BIOL 350 - Principles of Genetics Exam 1

KU Summer 2025

4 criteria for “genetic material”

1. Information

2. Transmission

3. Replication

4. Variation

Summary of Griffith’s Experiment on Genetic Transformation

Type S bacteria has a capsule that allows it to kill mice; type R bacteria does not have a capsule and cannot kill mice. Heat-killed type S bacteria and live type R bacteria together will kill a mouse because the type R uses the “transforming principle” to become type S (DNA)

Summary of Avery, MacLeod, & Mccarty’s experiment

Identified that DNA was the genetic material; cells with only DNA, not RNA or proteins, converted type R to type S. Additionally they added enzymes that destroy protein and RNA to ensure that DNA was the transforming principle

Summary of Hershey & Chase experiment

used microisotopes to distinguish DNA from proteins (phosphate for DNA and sulfur for proteins)

Which carbons of deoxyribose/ribose sugar does the dase, phosphate, and hydroxyl attach to?

base attaches to 1’

phosphate attaches to 5’

-OH hydroxyl attaches to 3’

What is a nucleotide made of? (3 parts)

Deoxyribose/ribose sugar

phosphate group

base

What is the structural difference between deoxyribose and ribose ?

ribose has a hydroxyl group on both the 2’ and 3’ carbon

deoxyribose has a hydroxyl group on only the 3’ carbon

Which bases are purines (how many rings) and which bases are pyrimidine (how many rings)

Purines (2 rings) are adenine and guanine and pyrimidines (1 ring) are thymine, uracil, and cytosine

Chagraff’s Rule

equal amounts thymine and adenine and equal amounts cytosine and guanine

3 stages of DNA replication

Initiation, Elongation, and Termination

Where is the prokaryotic origin of replication

oriC

3 types of DNA sequences at the oriC

AT-rich area

DnaA boxes

GATC methylation sites

What happens at the DnaA boxes?

DnaA proteins bind to DnaA boxes and bend DNA so it can be separated more easily

What is DnaB / helicase

unzips DNA for replication; travels 5’ to 3’

Function of GATC methylation sites

regulatie replication and ensure it only occurs once; daughter strand not immediately methylated, prevents second round of replication

Topoisomerase II / DNA Gyrase

travels ahead of replication fork and unwinds supercoiled DNA

Primase

synthesizes RNA primers and attaches them across the template strand

RNA Primer

allows DNA polymerase to attach nucleotides and create daughter strand of DNA

DNA polymerase III

adds nucleotides to make daughter strand

DNA polymerase I

removes RNA primers and puts DNA nucleotides in their place

DNA ligase

links okazaki fragments together

Name each labeled structure or protein of the replication bubble

1. Teloisomerase

2. single strand binding

3. RNA primer

4. DNA helicase

5. Primase

6. DNA polymerase III

7. okazaki fragment

8. DNA ligase

Leading strand

only one primer

Lagging Strand

multiple primers

What are okazaki fragments?

the fragments of replicated DNA that are attached to RNA primers in the lagging strand

What are the Ter sequences in prokaryotic DNA

termination sites opposite of oriC

What protein binds to the Ter sequences to stop the movement of the replication forks in prokaryotic DNA replication?

tus

What is termination utilization substance (tus)?

binds to Ter sequences to stop the replication fork in prokaryotic DNA replication

What are 3 fidelity mechanisms in DNA replication to minimize mistakes?

stability of correct base pairs

structure of the active site of DNA polymerase - distortion in shape due to mispairing prevents incorrect nucleotide fitting in active site

proofreading functions

What is the proofreading function of DNA polymerase?

3’ to 5’ exonuclease can digest the newly made strand and remove the mismatched nucleotide

Where is the origin of replication for eukaryotes?

ARS (autonomously replicating sequence)

How many origins of replication are present on a single chromosome of eukaryotic DNA? (1 or multilple?)

multiple

How does termination (DNA replication) work in eukaryotes?

The multiple replication bubbles meet each other and merge into completed chromosomes

Telomere

repetitive DNA sequences on 3’ overhang of linear chromosomes

Why can’t the 3’ ends of linear chromosomes be replicated?

DNA polymerase can only add DNA in 5’ to 3’ direction and cannot initiate synthesis. There is no room for an RNA primer at the 3’ end.

What does telomerase do?

adds RNA to the 3’ end of the template strand, allowing for an RNA primer to attach for the 3’ end DNA to be replicated as an okazaki fragment

What disease connects telomere length and aging?

Werner syndrome

Regulatory sequences (DNA transcription) binding site for ___ and function

binding site for regulatory proteins; influence the rate of transcription

Promoter (DNA transcription) binding site for ___ and function

binding site for RNA polymerase; signals start of transcription

Terminator (DNA transcription) function

signals the end of transcription

Start codon is usually ____ and/or ____

methionine or formylmethionine

Codon

3-nucleotide sequence of DNA that specifies a particular amino acid

Stop codon

specifes the end of polypeptide synthesis

Template strand

DNA strand that is “read” during transcriptionc

coding strand

RNA transcript is identical to it (T → U)

What do transcription factors do?

recognize promoter and regulator sequences to control transcription

3 stages of DNA transcription

1. initiation

2. elongation

3. termination

RNA polymerase

catalyzes the synthsis of RNA transcript

What groups compose the holoenzyme of RNA polymerase in prokaryotes like E.coli

core enzyme - 5 subunits

sigma factor - 1 subunit

Describe the initiation of prokaryotic DNA transcription, using the terms RNA polymerase, promoter, sigma factor, core enzyme, major groove, and open complex.

