Exam 1 - Translation & Protein Structure

What are the characteristics of hydrophobic (nonpolar) amino acid R groups? (2 items)

-Made of hydrocarbon chains or unchanged carbon rings -They stabilize through weak Van der Waals forces

What are the characteristics of hydrophilic (polar) R groups?

-Permanent charge separation -Form hydrogen bonds with each other or with H20 molecules

What are the 4 types of structure in a protein?

-Primary -Secondary -Tertiary -Quaternary

What happens at each step of translation regarding the ribosome and tRNA? (2 items)

-The ribosome binds to a tRNA (with an anticodon) that can base pair with a codon -The AA on the tRNA is attached to the growing transcript

What makes up the tertiary structure of a protein?

-whether or not the R groups are hydrophilic or hydrophobic interactions -Different types of bonds between various R groups

What are the 2 rules for transcription?

1. Complementary nucleic acids strands are antiparallel when they base pair 2. Incoming nucleotides are added to the 3' end only

Altogether, translation is made up of these steps (hint: they share the same names as those of transcription)

1. Initiation 2. Elongation 3. Termination

What makes up the alpha helix? (3 items)

1. Polypeptide backbone 2. The carbonyl and amide groups of each amino acid are stabilized by hydrogen bonds 3. The chem. properties of the R groups determine where the alpha helix is in the folded protein, and how it interacts with other molecules

What makes up the beta helix?

1. The polypeptide folds back and forth on itself, forming a pleated sheet stabilized by H-bonds b/t carbonyl group of one chain and the amide groups in the other 2. Have 4-10 polypeptide chains aligned side-to-side with amide groups in each chain h-bonded to carbonyl group 3. Can be formed by h-bonding b/t polypeptide chains that are parallel

What are the 3 rules of translation?

1. mRNA is read in the 5'-to-3' direction 2. The reading frame is set by the start codon 3. Translation stops just before the stop codon

What makes up the quaternary structure/shape of proteins?

2 or more polypeptide chains with tertiary structures

How many new proteins produced fold quickly once synthesized? (think in percentages)

75% -Proteins that are denatured have hydrophobic groups exposed to macromolecules in the cytoplasm

Translation requires many components, including ribosomes. What are ribosomes?

A structure of RNA and protein that binds with mRNA; is the site of translation

How are amino acids grouped?

According to the chemical properties of the R groups (mainly, if they're hydrophobic or hydrophilic)

Reminder: the _______ determines how a protein folds into a stable 3D figure

Amino acid sequence

What are amino acid residues?

Amino acids incorporated into proteins

This enzyme connects specific amino acids to specific tRNA molecules

Aminoacyl tRNA synthase

The tRNA structure contains 3 bases in the anticodon loop that make up the _______. These 3 bases are the 3 nucleotides that pair with the codon

Anticodon

Why does the tertiary structure determine the protein's function?

Because the 3D shape can serve as either the structural support, membrane channel, enzyme, or signaling molecule

What mechanism helps protect denatured proteins until the proper 3D structure is attained by a protein?

Chaperones

When are proteins made?

During translation

In addition to synthesizing proteins, what does a ribosome do?

Ensures the mRNA coding sequence is read in groups of 3 successive nucleotides, called codons which code for specific amino acids

Most codons specify an AA according to a ______

Genetic code

These 3 amino acids will affect protein structure

Glycine, Proline, Cysteine

Remember: In prokaryotes, translation happens when? In eukaryotes, transcription occurs in the nucleus while translation happens where?

Immediately after mRNA is made; in the cytoplasm

What makes up a protein's secondary structure?

Interactions between stretches of amino acids

Charged R groups can also form ______ bonds with each other or with other molecules.

Ionic

Can the protein coding sequence (amino acid sequence) be translated into a protein if translated in a different reading frame?

No, it must be translated through the proper reading frame

Reminder: amino acids connect with other AAs via _______ to form proteins.

Peptide bonds

A polymer of amino acids connected by peptide bonds is called a ______.

Polypeptide

What determines the primary, secondary, tertiary, and quaternary structure of proteins?

The amino acid sequence

What constitutes a protein's primary structure and why?

The amino acid sequence because it determines how a protein folds

Translation begins at which codon?

The start codon (AUG) -The codon's position in the mRNA establishes the reading frame

The actual translation of each codon is carried out by ______ while the ribosome establishes the correct reading frame

Transfer RNA (tRNA) - because tRNA carries individual amino acids

How do the ribosomes split up the amino acid sequence into groups of 3 nucleotides?

Using the reading frame

When does translation stop?

When the ribosome reaches a stop codon (UAA, UAG, UGA)

R groups of _______ amino acids are usually charged and ______.

acidic; strongly polar -Usually located on the outside surface of the folded molecule

What are the 2 types of the secondary structure?

alpha helix and beta helix

How can proteins be denatured?

changes in salt concentration, changes in pH, or high heat

In general terms, what happens during translation?

mRNA specifies the order that successive nucleotides are added to the transcript