Biochemistry: Protein Structures and Genetic Code

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Questions and Answers

What is the primary structure of a protein?

Association of multiple polypeptide chains.

The sequence of amino acids. (correct)

The further folding of secondary structures.

The interaction between neighboring amino acids.

Which type of protein structure is characterized by alpha helices and beta pleated sheets?

Tertiary

Primary

Secondary (correct)

Quaternary

What is the result of further folding of secondary structures in a protein?

Secondary structure

Tertiary structure (correct)

Primary structure

Quaternary structure

What is necessary for a protein to possess a quaternary structure?

Two or more polypeptide chains. Signup and view all the answers

What are domains in the context of a protein?

Discrete functional units formed by a group of amino acids. Signup and view all the answers

What primarily determines the secondary and tertiary structures of a protein?

The amino acid sequence. Signup and view all the answers

What is a codon?

A triplet of nucleotides that specifies a single amino acid. Signup and view all the answers

Why is a minimum of three nucleotides necessary to specify a single amino acid?

To ensure there are enough to code for the 20 different amino acids. Signup and view all the answers

What is the fundamental unit of the genetic code?

A sequence of three nucleotides. Signup and view all the answers

What was the initial challenge in determining the genetic code?

Determining the nucleotide sequence of an RNA. Signup and view all the answers

What role does polynucleotide phosphorylase play in the context of the genetic code?

It randomly links RNA nucleotides together without a template. Signup and view all the answers

What are homopolymers in the context of RNA synthesis?

RNA molecules consisting of a single type of nucleotide. Signup and view all the answers

What was the first codon-amino acid relationship identified using synthetic RNAs?

UUU encodes phenylalanine. Signup and view all the answers

What type of RNA was used to find out that UUU encodes phenylalanine?

Homopolymers Signup and view all the answers

Why were different amino acids radioactively labeled in different test tubes when testing poly(U)?

To see which amino acid was incorporated into a protein made from poly(U). Signup and view all the answers

After determining UUU, CCC and AAA, what was the NEXT step to determine more codon-amino acid relationships?

Using random copolymers Signup and view all the answers

How many potential reading frames are present in any given sequence of nucleotides?

Three Signup and view all the answers

What is the primary function of the initiation codon in mRNA?

It specifies the first amino acid in a protein and sets the reading frame. Signup and view all the answers

Which of the following codons typically serves as the initiation codon during translation?

AUG Signup and view all the answers

What is the difference between how AUG is used in bacterial cells versus eukaryotic cells, regarding the start of translation?

In bacteria, AUG encodes N-formylmethionine at the start; in eukaryotes, it encodes unformylated methionine. Signup and view all the answers

Which of the following is NOT a stop codon?

AUG Signup and view all the answers

What is a key feature of termination codons in translation?

They do not encode any amino acids and are not recognized by any tRNA. Signup and view all the answers

What is meant by the term 'universality of the genetic code'?

The genetic code is mostly, but not completely universal, with some exceptions known. Signup and view all the answers

What is the role of tRNA,Met with regards to methionine, in bacterial and/or eukaryotic cells?

They are the tRNAs that carry the methionine for the initiation position. Signup and view all the answers

What was the primary conclusion from Beadle and Tatum's experiments with biochemical pathways?

Mutations affecting a particular biochemical step occur at a single locus that encodes a particular enzyme. Signup and view all the answers

What is the updated name of the hypothesis originally proposed by Beadle and Tatum?

The one gene, one polypeptide hypothesis. Signup and view all the answers

If a mutation, auxotrophic mutation 106, allows growth only with supplements A or C, but not B, and mutation 102 only with C, with mutation 103 able to grow with A, B or C, what is the correct order in the biochemical pathway?

B → A → C Signup and view all the answers

What is the correct relationship between genes and enzymes based on the content?

Each gene encodes a separate enzyme involved in different steps of a pathway. Signup and view all the answers

What are the common components of all amino acids?

A central carbon atom, an amino group, a hydrogen atom, a carboxyl group, and a specific R group. Signup and view all the answers

What primarily determines the unique chemical properties of each amino acid?

The radical (R) group. Signup and view all the answers

What are the primary functions of proteins?

To act as enzymes, provide structural components, and transport substances. Signup and view all the answers

What is the role of enzymes in a cell?

To act as biological catalysts in chemical reactions. Signup and view all the answers

What enzyme is responsible for linking a specific amino acid to its corresponding tRNA?

Aminoacyl-tRNA synthetase Signup and view all the answers

Which part of the tRNA carries the attached amino acid?

3' end Signup and view all the answers

What is the energy source required for the charging of tRNA?

Adenosine triphosphate (ATP) Signup and view all the answers

What is the function of initiation factors in the translation process?

To bind mRNA to ribosome subunits Signup and view all the answers

In bacterial ribosomes, what are the sizes of the two subunits involved in translation?

30S and 50S Signup and view all the answers

What is the first step in the initiation of translation?

mRNA binds to the small ribosomal subunit Signup and view all the answers

Which codon is recognized by the initiator tRNA in the translation initiation phase of bacterial protein synthesis?

