Chapter 4: Translation and Protein Structure

Which statements about the simulation are TRUE? Select all that apply.

By changing zero, one, or two bases from each of the labeled codons, it is possible to create a tetrapeptide (four amino acids) of all methionines. Changing the guanine in the sixth codon of the original sequence to an adenine will not change the outcome of the simulation.

Imagine you are following a particular tRNA, called tRNAQ, through the process of translation in a eukaryote. In what order does tRNAQ go through the steps listed? Note that some steps may be used more than once.1. The polypeptide is transferred to tRNAQ.2. tRNAQ binds the A site of the ribosome.3. tRNAQ binds the P site of the ribosome.4. The ribosome shifts, with tRNAQ still bound.5. tRNAQ binds the E site of the ribosome.

2, 1, 4, 3, 4, 5

Which tRNA anticodon sequence is the correct match to the mRNA codon listed below? Note: codon-anticodon base-pairing is antiparallel. 5'-CGA-3'

3'-GCU-5' The tRNA anticodon always binds antiparallel to the mRNA codon. The 5'end of the tRNA anticodon is therefore complementary to the 3'end of the mRNA codon. Since the answer choices for the mRNA codon sequence are written 3'to 5', start with the 5'end of the tRNA anticodon and determine the complementary base of the mRNA codon written from the 3'end. Also, since we are looking for the mRNA codon sequence, it will include uracils and not thymines. This is why 3'-GCU-5' is correct and 3'-GCT-5' is incorrect.

For the numbered steps below, select the option that places them in the correct order.1) The ribosome binds to the mRNA and uses tRNAs to translate mRNA into the corresponding amino acid polypeptide sequence.2) The spliceosome removes introns.3) The primary structure of the polypeptide chain undergoes hierarchical foldings to form the tertiary structure.4) RNA polymerase binds to the promoter region of a gene and initiates transcription.

4 > 2 > 1 > 3

pH of a cell

7.35 - 7.45

20 common amino acids

9 essential 11 non-essential polar = hydrophilic

side chain (R group)

A chemical group attached to the central carbon atom of an amino acid, whose structure and composition determine the identity of the amino acid; also known as an R group.

Codon

A group of three adjacent nucleotides in RNA that specifies an amino acid in a protein or that terminates polypeptide synthesis.

Polypeptide

A polymer of amino acids connected by peptide bonds protein; residues: In the context of protein synthesis, any of the amino acids that is incorporated into a protein.

Enzymatic catalysis of the peptide bond between the growing polypeptide and the next incoming amino acid takes place in which binding site?

A site

3 binding sites of ribosomes

A site, P site, E site

amino group

NH2 ; a nitrogen atom bonded to two hydrogen atoms. An amino group is present covalently linked to the central carbon atom of an amino acid.

aminoacyl tRNA synthetases

An enzyme that attaches a specific amino acid to a specific tRNA molecule. - Responsible for actually translating the codon sequence in a nucleic acid to a specific amino acid in a polypeptide chain. - One aminoacyl tRNA synthetase for each amino acid; binds to multiple sites - catalyzes info of covalent bond between tRNA and amino acid

Successive amino acids in proteins are connected by peptide bonds.

Bond formed between two amino acids A covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group of another amino acid.

carbonyl group

C=O greater electronegativity of the O

carboxyl group

COOH; a carbon atom with a double bond to oxygen and a single bond to a hydroxyl group.

amino acid structure

Consists of a central carbon atom, called the α (alpha) carbon, connected by covalent bonds to four different chemical groups: an amino group (—NH2, shown in dark blue), a carboxyl group (—COOH, shown in brown), a hydrogen atom (—H, shown in light blue), and a variable side chain or R group (shown in green). - Tetrahedron - 4 covalent bonds equal angles - Amino group gains a proton; carboxyl group loses a proton - R-group differs by amino acid;amino acds differ by chemical/physical properties

In which ribosome site would you find the uncharged tRNA?

E site

reading frames

Following a start codon, a consecutive sequence of codons for amino acids. The different ways of parsing the string into three-letter words Ribosome establishes the correct reading frame for the codons, the actual translation of each codon in the mRNA into one amino acid in the polypeptide is carried out by means of transfer RNA (tRNA).

What are the three major groups of amino acids as categorized by the properties of their R groups? How do the chemical properties of each group affect protein shape?

Hydrophobic: nonpolar side chains, usually located in the interior of folded proteins, forms bonds with other hydrophobic amino acids or solvents. Hydrophilic: polar side chains, usually found on the outside surface of folded proteins, form bonds with other hydrophilic amino acids or water, also includes basic amino acids with side chains that are positively charged at pH and negatively charged pH. "Special": allow for more or less flexibility around side chains (cysteine).

amide group

N-H

Which components make up the ribosome? Select all that apply.

Protein and RNA

Glycine

R group is hydrogen not asymmetric nonpolar small enough to tuck into spaces where other R groups would not fit

Proline

R group is linked back to the amino group. This linkage creates a kink or bend in the polypeptide chain and restricts rotation of the C—N bond imposing constraints on protein folding in its vicinity

tRNA genes are transcribed by

RNA polymerase

Cysteine

SH group When two cysteine side chains in the same or different polypeptides come into proximity, they can react to form an S—S disulfide bond, which covalently joins the side chains.

