From DNA to Protein

What degrades

What eventually degrades mRNA in the cytosol

ribonucleases (RNases)

How is the degradation of mRNA differ from bacteria to eukaryotes

In bacteria, mRNA is rapidly degraded by ribonucleases. In contrast, eukaryotic mRNA undergoes a more complex degradation process that is determined in the untranslated region

what is the untranslated region in mRNA

The untranslated region is often between 3’ end of the coding sequence and the poly-A tail, and it controls the lifespan of the mRNA

how does the lifespan of mRNA help the cell

The lifespan of mRNA helps the cell by regulating protein synthesis; longer-lived mRNAs can produce more protein (Ex: beta-globin), while shorter-lived mRNAs allow for quicker responses to environmental changes.

An RNA chain is synthesized in which direction?

5’ to 3’ only

In eukaryotes, which parts of a gene are transcribed into RNA

introns and exons

The set of rules by which the nucleotide sequence of a gene is translated into the amino acid sequence of a protein is known as the ________

genetic code

how many combinations are possible for amino acids vs. the ones that are commonly found

There are 64 possible combinations for three nucleotides, but only 20 amino acids are commonly found in proteins.

each group of three consecutive nucleotides in RNA is called a

codon

where have differences been found from the basic genetic code

Occurs in mitochondrial mRNA in some fungi and protozoa because it has its own protein synthesis machinery apart from the rest of the cell.

on tRNA, where is the amino acid matching the codon covalently attached

the 3' end of the tRNA

what are the two unpaired nucleotides situated at either end of the L-shaped tRNA model

the anticodon and the amino acid attachment site

anticodon

a sequence of three nucleotides in tRNA that base pairs with the complementary codon in mRNA during translation

why is the fact that a single amino acid may be specified by several different codons in the genetic code relevant

Redundancy in the genetic code refers to the phenomenon where multiple codons can code for the same amino acid. This characteristic provides a buffer against mutations, as wobble base pairing with tRNA allows for some variation in the third position of the codon without affecting the protein sequence.

how does the number of tRNA differ in humans

humans have about 500 different kinds of tRNA molecules but includes only 48 different anticodons

aminoacyl—tRNA synthetases

Enzymes attach amino acids to their corresponding tRNA molecules in a process called charging, ensuring proper translation during protein synthesis. Each enzyme is specific to one amino acid, makes multiple contacts with its tRNA molecule, and uses ATP to connect it.

where does rRNA attach on mRNA

near the 5’ end, protein is synthesized 5’ to 3’

what do the large and small subunits of rRNA do

The large subunit catalyzes peptide bond formation, while the small subunit is responsible for decoding the mRNA sequence during translation.

how fast is bacterial rRNA to eukaryotic rRNA

Bacterial rRNA is generally synthesized and processed faster than eukaryotic rRNA, adding 20 amino acids per second

what are the three binding sites for tRNAs on rRNA

The three binding sites on rRNA are the A site where the tRNa attaches, P site that holds the growing polypeptide chain, and E site where tRNA exits the ribosome after attaching an amino acid

what is a ribosome made of

Ribosomes are made of 2/3 ribosomal RNA (rRNA) and 1/3 ribosomal proteins

Structure of rRNA

rRNA is folded compactly to form the core of the ribosome, while the ribosomal proteins are generally located on the surface, where they fill in the gaps of the folded RNA

what are ribosomal proteins purpose in ribosomes

Help fold and stabilize the RNA core, while permitting the changes in rRNA conformation to facilitate translation and ribosome function.

23S rRNA

This rRNA acts as an enzyme that links amino acids together, since ribosomal proteins are too far away. It acts as a tiny pocket that grabs the growing polypeptide chain and the next amino acid and holds them in exactly the right position so that they can bond together easily.

What does 23S rRNA also referred to as a peptidyl transferase suggest about the origin of catalysts?

It suggests that RNA may have once played a critical role as a catalyst in biochemical reactions, potentially being the first type of molecule to support life before proteins.

How does translation start with eukaryotic cells

1. AUG codon codes for the amino acid methionine via the initiator tRNA. This initiator tRNA and translation initiation factors are loaded directly onto the P site of the small ribosomal subunit, which no other tRNA can do

2. Translation starts when it recognizes an AUG codon while reading mRNA

How does translation for bacteria differ than eukaryotic cells

1. Bacterial mRNA only has a triphosphate at its 5’ end, with no 5’ cap to tell the ribosome where to begin searching for the start of translation, and instead uses a nucleotide-binding sequence upstream of AUG

2. Unlike a eukaryotic ribosome, a bacterial ribosome can readily bind directly to a start codon that lies in the interior of the RNA as long as it is preceded by a ribosome binding site by several nucleotides

3. Bacterial mRNA is usually polycistronic, meaning that it encodes multiple proteins on the same molecule; these contain a separate ribosome binding site for each protein sequence (operons)

What are the stop codons

UAA, UAG, and UGA—nonsense codons that signal the termination of protein synthesis

How do stop codons signal the end of protein synthesis

Stop codons are recognized by the A site in rRNA, and proteins called release factors bind to them, leading it to catalyze the addition of a water molecule instead of an amino acid, causing the polypeptide chain to be released from the ribosome.

what are polyribosomes or polysomes

Polyribosomes, or polysomes, are clusters of ribosomes located in the cytosol that simultaneously translate the same mRNA molecule, allowing for the rapid synthesis of multiple copies of a protein.

differences in bacterial and eukaryotic ribosomes is exploited by

antibiotics to selectively target bacterial infections while minimizing damage to eukaryotic cells.

protease

Proteases are enzymes that catalyze the breakdown of proteins by hydrolyzing peptide bonds, playing a crucial role in protein degradation and processing the process of this is called proteolysis

why are proteolysis pathways important

it is essential to quickly get rid of proteins that are only needed for a short time and to remove proteins that are damaged or built incorrectly, all proteins undergo this at some point, and the amino acids released in this process are recycled to build new proteins.

proteosomes function

Cylindrical protein complexes with binding sites found in the eukaryotic cells’ cytosol and nucleus that use ATP hydrolysis to unfold the protein and thread it into a cylinder lined with proteases, which break down the targeted proteins into short peptides.

ubiquitin

Ubiquitin is a small protein that tags other proteins for degradation by the proteasome, marking them for the proteolysis.

chaperone proteins

Chaperone proteins are crucial for assisting in the proper folding of other proteins, preventing aggregation, and helping to refold misfolded proteins. They play a vital role in maintaining cellular protein homeostasis.

how many different aminoacyl-tRNA synthetases do most organisms have

one for each amino acid, 20