Exam studies Chapter 7, 10, 12 and 13

Replication

The duplication of DNA in the cell by DNA polymerase for reproduction.

Transcription

The transfer of the genetic information of a gene from DNA into single-stranded RNA by RNA polymerase.

Translation

The synthesis of a protein using the genetic information encoded on mRNA.

Messenger RNA

A single stranded molecule that carries the genetic information from the DNA to the ribosome.

Transfer RNA

Converts the genetic information in the nucleotide sequences from mRNA into a defined set of amino acids in proteins.

Ribosomal RNA

Important catalytic and structural components of the ribosome.

What is considered the “Blueprint of Life”?

DNA

What process transfers genetic information from DNA into RNA?

Transcription

What is the structure of DNA?

A double helix composed of two complementary nucleotides strands.

What does complementary mean in DNA?

The bases pair specifically: A with T and G with C

What holds the two DNA strands together?

Hydrogen bonds betweeen complementary bases.

How many hydrogen bonds form between G and C, and between A and T?

G-C = 3; A-T = 2

What does it mean that DNA strands are antiparallel?

The two strands run in opposite directions: one 5′→3′ and the other 3′→5′

How is a bacterial chromosome replicated?

Replication begins at the origin of replication and proceeds bidirectionally, forming two replication forks.

What is bidirectional replication?

DNA replication that proceeds in two directions from the origin of replication.

What does DNA polymerase do during DNA synthesis?

It synthesizes a new DNA strand by adding one nucleotide at a time to the 3′ end of the elongating strand.

What determines which nucleotides are added during DNA synthesis?

Base-pairing rules.

What is a replication fork?

The Y-shaped region where the DNA strands separate during DNA replication.

What enzyme unwinds/unzips the DNA during DNA replication?

Helicase.

What enzyme makes the RNA primer?

Primase.

What enzyme synthesizes the new DNA strand?

DNA polymerase III.

What are the two types of newly synthesized DNA strands?

The leading strand and the lagging strand.

What are Okazaki fragments

Short DNA fragments formed on the lagging strand.

What does DNA polymerase I do?

Removes RNA primers and replaces them with DNA.

What does DNA ligase do?

Joins the DNA fragments together.

What are the three functional types of RNA?

mRNA, rRNA, and tRNA.

What do rRNA and tRNA do in protein synthesis?

They fold into characteristic three-dimensional structures that play roles in protein synthesis.

Which type of RNA is translated?

mRNA

What are mRNA, rRNA, and tRNA transcribed from?

Different genes.

What is a promoter?

A DNA sequence to which RNA polymerase binds to initiate transcription of a gene.

What is the function of an operator sequence?

It allows for the regulation of transcription.

Where can an operator sequence be located?

Between the promoter and the region transcribed or upstream of the promoter.

What is a terminator?

A DNA sequence at which transcription stops.

What do nucleotide sequences in DNA direct?

Transcription.

What does the promoter orient?

RNA polymerase.

What does the orientation of RNA polymerase determine?

Which DNA strand will be used as the template.

What is a codon?

An RNA triplet of three bases that encodes a specific amino acid.

How many codons and amino acids are there?

64 codons and 20 amino acids.

What is an anticodon?

The complementary sequence of a codon found on tRNA molecules.

What is wobble?

The variation at the third base of codons that allows most amino acids to have more than one codon.

What is the start codon?

The first codon of an mRNA that is translated, usually formyl-methionine.

What is a stop codon?

One of three codons that signals translation to stop.