Messenger RNA

The RNA molecule that combines with a ribosome to direct protein synthesis; it carries the genetic "message" from the DNA to the ribosome.

Draw one of the 20 amino acids and label the amino group, the carboxyl group, the R group (side chain), and the α carbon.

The carboxyl and the a-carbon the same for all amino acids. The amino group is the same for almost all the amino acids, with proline being the exception. The variety of functions and forms among the amino acids is mainly due to their different side chains (R groups).

amino end

The end of a polypeptide chain that has a free amino group. NH+3

carboxyl end

The end of a polypeptide chain that has a free carboxyl group COO−

What ultimately determines the three-dimensional shape of a protein?

The order of amino acids in the polypeptide chain determines the way in which proteins fold because of various interactions and bonds formed between the amino acids. These interactions can give rise to specific secondary and tertiary structures.

tertiary structure

The overall three-dimensional shape of a protein, formed by interactions between several secondary structures. Result from interactions between amino acid side chains, largely R groups serve as structural support, membrane channel, enzyme, or signaling molecule

Which of the statements is true regarding a basic amino acid?

The positively charged R group of a basic amino acid could bind DNA.

A mutation leads to a change in one amino acid in a protein. The result is that the protein no longer functions properly. How is this possible?

The sequence determines how the protein folds and can disrupt its function. The hydrophobic R groups of two amino acids must aggregate for proper structure and function, then a mutation that changes a hydrophobic amino acid to an acidic or basic will prevent this aggregation and disrupt structure and function. If proper folding requires interaction between T groups of basic or acidic amino acids then changing either one to hydrophobic means proper folding won't take place.

Anticodon

The sequence of three nucleotides in a tRNA molecule that base pairs with the corresponding codon in an mRNA molecule.

secondary structures

The structure formed by interactions between stretches of amino acids in a protein. result from hydrogen bonding in the polypeptide backbone; Hydrogen bonds can form between the carbonyl group in one peptide bond and the amide group in another, thus allowing localized regions of the polypeptide chain to fold 2 types: α (alpha) helix, β (beta) sheet

quaternary structure

The structure that results from the interactions of several polypeptide chains/subunits; various tertiary structures subunits can be different or identical

denatured protein

The unfolding of proteins by chemical treatment or high temperature; the separation of paired, complementary strands of nucleic acid.

Amino Acids that affect protein structure

glycine, proline, and cysteine

anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

Which of the following is the actual event that translates the language of nucleic acids (the sequence of bases, A, T (U), C, and G) to the language of proteins (determining which amino acid will be added to the polypeptide)?

attachment of the appropriate amino acid to the tRNA by aminoacyl tRNA synthetase

amino acids

building blocks of proteins

Proteins that do not refold properly after being heated generally require the assistance of which type of molecules in cells?

chaperones

The bond that forms between amino acids:

connects amino groups and carboxyl groups of adjacent amino acids.

How is the amino acid held on the charged tRNA?

covalent bond

The correspondence between codons and amino acids, in which 20 amino acids are specified by 64 codons

genetic code AUG is beginning code

Amino acids with polar R groups

have a permanent charge separation, in which one end of the R group is slightly more negatively charged than the other Basic & acidic amino acids = charged/strongly polar Basic gain proton Acidic lose proton; negatively charged

Chaperones are proteins that

help other proteins fold properly; help protect slow-folding or denatured proteins until they can attain their proper three-dimensional structure A protein that helps shield a slow-folding protein until it can attain its proper three-dimensional structure.

Which process is carried out by the spliceosome?

intron removal

Where is transcription located? Where is translation located?

nucleus Cytoplasm

protein structures (amino acids)

primary, secondary, tertiary, quaternary

Which enzyme is made up of both RNA and protein?

ribosome

The sequence of amino acids dictates protein folding, which determines function.

sequence is called a protein

protein roles

structural, mechanical, cell signaling, immune responses, cell adhesion, cell cycle hen fully folded, some proteins contain pockets with positively or negatively charged side chains at just the right positions to trap small molecules; others have surfaces that can bind another protein or a sequence of nucleotides in DNA or RNA; some form rigid rods for structural support; and still others keep their hydrophobic side chains away from water molecules by inserting into the cell membrane.

The fully folded structure of a functional protein composed of a single polypeptide chain is referred to as:

tertiary

When a peptide bond is created between two amino acids:

the carboxyl group of the first amino acid is joined to the amino group of the second.

only the primary structure (amino acid sequence) is encoded by a protein-coding gene

true

Which base is not found in DNA?

uracil

α (alpha) helix, β (beta) structure

α (alpha) helix: 3.6 amino acids per turn; polypeptide is twisted tightly in right-handed coil; stabilized by hydrogen bonds that form between each amino acid's carbonyl group (C=O) and the amide group (N—H) four residues ahead in the sequence; R groups project outward β (beta): 4 to 10 polypeptide chains side by side; polypeptide folds back and forth on itself, forming a pleated sheet that is stabilized by hydrogen bonds between carbonyl groups in one chain and amide groups in the other chain across the way; R groups project alternately above and below the plane of the β sheet; amide groups hydrogen bonded to carbonyl groups; chains antiparallel