Unit 3 Genetics

rRNA

mRNA

tRNa

snRNA

snRNPs

snoRNAs (small nucleolar RNA)

miRNA (microRNA)

siRNA (small interfering RNA)

piRNA (piwi-interacting RNA)

lncRNAs (long noncoding RNA)

long, noncoding RNA segments

crRNA (crisprRNAs)

Assist in destruction of foreign DNA

Transcription Unit

The stretch of DNA that is transcribed that includes a promotor and terminator

Ribonucleoside Triphosphate (rNTPs)

The enzyme/molecule that makes RNA, made of sugar, a base, and triphosphate

Core Enzymes

The two subunits of a ribosome

Sigma Factor 

The part of RNA Polymerase that binds to the promotor

Holoenzyme

Part of a ribosome made of the sigma factor and a core enzyme

RNA Polymerase I

All Eukaryotes; transcribes rRNA

RNA Polymerase II

All Eukaryotes; transcribes pre-mRNA, snoRNAs, miRNAs, and snRNAs

RNA Polymerase III

All Eukaryotes; transcribes tRNAs, rRNAs, mrRNAs, and siRNAs

RNA Polymerase IV

Some Eukaryotes; transcribes siRNA and silences transposons

Transposons

Genes that can move throughout the genome

RNA Polymerase V

Some Eukaryotes; transcribes siRNA.

Consensus Sequences

Sequences conserved among multiple species/the “equilivant” sequence. -10 and -35 are important in bacteria.  

Upstream Element

A consensus sequence in the promotor

Abortive Initiative

When RNA Polymerases fail to transcribe the entire gene, often repeated several times before successful transcription occurs

Polycistronic mRNA

mRNA containing multiple genes

General Transcription Factors

Transcription factors that form the basal transcription apparatus

Basal Transcription Apparatus

A group of proteins that initiate transcription in RNA Polymerase II

DNA Polymerase I

Prokaryotes; Removes & replaces primers (created by primase)

DNA Polymerase II

Prokaryotes; Repairs DNA and stops replication is damage to DNA is detected

DNA Polymerase III

Prokaryotes; Elongates DNA, does most of the DNA replication

DNA Polymerase alpha α

Eukaryotes; has primase activity and initiates nuclear DNA synthesis by synthesizing an RNA primer, followed by a short string of DNA nucleotides

DNA Polymerase delta δ

Eukaryotes; follows DNA polymerase alpha to replicate the lagging strands

DNA Polymerase gamma γ

Eukaryotes; replicates and repairs mtDNA

DNA Polymerase epsilon ε

eukaryotes; replicates on the leading strand(s)

Enhancers

Distant DNA sequences that can be bound to transcription factors to increase transcription

Non-template Strand

Coding Strand

Template strand

Non-coding strand

Template strand

Antisense Strand

Template Strand

Negative Strands

TATA-binding Proteins

How do Rho-dependent terminators works?

The Rho protein binds to the rut site on the mRNA and moves toward the 3' end, degrading the extra noncoding RNA.

Polycistronic mRNA

A group of bacterial genes transcribed together; no terminator after each gene

RNA Polymerase I Termination

Termination requires a termination factor that binds to a sequence downstream of the termination

RNA Polymerase III Termination

Ends after transcribing a terminator sequence that produce a string of uracil molecules, sometimes needing hairpins/secondary structures

RNA Polymerase II Termination

Transcribes well past the coding sequence, more being cleaved and degraded back towards the terminator via exonuclease like RAT1

Exonuclease

Enzymes that cleave nucleotides one at a time from the ends of a nucleic acid polymer, either the 5’ or 3’ end

RAT1

a 5’→3’ exonuclease found in yeast

Core Promotor

A promotor where the Basal transcription complex binds

Intron Early Hypothesis

The idea that early organisms had introns and they were lost in prokaryotes

Intron Late Hypothesis

The idea that early organisms did not have introns and eukaryotes later acquired them

Group I Introns

Self-splicing introns found in bacterial, viruses, and eukaryotes

Group III Introns

Self-splicing introns found in mitochondria, chloroplasts, bacteria, and archea

Nuclear pre-mRNA introns

Non-self-splicing (requires a spliceosome) introns found in the eukaryotic nucleus

Transfer RNA introns

Non-self-splicing introns found in tRNA genes of bacteria, archaea, and eukaryotes

Lariat

A structure formed during RNA splicing where the 5’ splice site binds to the branch site

Alternative Processing Pathways

Pathways that allow one pre-mRNA to produce different proteins

Guide RNAs (gRNAs)

Partially complementary RNA segments to unedited mRNA that binds to mRNA to modify the mRNA.

The TΨC arm

An arm of tRNAs

The DHU arm

An arm of tRNAs

RNA-induced silencing complex

a combination of siRNA, miRNA, and proteins that degrade mRNA

CRISPR RNAs (ciRNAs)

RNAs that work w/ CRISPR Cas-9 to combat foreign DNA

Scientists behind the one gene one polypeptide theory

Beetle and Tatum

The organism studies by Beetle and Tatum

Neurospora

Why is studying Neurospora advantageous?

They are easily cultivated and haploid so recessive mutations can be viewed

Neurospora Group I

The mutant group of neurospora that lacks the enzyme to synthesize ornthine, and therefore citrulline, and arginine.

Neurospora Group II

The mutant group of neurospora that lacks the enzyme to synthesize citrulline, and therefore arginine.

Neurospora Group III

The mutant group of neurospora that lacks the enzyme to synthesize arginine

The chemical synthesis pathway of Neurospora

Precursor → ornithine → citrulline → arginine

Primary Structure of proteins

Sequence of amino acid

Secondary Structure of proteins

Formed by interactions between amino acids (alpha helixes, beta pleated sheets)

Tertiary structure

Overall three-dimensional shape, determined by the primary structure interactions.

Quaternary Structure

Association of two or more polypeptide chains

Scientists who discovered what amino acid some codons code for

Nirenberg and Matthaei

TFIID

TATA-Binding Protein (Transcription)

TBP

TATA-Binding Protein (Transcription), binds with TFIID

TFIIA

Transcription Factor

TFIIH

Transcription Factor

TFIIF

Transcription Factor

TFIIE

Transcription Factor

IF-3

Prevents the large subunit from binding to the small subunit prematurely

IF-2 & IF-1

Binds with GTP and initiator tRNA to help it attach to the P site of small ribosomal subunit

EF-Tu

Binds with GTP and tRNA and attaches it to the A site

EF-G

Assists with translocation

RF-1 & RF-2

Help release the polypeptide chain from the ribosome

RF-3

Release RF-1 and RF-2 from the ribosome

Histones

H1, H2A, H2B, H3, H4