BIO340 Mangone Homework

Exam 3 Prep

What did Meischer extract from the nuclei of human white blood cells?

‘nuclein’; consisted mainly of DNA and some contaminants

Bacteriophage contents

DNA and protein

Hershey-Chase Experiment

1. incubated S or P labeled bacteriophages with Ecoli in separate flasks

2. allowed time for virus infection

3. sheared virus coats from cell walls of Ecoli

4. cenrifuged blended Ecoli-virus mixture

5. measured radioactive P or S in pellet or supernatant

Explain results of Hershey-Chase

• infected cells were heavier and went into the pellet; noninfected in supernatant

• P labeled cells in pellet; S labeled in supernatant

• means that infecting material of bacteriophage was DNA

3 parts of nucleotide

1. pentose sugar

2. phosphate group (attached to 5’)

3. nucleotide (attached to 1’)

nucleoside

A sugar attached to a base but not a phosphate group

Where is the hydroxyl group attached deoxyribose

3’ of the carbon

How many rings are found in a purine vs pyrimidine?

2 vs 1

What is the name of the bond that connects two sugar molecules via a phosphate group in the backbone of DNA

phosphodiester

What year was the DNA double helix structure first published/discovered

1953 (watson and crick)

Based on Xray imgs we know a single turn of the DNA double helix measures…

34 angstroms

How many hydrogen bonds are between GC vs AT

3 vs 2

which direction does the sugar phosphate backbone vs bases face in DNA

outward vs inward

What was the name of the project that challenged our understanding of what a gene is?

ENCODE project

True or False:'Alternative splicing' is one gene locus producing multiple different mRNA transcripts.

True

Which scientists proposed the one gene, on enzyme theory

Beadle and Tatum

When was splicing discovered?

1977 by Sharp and Roberts

What phenomenon involves the ligation of two separate mRNA molecules and complicates the classical 'locus' definition of a gene?

Trans-splicing

T or F: The ENCODE project found that the distinction between 'genic' and 'intergenic' regions of the genome is less clear than previously thought.

False, ENCODE revealed transcription and regulatory activity throughout the genome, blurring the line between genic and intergenic regions.

What % of human DNA bases actually encodes exons

~1.2%

T or F: Under the updated definition proposed by Gerstein et al. 2017 (Genome Research 17:669-681) regulatory regions like enhancers are considered part of a gene.

False; UTRs are classified as gene associated rather than a part of the genes themselves

T or F: The ENCODE project found that only protein-coding regions of DNA are ever transcribed into RNA.

False

What are pseudogenes?

genes derived from functional genes that have lost their original function due to mutations

Due to the twisting of the 2 DNA strands, what two structures form on the surface of the molecule?

Major and Minor Grooves

Meselson and Stahl distinguished paternal DNA from newly made DNA by…

labeling paternal DNA with 15N

Meselson Stahl Experiment steps

1. Ecoli grown in 14N media = 14N14N ‘light’ band

2. Ecoli grown in 15N media = 15N15N ‘heavy’ band

3. 15N Ecoli grown in 14N media; after 1 gen = 15N14N ‘intermediate’ band

4. 2nd gen = 1 14N14N light band; 1 15N14N intermediate band

What idea did the Meselson Stahl experiment support

Supports semiconservative replication

What molecule is cleaved to supply energy for DNA replication?

dNTP

What area unwinds to initiate DNA sunthesis?

origin of replication

1 in prokaryotes

many in eukarya

Enzyme that unwinds DNA before replication; creates a replication bubble w 2 rep forks

DNA helicase

short molecules of RNA that start DNA rep process

RNA primers

This strand is synthesized discontinuously during DNA rep

lagging strand

Pieces that form as a result of rep of lagging strand

okazaki fragments

Stage of DNA rep where proteins open up double helix and prep it for complementary base pairing

Initiation

What does the enzyme primase do in DNA rep?

synthesize RNA primers

What does DNA polymerase I do

fills gaps between okazaki fragments

Stage of DNA rep where nucleotides connect together to make daughter strand complementary to template strant

Elongation

enzyme that forms covalent phosphodiester bonds btwn adjacent okazaki fragments

DNA ligase

How many directions does replication proceed from in bacterial chromosome

2 (bidirectional)

what does ‘n’ refer to in 2n

a single set of chromosomes (typically the haploid #)

Name of location when 2 replication forks moving in opposite directions around bacterial chromosome meet

termination region

During replication of circular chromosome, unwinding of 1 region creates ____ bc other regions get overwound

supercoiling

enzyme that gets rid of supercoils

topoisomerase

Is replication bidirectional in euks?

YES

Where is the centromere located in a metacentric vs acrocentric chromosome?

metacentric: in the middle ish ; acrocentric: closer to one end (recall p and q arm)

what do you call a chromosome that is not a sex chromosome?

autosome

At which stages does transcription occur?

initiation, elongation, termination

What enzyme synthesizes RNA during transcription

RNA polymerase

What sequence on DNA tells RNA Pol where to bind in transcription?

promoter

What is RNA polymerase holoenzyme composed of?

core enzyme + sigma factor

what does the term closed promoter complex refer to

initial binding of RNA polymerase holoenzyme to promoter

how is energy obtained for transcriptional elongation?

breaking bond in ribonucleotide triphosphate

what does open promoter complex refer to?

bubble like structure that forms uring initiation of transcription