Biol 200

Information Biopolymers (examples)

Informational Biopolymer Monomer structure

Polymer backbone (formed by what?)

Informational Biopolymers made from what?

Characteristic element of nucleotides

Common element of Nucleotides

Two joining sites in nucleotides

Link between Nucleotides

Protein Characteristic element

Protein common element

Protein joining sites

Protein growth starts on this end

3 main AA classes

Form of Amino Acid Monomers

Watson-Crick base pairs (What are they?)

Tm is a function of what?

G-C pair (number of H bonds?)

A-T pair (how many H-bonds)

Growth direction of nascent RNA chain

Unwinds DNA duplex

RNA exits polymerase how?

Facilitate binding of RNA polymerase to DNA

Transcription Monomers

DNA replication Monomers

Stop codons

Amino acid Monomers for translation

Number of polymerase molecules recruited per start site for DNA replication

Direction of DNA replication

Unwinding bubble state for DNA replication

Unwinding bubble state, tranqqscription

Oligopeptides (composition)

Proteins (What are they?)

Mass units used for proteins

Dalton to atomic mass unit conversion

Average mass of 1 aa

Largest known polypeptide

Weight of largest known polypeptide

How many aa's in largest polypeptide?

Two major classes of amino acid side chains

Functions of proteins

Levels of proteins Structure

Primary protein Structure (what is it?)

Secondary protein Structure (what is it?)

Tertiary protein Structure (What is it?)

Quaternary structure (what is it?)

Supramolecular protein Structure (what is it?)

Two major peptide chain backbone conformations

Absence of secondary structure

Backbone configurations based on?

Three motifs of protein secondary structure

Coiled-Coil motif (involved in?)

Helix-loop-helix motif (involved in?)

Zinc Finger motif (Involved in ?)

Four structural classes of proteins

Length of a domain

Chaperones (What are they?)

What were chaperones originally identified as?

Two major classes of chaperones

Hsp 70 (What is it?)

Hsp60 (also called what?)

Ubiquitin (What is it?)

Molecule to which protein binds

Important properties in ligand binding

Specificity (ligand)

Affinity (ligand)

Antibodies contain what?

Where do substrate binding & rxn catalysis occur?

Vmax (what is it?)

Km (What is it?)

What does the Vmax depend on?

What does the Km depend on?

What does the catalytic mechanism of serine proteases involve

Widely used as allosteric switches to control protein activity

DNA polymerase error rate

RNA Polymerase error rate

Point Mutation (What is it?)

Missense Mutation (what is it?)

Nonsense mutation

Silent Mutation

Excision repair systems

What does DNA glycosylase do in Base excision repair

APEI endonuclease (does what in Base excision repair? )

AP Lyase (Does what in Base excision repair?)

Binds at mismatch site in mismatch excision repair

Removes Nucleotides on newly synthesized daughter strand in mismatch excision repair

Recognizes backbone kink induced by thymine dimers in Nucleotide excision repair

XP-G/RPA does what in Nucleotide excision repair

What is XP-G/RPA?

Cut damaged strand 25nt apart in Nucleotide excision repair

Xderoma Pigmentosum Cancer Syndrome (Caused by what?)

Fills in gap in Nucleotide excision repair

Causes DNA double strand break

Fragmentation in tandem MS occurs where?

Nucleosome

Karyotype

Required for replication/stable inheritance

Telomeres (role)

CENP-A

Telomerase (does what?)

Telomerase (found where?)

15N DNA vs. 14N density difference

Replication region usually rich in what?

Removes RNA Nucleotides from RNA Primer

Keeps single stranded DNA in favorable conformation coat

Sliding Clamp that keeps cruising DNA polymerase connected to template strand

Loads PCNA on DNA

Pol. epsilon (responsible for which strand)

Pol gamma (responsible for which strand) poop

Two repair mechanisms for DNA Double-Strand Breaks

Homologous recombination plays a role in which type of breast cancer?

Forms a synapse in Non-homologous end joining

Non-homologous end joining problems

Local unwinding or unbroken DNA in homologous recombination

Heteroduplex (What is it?)

Fluorescent DNA binding dye

PCR primer

How many primers in PCR

PCR steps

DNA cloning (goal)

DNA cloning inserts

Recombinant DNA

Restriction site (What type of sequence?)

Dilution Cloning (What is it?)

cDNA (What is it?)

Genomic DNA vs cDNA

Produces blue product from X-Gal

Transient Transfection (requires what?)

G-418 (What is it?)

Protein separation methods

Protein Phys./Chem. Properties

Centrifugation size unit

Electrophoresis direction of migration (determined by what?)

Electrophoresis speed of migration determined by what?

Isoelectric point

Isoelectric point depends on what?

Gel Filtration Chromatography (Based on what?)

Ion-Exchange Chromatography (Based on What?)

Western blot (principle)

Sandwich immunodectetion (What is it?)

Immunoprecipitation (What is it?)

Immunoprecipitate contains what?

GFP promoter fusion (what is it?)

GFP protein fusion (what is it?)

Mass spectrometry: determination of what?

Acceleration in electric/magnetic field depends on what?

How many bonds/molecule broken in tandem MS?

Tandem MS identifies what?

Proteomics (what are they?)

genome (what is it?)

Simple sequence DNAs (what are they?)

Mobile element interspersed repeats (account for what percentage of human genome?)

Selfish DNA (also known as?)

two major classes of selfish DNA

DNA transposon (what enzyme is used?)

Retrotransposons (what enzyme is used?)

Retrotransposons (related to what?)

LTR elements (what are they?)

LINEs (what are they?)

Two mechanisms of genome evolution

Orthologues (what are they?)

Paralogues (what are they?)

