Synthetic Biology Exam 2

What is Synthetic Biology

“Synthetic biology is a) the design and construction of new biological parts, devices, and systems and b) the re-design of existing natural biological systems for useful purposes.”

Housekeeping

Gene products are required by the cell under all growth conditions

Gene Regulation

How bacteria regulate the expression of their genes. How living organisms regulate the expression of their genes and genes that are being expressed meet the needs of the cell for a specific growth condition.

Transcriptional

When the transcription of the gene(s) can be regulated

Translational Regulation

Regulation at the level of a protein

Transcription

In this process RNA is chemically synthesized by the action of RNA polymerase

template

Strand complementary to the RNA

Terminator

Causes RNA polymerase and the newly synthesized RNA disassociate from the DNA to end transcription

nontemplate strand

coding strand, contains the samesequence as the RNA exceptfor the substitution ofuracil for thymine

core rna polymerase

A complex composed of the proteins beta, beta prime and two subunits of alpha

holoenzyme

Core RNA polymerase + sigma factor

promoters

The sigma factor directs RNA polymerase to these specific sequences in the DNA so that transcription initiates at the proper place

+1 site

the transcriptional start site

-10 region

The motif at ~10 bases upstream of the +1 site

-35 region

The motif at ~35 region upstream of the +1 site

promoters consensus sequence

consist of TAATAT at the -10 region and TTGACA at the 35 region.

stem loop structure

Secondary structure forms in the RNA which can be associated with terminating transcription

ribosome binding site

Ribosomes are able to bind to this site in the mRNA and initiate translation at the starting methionine codon (AUG)

Shine Delgarno Sequence

Another name for ribosome binding site

operators

These DNA sequences are control region found adjacent to or overlapping the -35 and -10 regions of the promoter

repression

The process in which regulatory proteins have the ability to bind to their control region and prevent transcription

activation

The process in which regulatory proteins can also bind to their control regions and promote RNA polymerase binding to the promoter

operon

A group of genes physically linked on the chromosome and under the control of the same promoter(s)

polycistronic mRNA

In an operon, the linked genes give rise to a single mRNA that is translated into the different gene products.

regulon

Group of genes all needed for the same process but physically located in different parts of the chromosome and containing their own promoter(s)

catabolic

The process when a compound is broken down

anabolic

biosynthetic pathway

How do bacteria protect their DNA?

By adding methyl groups to prevent cutting by restriction enzymes.

What are the three types of bacterial protection systems that use restriction enzymes, and how do they differ?

• Type I: Cuts far from the recognition site, needs ATP.

• Type II: Cuts at the recognition site, no ATP needed.

• Type III: Cuts near the recognition site, needs ATP.

What is a Palindrome?

A DNA sequence that reads the same in both directions (e.g., GAATTC and CTTAAG).

What are the features of cloning vectors?

• Origin of replication.

• Selectable marker (e.g., antibiotic resistance).

• Unique restriction sites for inserting DNA.

For the pUC19 plasmid, where are the unique restriction sites located?

Within the multiple cloning site (MCS), near the lacZ' gene.

At what temperature do many restriction enzymes work best?

37°C

What is the consequence of using room temperature for the restriction digest?

Reduced enzyme activity or incomplete digestion

How are partial digests created?

By using less enzyme, shorter incubation times, or suboptimal conditions