation

• Transcriptional

• Translational

• Post-transcriptional

• Epigenetic

What molecular interactions could lead to an increase in transcription?

more frequent recruitment of RNA Pol II to a promoter region

What can you recall about the lac operon and how genes are regulated?

CAP binding protein in the Lac operon

Enhancer element

region of DNA, which can contain multiple cis-elements for transcription factors to bind

What is true about eukaryotic transcriptional regulation?

• co-regulated genes are transcribed as separate transcripts

• Co-regulated jeans are located on different chromosomes

• The same cis- elements are found in promoters of co-regulated genes

What can reporter gene essays answer?

1. Where are the cis-regulatory elements located in a promoter?

2. How many cis-regulatory elements are there?

3. What is the impact of cis-regulatory element on gene expression?

What are the potential impacts of transcription factors not working in isolation but in combination with others?

is transcription factors working combination that supposed to be the potential for controlling regulation, by altering the presence or absence of one of the transcriptional factors. This has the potential to produce complex gene expression patterns by integrating multiple environmental signals.

What can affect transcription association with DNA and subsequently RNA Pol

1. Spacing of cis-elements

2. Order of cis-elements

3. Orientation of cis-elements

4. Affinity of binding

Kr enhancer

LacZ reporter construct

At high concentration of hb you would expect:

1. Hb infinity sites in Kr promoter to be occupied

2. Hb low affinity sites in Kr promoter to be occupied

At a low concentration of hb you would expect:

1. Hb high affinity site in Kr promoter to be occupied

Enhancer reppressors

integrate signals from multiple transcription factors to allow for specificity and gene regulation. This is achieved by cooperative binding of transcription factors.

Constitutive heterochromatin

densely packed chromatin, always condensed, found in non-coding and repetitive regions of the genome

Nucleosome

the basic repeating unit of a chromatin package in eukaryotic nucleus consists of 150bp of DNA wrapped around proteins

Histone

Positively charged protein which provides structural supports DNA in the for of chromosomes or chromatin

Euchromatin

lately packed chromatin, usually found in regions of chromosomes containing protein, coding genes, and is associated with active transcription

Facultative Heterochromatin

complex of DNA and protein found in eukaryotic nuclei

Constitutive Heterochromatin

sometimes condensed DNA, can depend on cell type or developmental stage, associated with an act of genes

What is epigenetic regulation?

mechanism by which axis of RNA Pol II to a promoter is controlled by altering chromatin state

What is associated with ZGA?

• Finding a pioneer transcription factors to close chromatin regions

• ATP dependent movement of nucleosomes

In what situation can you think of where post transcriptional regulation might be beneficial?

when the cell needs to respond quickly by adjusting protein levels, fine-tuning of expression, or controlling the production of pathogenic RNA

m⁷G 5’ cap

modified base that allows ribosome to bind and prevent degradation

Start codon

positions ribosome in correct frame for translation

Stop codon

bound by release factors triggering ribosome dissociation

Poly A tail

sequence, not encoded in DNA, protect transcript from degradation

5’UTR

non-coding sequence that contains cis-elements to regulate expression

3’UTR

non-coding sequence that contains cis-elements to regulate expression

What are miRNAs transcribed from?

zygotic genome

RISC

RNA induced silencing complex

siRNAs

• Produced as an immune response to viral infections and triggered destruction of viral RNAs

• Derived from dsRNA molecules to produce multiple sequences

• Specificity is provided by complementary base pairing, perfect match to a single target sequence

miRNAs

• Encoded by jeans and the host gino and play a role in development and regulation of native genes

• Evolutionary conserved, derived from distinct hairpin precursor to produce a single sequence

• Specificity is provided by complementary base pairing, allows some mismatches, and target multiple genes

• Work by blocking translation

siRNAs and miRNAs

• Produced by the action of a DICER nuclease an incorporated into an RISC to achieve silencing

• Work by Cleveland target sequences leading to degradation

Smaug protein

• maternal gene

• accumulates overtime by translation of maternal mRNA

What is the function of the 3’ UTR

It contains cis-elements to regulate expression

Under normal circumstances, what would be the first step of a translation?

finding a eukaryotic initiation factor to the 5’ cap and recruitment of the pre-initiation complex

Readers

proteins which recognized and bind to histone tails with specific modification

Writers

proteins which add specific modification to histone tails

Erasers

proteins which remove specific modifications to histone tails

PRC2

deposit methyl groups

PRC1

oligomerizes holding nucleosomes close together

Acetylation associated with euchromatin

loosely packed active genes

Instances of epigenetic regulation

• Developmental

• X-in activation

• Genomic imprinting

• Transgenerational inheritance

X-inactivation

• required to prevent excessive gene expression leading to developmental issues

• Gene dosage compensation

• Random chance

• Impact chromosome

• Function is gene dosage

genomic imprinting

• Silences one allele

• A small number of autosomal genes require one allele to be silenced, linked to maintaining the correct gene dosage

• Determined by parental sex

• Impacts the number of genes

Transgenerational inheritance

• Determined by environmental

• Impacts individual genes

• The function is unknown

Developemental

• Determined by gene function

• Impacts individual genes

• The function is cell differentiation