Polynucleotide Kinase (does what?)

What must be incorporated into PCR amplified DNA for the production of labelled probes?

Membrane Material for DNA

Membrane Material for RNA

Northern Blot gel contains what special ingredient?

Primer used for RNA seq

Three stages of RNA transcription

o factors (play what role in transcription)

DNA binding protein (play what role in transcription)

Polycistronic

Monocistronic

Polymerase with highest sensitivity to mushroom toxin

RNA polymerase II (role)

Common features of Eukaryotic RNA polymerases

TATA box binding protein (does what?)

TFIIA (role?)

TFIIE (role?)

TFIIF (role?)

Needed for formation of open complex

Presence of NTPs (does what?)

Elements of TFIIH critical for formation of open complex

What precentage of the genome is transcribed?

In what types of genes does transcription occur bidirectionally (example)

Use of recombinant technology in mammalian cells (what term applies?)

Use of recombinant technology in live animals/plants (what term applies?)

Reporter genes (what are they?)

Linker Scanning Mutational Analysis (used for what?)

Common reporters

Recognition helix (what is it?)

GAL4 (responsible for what function in yeast ?)

Cis-acting (definition)

Trans-acting (definition)

GAL 4 contains which domains?

Various domains found on transcription factors?

homeobox gene

3 categories of Zinc Fingers?

C4 Zinc finger characteristics

What are helix-loop-helix proteins?

How are molecules cross-linked in ChIP

heterodimer

homodimer

Nucleosomes (use?)

Heterochromatin, characteristics

Heterochromatin (found where?)

Loci for reproductive types in yeast

SIR 3,4 proteins (role?)

SIR2 protein (role?)

In histone deacetylation complexes, Ume6 binds what?

Rpd3 (role?)

Examples of protein complexes that acetylate

Chromatin readers (role?)

Types of histone tail markings

Methylation of lysine 4 on histone 3 (associated with what?)

Methylation of lysine 9 on histone 3 (associated with what?)

XIST locus (what does it do?)

Epigenetic Trait (what are they?)

Marks on Histones (what are they called?)

Modify and mark naive histones (what does this?)

What does LacI interact with to create repression in bacteria?

What is VP16?

Pioneer Transcription factors (what do they do?)

Where is the CTD found?

How many YSPTPS repeats in humans?

Exonic Splicing Enhancers (what is their role?)

U2AF (what is its role?)

Catalyzes formation of Poly A tail

Factors involved in cleavage of RNA and polyadenylation

Mediates polyadenylation slow phase

What happens in the polyadenylation slow phase

Protein used in rapid phase of polyadenylation

What happens in the rapid phase of polyadenylation

Which mRNA transcripts are NOT polyadenlyated?

What is a nucleolus?

snoRNAs (what do they do?)

What is the difference between fibronectin in fibroblasts and hepatocytes?

Sexually dimorphic characteristics (what are they?)

Dsx exon 4 (does what?)

Dsx exons 5-6 (do what?)

Deamination reactions (two types)

Enzyme responsible for editing apo-B

Nuclear Pore Complexes (role?)

Size of a nuclear pore complex

FG-nucleoporins (role?)

Nuclear Localisation signal (role?)

Ran (what is it?)

Nuclear Transport Receptors (role?)

What are the two subunits of the mRNA exporter

NXF1 (role?)

NXT1 (role?)

Insect Polytene chromosomes (also know as?)

Dominant Negative Effects (what are they?)

When are pre-mature stops detected

Sequence which destabilizes Eukaryotic mRNAs

Deadenylase Complex (does what?)

XRN1 (role?)

ferritin (what does it do?)

What percentage of cellular RNA is comprised of rRNA?

rRNA folds into what structures?

What transcribes tRNA?

aminoacyl-tRNA synthetase (role?)

How are aa's linked to tRNA?

How is Methionine modified in bacteria?

What forms the eIF2 ternary complex?

Initiator factors which keep small ribosomal subunit alone

What forms the 43S complex?

What is the eIF4 complex composed of?

What type of protein is eIF4A (what role?)

What does the Shine-Dalgarno box bind to in bacteria

position AUG for pairing with tRNA in mammalians

what is the Kozak sequence

eIF4G (binds to what?)

Cause of conformational change which brings A site aa close to P site chain

rRNA used for peptidyl transferase reaction in bacteria

rRNA used for peptidyl transferase reaction in eukaryotes

Forward translocation of ribosome (carried out by what?)

recognition of codon (by what?)

What does eRF1 associate with?

dsRNA (causes what?)

Snapback constructs (composed of what?)

T7 promoter (composed of what?)

DICER (role?)

Binds siRNA

Argonaute protein (role?)

degrades cleaved mRNA transcripts

miRNA (how does it affect RNA?)

siRNA (how does it affect RNA?)

viral sponge RNA (plays what role?)

Cas9 (what is it?)

sgRNA (combination of what?)

PAM sequence (what is it?)

disruption construct (yeast) (made how?)

streptavin (What is it?)

How many YSPTPS repeats in humans?

How many YSPTPS repeats in yeast?

Where does RNA Polymerase stop (near promoter)

What does the cApping enzyme add to the 5' end of RNA

How is the 5' cap linked to the 5' cap end?

What is P-TEFb's role in CTD phosphorylation

What are the further proteins attracted by S5 phosphorylation?

What does the Ribonucleotin complex participate in?

In introns, what are the usual Nucleotides at the 5' end?

In introns, what are the usual Nucleotides at the 3' end

What is the spliceosome composed of

Contacts intron border (which snRNP)

Contacts branch point region (which snRNP)

How are the two intro splicing trans-esterification reactions mediated

Enzyme which linearizes lariat