Protein Synthesis and Genetic Engineering

What phases of the cell cycle does protein synthesis take place?

Protein synthesis takes place in the G1 and G2 phases.

What do we call the process where DNA is copied to make RNA?

Transcription.

Where does transcription occur in eukaryotes?

In the nucleus.

Where does transcription occur in prokaryotes?

In the cytoplasm.

What enzyme adds nucleotides to the template strand during transcription?

RNA polymerase.

Why are the two structural differences between DNA and RNA?

DNA uses deoxyribose sugar while RNA uses ribose. DNA uses thymine while RNA uses uracil

What is messenger RNA?

mRNA is a single stranded RNA molecule that carries genetic instructions needed to make proteins from DNA in the nucleus to ribosomes in the cytoplasm.

What is ribosomal RNA?

rRNA is a type of non-coding RNA that is a primary component of ribosomes.

What are transfer RNAs (tRNAs)?

Small molecules that translate the genetic code in mRNA into the amino acid sequence of proteins during protein synthesis.

How is mRNA edited before it leaves the nucleus?

Non-coding introns are removed and coding exons are joined together in a process called splicing.

What is a ribozyme?

An RNA molecule that can catalyze specific biochemical reactions, similar to protein enzymes.

What is RNAi?

RNA interface is a biological process where RNA molecules inhibit gene expression by neutralizing specific mRNA molecules

How do scientists use RNAi?

Scientists use it to study gene function, develop therapies for disease, and manipulate gene expression

What process uses RNA to synthesize proteins?

Translation.

What is the ratio of nucleotides to amino acids?

3 nucleotides : 1 amino acid.

What do we call a group of three consecutive nucleotides on mRNA that codes for a single amino acid?

Codon.

How many different ways can 4 letters be arranged in triplets?

64 different ways.

Why is the genetic code described as redundant?

Multiple codons can code for the same amino acid, minimizing the impact of mutations

What is the start codon?

AUG, which codes for methionine.

How many stop codons are there?

Three stop codons: UUA, UAG, and UGA.

Where are ribosomal subunits assembled in eukaryotic cells?

In the nucleolus.

What besides RNA makes up ribosomes?

Ribosomal proteins.

What are the three tRNA binding sites on a ribosome in order?

The A (aminoacyl) site, P (peptidyl) site, and E (exit) site.

What type of RNA binds to the binding sites on the ribosome?

tRNA

What role does tRNA play?

tRNA acts as adaptors, translating genetic code in mRNA into the amino acid sequence of proteins.

What do we call the three nucleotides at the bottom of tRNA that bind with mRNA?

Anticodon.

What are the three stages of translation?

Initiation, where the ribosome binds to the mRNa, elongation, where amino acids are added to the growing polypeptide chain, and termination, where the process stops and the completed protein is released.

What codon appears on the A site during initiation?

AUG codon.

Which translation stage is the longest? Why?

Elongation, because the ribosome needs to traverse the entire mRNA and read each codon to create the protein.

How much energy is used per peptide bond in protein synthesis?

1 ATP and 2 GTP

When does the protein release factor bind to the mRNA codon?

During the termination stage of translation.

How do protein release factors differ from tRNAs?

Release factors recognize stop codons; tRNAs deliver amino acids.

Where in the cell does translation take place?

On ribosomes in the cytoplasm.

What is a polyribosome?

A group of ribosomes bound to a single mRNA molecule, simultaneously translating that single mRNA molecule.

What type of endoplasmic reticulum has ribosomes attached?

Rough endoplasmic reticulum.

Where do proteins go to get a small sugar attached after synthesis?

To the Golgi apparatus.

What structures do proteins travel in from the ER to the Golgi?

COPII-coated transport vesicles.

What moves transport vesicles along microtubule tracks from the ER to the Golgi

Motor proteins.

What evidence supports that the 'RNA World' predates the DNA World?

RNA can store genetic information (like DNA) and catalyze reactions (like proteins)

What is a mutation? What can cause it?

A mutation is a change in the DNA sequence caused by replication errors, exposure to radiation or chemicals, or viral infections

Define point mutation.