UUU, UUC

Phenylalanine

UUA, UUG, CUU, CUC, CUA, CUG

Leucine

AUU, AUC, AUA

Isoleucine

AUG

Methionine (Start)

GUU, GUC, GUA, GUG

Valine

UCU, UCC, UCA, UCG, AGU, AGC

Serine

CCU, CCC, CCA, CCG

Proline

ACU, ACC, ACA, ACG

Threonine

GCU, GCC, GCA, GCG

Alanine

UAU, UAC

Tyrosine

UAA, UAG, UGA

None (Stop)

CAU, CAC

Histidine

CAA, CAG

Glutamine

AAU, AAC

Asparagine

AAA, AAG

Lysine

GAU, GAC

Aspartic acid

GAA, GAG

Glutamic acid

UGU, UGC

Cysteine

UGG

Tryptophan

CGU, CGC, CGA, CGG, AGA, AGG

Arginine

GGU, GGC, GGA, GGG

Glycine

How many reading frames are typically used for translation?

One, which makes the correct protein.

How many potential reading frames does an ORF nucleotide sequence have?

Three

Where does translation end?

At the stop codon.

Where does translation begin?

At the start codon.

Where does the ribosome begin to assemble?

At the ribosome-binding site.

What do nucleotide sequences in mRNA direct?

Translation.

What are the three stages of translation (protein synthesis)?

Initiation, elongation, and termination.

How many ribosomes can translate the same mRNA molecule?

More than one ribosome.

When does translation begin in relation to mRNA synthesis?

Ribosomes begin translating the 5′ end of mRNA before transcription is complete.

What happens to complete proteins after they pass through the membrane?

They fold into globules and are sent to the Golgi for distribution.

Where is mRNA made?

In the nucleus.

How does mRNA leave the nucleus?

Through a nuclear pore.

Where is mRNA transported for protein synthesis?

To the rough ER.

Where are ribosomes and other components for protein synthesis concentrated?

At the rough ER.

Where are complete proteins sent for distribution?

To the Golgi

Can the level of gene expression be controlled?

Yes

How is gene expression generally regulated in cells?

It is very specific and tightly regulated, using multiple ways and types of mechanisms.

What do DNA-binding proteins interact with?

Two, often repeated, sequences near each other but separated by a gap.

What are the three terms associated with transcriptional regulation by repressors?

Inducer, repressor, and co-repressor.

What terms are associated with transcriptional regulation by activators?

Activator and inducer.

Where do repressors and activators bind relative to the promoter?

Repressors bind to the operator between the promoter and gene sequence, while activator-binding sites can be some distance upstream from the promoter.

Which sugar do E. coli cells preferentially use when both glucose and lactose are available?

Glucose.

When do E. coli cells begin metabolizing lactose?

After the glucose supply is used up.

How does growth on lactose compare with growth on glucose?

Growth on lactose is slower than growth on glucose.

What is the lagging strand?

The DNA strand synthesized discontinuously in short fragments called Okazaki fragments.

What is the leading strand?

The DNA strand synthesized continuously during replication.

Gene

A specific section of DNA that holds the instructions to make a protein, which determines a specific trait.

Genome

An organism's complete set of DNA. It includes all of its genes and genetic instructions needed to build and maintain that organism.

Operator

A segment of DNA that acts as the regulatory switch.

Quorum Sensing

A method of cellular communication used by bacteria to monitor their population density and coordinate group behaviors.

Two-Component Regulatory System

A bacterial signaling system consisting of a Sensor Kinase (detects environmental stimuli and autophosphorylates) and a Response Regulator (receives the phosphate and alters gene expression)

Operon

The entire stretch of DNA needed for enzyme production. It includes the operator, the promoter, and the cluster of genes they control.

Which sugar do E. coli preferentially use when both glucose and lactose are available?

Glucose

When do E. coli begin metabolizing lactose?

After the supply of glucose is used up.

How does growth on lactose compare with growth on glucose?

Growth on lactose is slower than growth on glucose.

In what direction are DNA and RNA always produced?

5′ to 3′ direction.
(The numbers 5' and 3' refer to the order of carbon atoms in the sugar chain, starting at the oxygen without a side chain).

What holds the antiparallel chains of DNA (or RNA in double-stranded RNA viruses) together, and how many bonds do the bases share?

They are held together by hydrogen bonds. C and G share 3, while A and T (or U in RNA) share 2