GN 311 Module 3

Miescher

First to isolate DNA

Kossel

First to identify 4 nitrogenous bases

Levene

First to say DNA made of nucleotides

Griffith

Transformation

Avery, MacLeod, and McCarty

DNA is transforming principle

Hershey and Chase

DNA is genetic agent in bacteriophages

Heinz Conrad and Bea Singer

RNA is genetic material in virus

Yanofsky

Collinearity between DNA and protein

Franklin

Discovered shape of DNA

Watson and Crick

Released shape of DNA

RNA

Ribonucleic acid

DNA

Deoxyribonucleic acid

Purines

A and G

Pyrimidines

C, T, and U

Nucleoside

Sugar and base

Nucleotide

Sugar, base, and phosphate

Which carbon distinguishes DNA from RNA

2’ carbon

Hydrogen Bonds

Weak attractions between positive and negative charged molecules; NOT main force of joining two strands of DNA

Phosphodiester Bonds

Connect the sugar-phosphate backbone

Hydrophobic Interactions

Main force in stabilizing the double helix

What does electrophoresis do?

Separates DNA fragments based on size

What is DNA absorbed at?

260nm

Denaturing

Breaking hydrogen bonds and hydrophobic interactions with heat or chemicals; becomes single stranded

Hyperchromic Effect

Increase in UV absorption due to denaturation

Melting Curve

Shows melting temperature; midpoint of thermal denaturation

Chromatin

The complex of DNA, chromosomal proteins, and RNA within the nucleus

Euchromatin

Lighter staining parts of the chromosome during interphase

Heterochromatin

Darker staining parts of chromosome

Histones

Basic proteins and have lots of positive charged amino acids; all binding electrostatic to DNA; highly conserved

11nm Fiber

Tandem nucleosomes; beads on a string

Nucleosome

Core and linker DNA

Nucleosome Core

Core histones and DNA

How long are chromatin strands?

5-24nm

Nuclear Matrix

Fibrous network throughout the nucleus that anchors a series of DNA loops

Supercoiling

Occurs when DNA coils back on itself when it is overwound or underwound

Postitive Supercoiling

Over-rotated in same direction as DaN coil left-handed supercoil compensates

Negative Supercoiling

DNA is underwound so right-handed supercoil compensates

What are the most compacted chromatin?

Mitotic chromosomes

Bands

Characteristic for a strain of organism that can be used to identify specific chromosomes

Endopolyploidy

Several rounds of DNA replication without separation of replicated chromosomes

Puffs

Areas where the DNA is loosely coiled so that transcription can occur

Telomeres

Provide stability for ends of chromosomes so that they are not degraded by exonucleases

Theta Replication

Common in bacteria and other circular DNA molecules

Rolling Circle Replication

The F factor and some viruses

Linear Eukaryotic Replication

Will have multiple origins of replication along their length

Bidirectional Replication

Replication can proceed in both directions from the origin

DNA Pol III

Responsible for most DNA synthesis; elongates DNA

DNA Pol I

Discovered first; removes and replaces primers

What catalyzes phosphodiester bond reaction?

DNA polymerase

Continuous Strand

Leading strand

Discontinuous Strand

Lagging strand

Initiator Protein (DnaA)

Binds to origin of replication causing local unwinding and short stretch of ssDNA

Helicase

Attaches at replication fork and moves into fork breaking H-bonds as fork moves along DNA

SSB: Single Stranded Binding Proteins

Coat single-stranded dNA to protect, stabilize, and prevent hairpins

Gyrase

Topoisomerase that relieves supercoiling ahead of replication fork

Topoisomerase

Nick DNA to relieve tension due to supercoiling

Primase

RNA polymerase that makes RNA primers

Primosome

Helicase and primase

Nick

Missing a sugar-phosphate bond

DNA Ligase

Seals nick

Replication Licensing Factor

Attaches to each origin of replication early in the cell cycle

Telomerase

Contains RNA which it uses to make several repeats of DNA to extend 3’ end of telomere

rNTPs are added?

5’ to 3’

What are prokaryotes?

Polycistronic

What are eukaryotes?

Monocistronic

Coding Strand (sense strand)

Contemplate DNA strand

Transcription Unit

Segment of DNA that codes for an RNA molecule and sequences necessary for transcription

Core Enzyme

alpha 2 beta beta prime

Holoenzyme

alpha 2 beta beta prime sigma

Consensus Sequence

A sequence that describes the nucleotides most often in a segment of interest

Upstream

Sequences prior to start of transcription (left)

Downstream

Sequences after start of transcription (right)

What does the sigma subunit?

\-10/-35 and TATA box

Direct Repeat

Same sequence copied

Inverted Repeat

Leads to hairpin formation in the RNA during transcription; are present near termination and are transcribed

Bacteria Termination

Using rho; has helicase activity

RNA Pol I

Large rRNA

RNA Pol II

mRNA, snRNA, snRNA, miRNA

RNA Pol III

small rRNA, tRNA, snRNA

Where does transcription in eukaryotes happen?

Nucleus

Where does transcription in prokaryotes happen?

Cytoplasm

Cis Elements

Nucleotide sequences that are close to the coding region of a gene

Trans-Acting Factors

Proteins or RNAs from other genes

Core (basal) Promoter

Upstream of gene and where the basal transcription apparatus binds; has TATA box

Regulatory Promoter

Upstream of core promoter; variety of consensus sequences

What is first type or processing?

Capping of 5' end

What is second type of processing?

PolyAtail added to 3’ end

What is third type of processing?

Removal of introns

RNAi

RNA interference

Precursor rRNA

Contains all rRNAs except 5S rRNA in eukaryotes

Methylation

Adding a methyl group to identify separate rRNA-to-be molecules

snoRNAs

Help slice precursors

Inosine

Derivative of guanine

Capping mRNA

Occurs as soon as 5’ end of pre-mRNA is free of RNA pol

PolyATail

Protects the mRNA, helps initiate translation, involved in termination of transcription

Spliceosome

snRNPs and pre-mRNA complex - structure at which introns are removed and exons are joined together

snRNPs

Small nuclear ribonucleoproteins; 300 proteins and 5 snRNAs

snRNAs

Have regions complementary to ends of exons, sites in introns or sites on others

Intron Removal Consensus

GTAG

Guide RNAs (gRNA)

Aid in insertion and deletion types of editing