RNA polymerase moves along the DNA strand and scans until it encounters the promoter. Sigma factor recognizes this -35 to -10 reguin and binds to the major groove to create an open complex and then is released and the core enzyme.

2 mechanisms for termination of DNA transcription in E.coli

1. rho-dependent

2. rho-independent

steps of rho-dependent termination using terms rho recognition site (rut), rho protein, RNA polymerase, and stem loop

rho protein binds to the rho recognition site and moves in the 3’ direction. at the same time, RNA polymerase transcribes a region that forms a stem root, causing the polymerase to pause. during the pause, rho protein catches up to the open complex and separates the RNA-DNA hybrid.

two RNA sequences that facilitate rho independent termination

1. uracil rich sequence at 3’ end of the RNA

2. stem loop structure upstream of the uracil-rich region

Why is it that an enhancer can be thousands of nucleotides upstream of the promoter but is still able to facilitate RNA polymerase attachment?

enhancer can still be in close proximity to the promoter because of the folded and coiled nature of DNA

Label each number in the open complex figure

1. RNA transcript

2. coding strand

3. template strand

4. RNA polymerase

5. new nucleotide

Label each number in the eukaryotic gene and processed mRNA transcript figure

1. enhancer

2. promoter

3. 5’ UTR

4. start codon

5. stop codon

6. 3’ UTR

7. termination site

8. 5’ cap

9. 5’ UTR

10. exon 2

11. 3’ UTR

12. poly A tail

2 Functions of the 5’ cap on mRNA transcript

prevents degradation and aids in transportation of the transcript

Function of poly A tail in mRNA transcript

protects transcript at the 3’ end from being degraded

what binds to enhancers

transcription factors

function of enhancers

increase rate of transcription by helping recruit RNA polymerase

TFIID general transcription factor function

recognizes the TATA box

how does TFIID recognize TATA box?

TATA binding protein

what type of protein is GAL4

regulatory transcription factor

GAL4 aids transcription for what genes?

GAL enzymes

GAL 80 function

binds to GAL4 and inhibits transcrtiption

GAL3 function

bind to GAL80 in presence of galactose

the UAS (upstream activator sequence) is an ______?

enhancer

how does GAL4 initiate transcription?

recruits transcription complex

Why do you not want to transcribe genes when their encoded protein is not needed at the moment?

To save energy and efficiency

How does chromatin conformation affect transcription?

Closed conformation prevents transcription while open conformation DNA is accessible to transcription factors

Levels of Gene Regulation:

1. high level

2. binding to DNA

3. influence RNA pol ability to initiate transcrtiption

4. up- and down-regulation

1. chromatin conformation

2. DNA methylation

3. regulatory transcription factors

4. enhancers and silencers via activators and repressors

Acetylation of histone makes DNA ____

less tightly bound to the histone

Four levels of combinatorial control of gene transcrtiption

1. two or more regulatory transcription factors acting on same gene at once

2. modulation of activators and repressors

   a. binding of small effector molecules

   b. protein-protein interactions

   c. covalent modifications

3. DNA methylation

What does DNA methylation do?

block transcription by preventing activators from binding

housekeeping genes

genes that are expressed consistently and constantly in most cell types

methylation ______ ______

inhibits transcription

gene regulation often occurs over ____ distances

long

acetylated DNA (is/is not) being actively transcribed

is

cis-acting elements

DNA sequences; exert effect over single gene

trans-acting elements

protein

What is promoter region on DNA called in 1. eukaryotes and 2. prokaryotes?

1. TATA box

2. -35 and -10 region

what recognizes promoter in prok. transcription?

sigma factor on RNA polymerase

what recognizes promoter in euk. transcription?

TFIID general transcription factor

What is the benefit of alternative splicing?

differential splicing allows different proteins created from same gene

What splices RNA transcript?

spliceosome

The two terminus names in a polypeptide chain

n terminus / amino

c terminus / carboxyl

The first amino acid in a chain is attached to what terminus?

n terminus

what is a charged tRNA

tRNA with an animo acid attached

what enzyme charges tRNA?

aminoacyl-tRNA synthetase

2 ribosome subunits:

large subunit

small subunit

translation initiation in 1. prokaryotes and 2. eukaryotes

1. 16s rRNA recognizes shine delgarno sequence in 5’ UTR

   1. small subunit attaches to 5’ cap and scans for start codon

Why do stop codons terminate translation?

No tRNA can recognize the codon. No new animo acids can be added to the chain

What recognizes the stop codon(s) in translation?

release factors that mimic tRNA shape

How can antibiotics target bacterial RNA translation but not harm human RNA translation?

bacterial ribosome is smaller than eukaryote

What does a repressor protein do?

blocks transcription when bound to DNA

What does an activator protein do?

starts transcription when bound to DNA

What does an inducer molecule do in gene regulation?

binds to a protein to induce a conformational change in shape

2 functions of inducer molecules in gene regulation

facilitate or inhibit the ability of a protein to bind to DNA

What is an operon?

regulatory unit of DNA encoding multiple genes under one promoter