A genetic alteration where a single nucleotide base is changed, inserted, or deleted.

Why are insertion/deletion mutations considered worse?

They cause a frame-shift, altering the reading frame of the DNA sequence, leading to a completely different protein being produced

What is the mutation rate in humans?

About 1.1-1.7 × 10^-8 per base pair

Why are most point mutations considered neutral? (what percent of the human genome actually codes for proteins, and what often happens when a point mutation occurs on the third nucleotide of a codon).

Because only 1-2% of the human genome actually codes for proteins and point mutations in the third nucleotide of a codon often don’t change the resulting amino acid.

What is a transcription factor?

A protein that regulates transcription by binding to specific DNA sequences, either promoting or inhibiting the process.

What is an operon?

A unit of DNA where a set of genes are transcribed together under the control of a single promoter and operator

How many genes are in the lac operon (that code for enzymes)?

Three genes

What molecule prevents transcription when attached to a histone tail?

A methyl group.

What tool do scientists use to transfer small amounts of liquid?

Micropipettes.

What is the first restriction enzyme discovered in E. coli?

EcoRI.

What gene is included on a plasmid to isolate bacteria on ampicillin?

Ampicillin resistance gene (ampR).

What is the process of inserting foreign DNA into a bacterial cell called?

Transformation.

What are sticky ends?

Single-stranded overhanging ends that allow easy joining of DNA fragments.

What is the role of mutations and evolution?

Mutations play a crucial role in evolution as they are the primary source of genetic variation, ultimately driving evolution

What did Linus Pauling use the amino acid sequence of hemoglobin of three different animals to figure out? (what does mutation rate tell us)?

He used it to figure out the mutation rate, which helps us determine the evolutionary time between species

Why are mitochondrial mutation rates used as evidence for human evolution?

Mitochondrial mutation rates are used in human evolution because mitochondrial DNA is passed down maternally

Does every cell in a multicellular organism transcribe the same genes? Why?

No, not every cell in a multicellular organism transcribes the same because gene expression is regulated, meaning specific genes are turned on or off in different cell types to enable specialization.

Give an example of a protein that is produced in the cells of the pancreas cells that is not produced in a skin cell. 

Insulin, which is a protein that regulates blood sugar levels

What tool do scientists use to separate/identify DNA fragments  by size?

Gel electrophoresis

What is the gel for gel electrophoresis made of?

Agarose

What is the overall charge on a molecule of DNA?

The overall charge on a molecule of DNA is negative, primarily due to the presence of negatively charged phosphate groups.

In gel electrophoresis, what pulls the DNA?  What goes faster, a small or large fragment of DNA? Why?

In gel electrophoresis, an electric field pulls negatively charged DNA fragments towards the positive electrode, with smaller fragments moving faster than larger ones

What is the promoter site in an operon?

The promoter site in an operon is the binding site for RNA polymerase, the enzyme that performs transcription.

What attaches to the promoter site that will transcribe the genes?

Both RNA polymerase and transcription factors

What will block the promoter site?

Repressor proteins

What will release a repressor protein from blocking the promoter site?

When an inducer molecule binds to the repressor protein

What is the “on” switch for the lac operon?

The lac operon is turned on when lactose is present and glucose levels are low.

Why do you include a DNA marker (ladder)?

it allows you to estimate the approximate lengths of DNA fragments in your samples.

What is a plasmid?

 a small, circular piece of DNA. They often carry genes that provide the host cell with genetic advantages, such as antibiotic resistance. 

Humans use plasmids as a tool for what?

Humans use plasmids for genetic engineering and transformation

What tool (enzyme from bacteria) do scientists use to cut DNA at specific sites to create sticky ends?

Restriction enzymes

What gene (for a protein) do scientists attach to make a molecule glow red?

Red fluorescent protein (RFP)

How do we control the expression of rfp in our transgenic bacteria? What “turns on” the arabinose operon in pARA-R plasmid?

The expression of rfp in our transgenic bacteria is controlled by the arabinose operon which is turned on when arabinose is present in the pARA-R plasmid.