TF Questions Exam 2

Regulatory genes (L7)

Genes whose products control the transcription or translation of other genes

Where does a repressor bind in a bacterial operon to negatively regulate transcription? (L7)

The operator (not the promoter)

Repressible gene control (L7)

Controlled by a repressor (negative control)

Regulator protein in negative control (L7)

A repressor

Regulator protein in positive inducible control (L7)

An activator; the gene is normally inactive in transcription

Lac operon in the absence of lactose (L7)

Repressed (not transcribed) because the repressor binds the operator

Types of control on the lac operon (L7)

Both negative (repressor) and positive (cAMP-CAP) control

When does cAMP-CAP activate the lac operon? (L7)

When glucose level is low (cAMP is high)

trp operon in the absence of tryptophan (L7)

The trp genes are expressed (tryptophan is synthesized)

Where are most structural genes found in eukaryotes? (L8)

Individually regulated, not in operons (operons are mainly prokaryotic)

Effect of highly condensed DNA bound to histones on gene expression (L8)

Represses gene expression

Importance of mRNA degradation rate in eukaryotes (L8)

It is important in regulating gene expression

Effect of adding acetyl groups to histone tails (L8)

Loosens chromatin and usually stimulates transcription

Function of FLD in the FLC gene (L8)

FLD deacetylates histones at FLC, which represses FLC transcription

GAL4 (L8)

A transcription activator for galactose-digesting enzyme genes

GAL80 when there is no galactose (L8)

GAL80 binds GAL4 and blocks it, so the galactose-metabolizing genes are not transcribed

Alternative splicing in Drosophila (L8)

Important in regulating sexual development

Tra mRNA in male fly embryos (L8)

Processed Tra mRNA is longer, but a nonfunctional Tra protein is produced

RNA interference (RNAi) other names (L8)

RNA silencing and posttranscriptional gene silencing

Effect of siRNAs on target mRNA (L8)

Increase degradation of the target mRNA, so protein production decreases

Role of miRNA in RISC (L8)

Pairs imperfectly with mRNA and inhibits translation of the targeted mRNA

Role of siRNA in RISC (L8)

Pairs with mRNA, and RISC cleaves the mRNA

RITS composition (L8)

siRNAs and proteins

Role of siRNA in RITS (L8)

Binds DNA, causing methylation and restricting transcription (transcriptional silencing)

Somatic mutations and daughter cells (L9)

Somatic mutations ARE passed to daughter cells when the cell divides (but not to offspring)

G/C to A/T base pair change (L9)

A transition mutation (purine-to-purine or pyrimidine-to-pyrimidine)

Effect of nonsense mutations (L9)

Change an amino acid codon into a stop codon, causing premature termination and a truncated protein

Missense mutation (L9)

Changes a codon so it specifies a different amino acid

Insertion or removal of nucleotides in a gene (L9)

Usually causes a frameshift mutation

Cause of spontaneous mutations (L9)

DNA replication errors

Cause of grape color variation (L9)

Gene mutation via transposition

Effect of UV light on DNA (L9)

Absorbed by pyrimidines, forming pyrimidine dimers

Effect of incorporating 5-bromouracil during replication (L9)

Can lead to transition mutations

Why base analogs are mutagenic (L9)

They resemble normal bases but mispair, causing replication errors (they do not destroy the sugar backbone)

What does mismatch repair recognize? (L9)

The newly synthesized strand (unmethylated), using the methylated parental strand to identify which base to correct

Photoreactivation (L9)

A form of direct repair (reverses pyrimidine dimers using light)

DNA glycosylase (L9)

Recognizes and removes a specific damaged base in base excision repair

Malignant tumor (L10)

Cells are invasive and can spread (benign tumor cells stay localized and noninvasive)

Metastatic tumor (L10)

Cells invade surrounding tissues and spread to distant sites in the body

Most common type of cancer (L10)

Sporadic cancer (familial cancer, passed from parent to child, is a minority)

How is an oncogene formed? (L10)

Changes in the DNA sequence of a proto-oncogene give rise to an oncogene

Function of proto-oncogenes (L10)

Promote cell proliferation, growth, and survival

Ras gene mutation (L10)

A missense mutation in ras can cause human bladder cancer

Human src gene (L10)

A proto-oncogene that can be changed to an oncogene through virus infection

MYCN gene (L10)

A transcription factor gene that can be amplified to cause neuroblastoma

CML and Burkitt's lymphoma cause (L10)

Chromosome translocation and activation of an oncogene

Effect of tumor suppressor genes being inactivated (L10)

Cells grow out of control

RB and p53 (L10)

Tumor suppressor genes (not oncogenes) involved in cell cycle checkpoint regulation

p53 protein function (L10)

Acts as a "brake" to halt cells at the G1 checkpoint, allowing DNA repair

RB gene mutation (L10)

Cells pass the G1/S checkpoint without normal controls, causing retinoblastoma

DNA repair genes (L10)

Tumor suppressor genes (not oncogenes)

Three recurring steps of PCR (L11)

Denaturation, primer annealing, and extension

Taq polymerase (L11)

Heat-stable DNA polymerase used in PCR; it survives the 94°C denaturation step

What does agarose-gel electrophoresis separate DNA/RNA by? (L11)

Size (charge-to-mass ratio is similar, so smaller fragments move faster)

How do restriction enzymes cut dsDNA? (L11)

At specific recognition sequences, producing cohesive (sticky) or blunt ends

Plasmid (L11)

Small circular DNA of thousands of bp with functional genes and its own origin of replication

Three important characteristics of a cloning vector (L11)

1. Origin of replication 2. Selectable marker 3. Unique restriction enzyme sites

Recombinant plasmid in gene cloning (L11)

Replicates independently in the host; when the host divides, copies are passed to the progeny

Color of bacteria with empty (no insert) plasmids (L11)

Blue, because they have a functional lacZ; the blue colony is NOT selected for the cloned gene

Vector needed for a GMO (L11)

An expression vector

Ti plasmid (L11)

Can be modified or engineered as a vector for plant transformation

Tumor-inducing genes in the Ti plasmid (L11)

Can be removed and replaced by your gene of interest for plant transformation

Why Sanger sequencing terminates DNA synthesis (L12)

A dideoxynucleotide (ddNTP) is incorporated, and it lacks a 3'-OH

How is the sequence read from a Sanger gel? (L12)

From bottom to top, giving the newly synthesized strand 5' to 3' (the template is its complement)

Value of Sanger sequencing vs Illumina (L12)

Sanger is still valuable (longer reads, high accuracy, validation of results)

Read length: Illumina vs Sanger (L12)

Illumina reads are much shorter than Sanger reads

Illumina vs Sanger throughput (L12)

Illumina has much higher throughput

Why DNA fragment clusters are generated in Illumina (L12)

So the optical detector can detect a strong enough signal during sequencing

Illumina sequencing method (L12)

Sequencing by synthesis, relying on incorporation of nucleotides with a reversible terminating group by a DNA polymerase