Start codon Signup and view all the answers

What is the composition of the reaction that charges tRNA?

Amino acid + tRNA + ATP Signup and view all the answers

What role does rRNA play in the formation of peptide bonds during elongation?

It acts as a catalyst in the process. Signup and view all the answers

Which factor is required for the translocation step in the ribosome during elongation?

Elongation factor G (EF-G) Signup and view all the answers

What happens to the tRNA that occupied the P site after translocation?

It moves to the E site and then into the cytoplasm. Signup and view all the answers

Which site in the ribosome does the initiator tRNA attach to during translation?

P site Signup and view all the answers

What is the primary consequence of the absence of elongation factor P (EF-P) during translation?

Ribosomes stall during translation of polyproline-containing proteins. Signup and view all the answers

How does the ribosome move during translocation?

In the 5→3 direction. Signup and view all the answers

How does peptide-bond formation influence the tRNA in the P site?

It causes the tRNA to release the amino acid. Signup and view all the answers

What pattern summarizes the progress of each tRNA through the ribosome during elongation?

Cytoplasm → A site → P site → E site → cytoplasm Signup and view all the answers

Study Notes

Protein Synthesis

Proteins are essential components in living organisms, acting as enzymes, structural components, or having regulatory or communication functions
Genes encode proteins, and a single gene encodes a single protein

The One Gene, One Enzyme Hypothesis

Beadle and Tatum studied mutations in the bread mold Neurospora to investigate the relationship between genes and proteins
Neurospora is easily cultivated in labs and its main vegetative part is haploid, making it easy to observe recessive mutations
Wild-type Neurospora can grow on a minimal medium (inorganic salts, nitrogen, a碳 source, and biotin). Mutants (auxotrophs) can't grow on minimal medium but grow on a medium containing the substance they cannot synthesize themselves.
Irradiating Neurospora spores creates mutations
Mutations were identified by their inability to grow on a minimal medium
The results led to the conclusion that each step in a biochemical pathway is catalyzed by a different enzyme, which is encoded by a separate gene (one gene, one enzyme hypothesis)

Protein Structure

Proteins are polymers of amino acids
Twenty common amino acids are found in proteins
All amino acids share a similar structure with a central carbon atom, an amino group, a carboxyl group, a hydrogen atom, and an R-group (side chain)
Amino acids are linked together by peptide bonds to form a polypeptide chain

The Genetic Code

DNA base sequences carry genetic information
Determining how base sequences specify amino acid sequences (the genetic code) proved challenging
A codon is a set of three nucleotides that specify a particular amino acid
Three nucleotides per codon provide sufficient combinations to encode all 20 amino acids
Francis Crick and his colleagues confirmed that the genetic code is a triplet code in 1961
A codon consists of three nucleotides

The Genetic Code (continued)

Marshall Nirenberg and Johann Matthaei cracked the code by using synthetic RNAs (homopolymers
Poly(U) RNA produced a protein containing only phenylalanine
Other synthetic RNAs were also used
The genetic code was completely deciphered by 1968
The genetic code is considered to be universal, with a few exceptions, especially in mitochondrial genes
The genetic code is non-overlapping with 61 sense codons to specify 20 amino acids
Stop codons include UAA, UAG, and UGA

Protein Synthesis (continued)

Translation occurs on ribosomes which are responsible for assembling amino acids into proteins
mRNA serves as a template for the translation process

Protein Synthesis in Bacterial and Eukaryotic Systems

Bacterial translation initiation requires the Shine-Dalgarno sequence in the mRNA to allow ribosome binding and the initiator tRNA
Eukaryotic translation initiation involves a series of steps involving the 5' cap of the mRNA, initiation factors, and the initiator tRNA
Polypeptides in a polyribosome grow proportionally longer as translation proceeds

Messenger RNA (mRNA) Surveillance

Cells have evolved several quality control mechanisms for protein synthesis, known collectively as mRNA surveillance, to detect and deal with errors that could create issues during translation

Protein Synthesis Processes

Initiation: Components necessary for synthesis assemble at the ribosome
Elongation: Amino acids are joined one at a time, the polypeptide chain grows
Termination: Protein synthesis stops when the ribosome reaches STOP codons; release factors aid in releasing the polypeptide from the ribosome

Ribosomes

Ribosomes are the site of protein synthesis
Ribosomes consist of two subunits (small and large)
Ribosomes have three sites for tRNA attachment (A, P, and E sites)
tRNA, a molecule that recognizes specific codons and brings the corresponding amino acid to the ribosome, participates in the process

Antibiotics

Many antibiotics target bacterial translation machinery, inhibiting specific steps in the process
The structure of antibiotics is similar to components of tRNA, mRNA, or ribosomes
Antibiotics block essential components of bacterial protein synthesis

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Description

This quiz covers essential concepts in biochemistry, focusing on the structures of proteins and the genetic code. It explores primary, secondary, tertiary, and quaternary structures, along with the significance of codons and RNA synthesis. Test your knowledge on how proteins fold and their genetic encoding!