Study Unit 2

Question 1

Introduction to Proteins
What are proteins and their importance in cellular functions?

Answer 1

Proteins are diverse, ubiquitous, and versatile molecules that mediate many reactions and cellular processes essential for cellular function.

Question 2

Amino Acids and Their Components. What are the building blocks of proteins and their components?

Answer 2

Proteins are made up of amino acids. Each amino acid has four components bound to the alpha carbon: a carboxyl group, an amino group, a hydrogen, and a unique R group.

Question 3

Role of the R Group, How does the R group affect a protein?

Answer 3

The chemical properties of each amino acid’s R group affect how the protein folds and its three-dimensional shape, ultimately governing the protein’s function.

Question 4

Histone Protein Evolution. Why are histone proteins among the most slowly evolving proteins?

Answer 4

Histone proteins, such as histone H4, evolve slowly because their function requires binding to negatively charged phosphate groups in DNA, necessitating richness in basic amino acids like lysine and arginine.

Question 5

Peptide Bonds and Polypeptides. What are peptide bonds and how are they formed?

Answer 5

Peptide bonds are covalent bonds that join two amino acids through a dehydration synthesis reaction, removing a molecule of water. These bonds are shorter than other single bonds, limiting rotation.

Question 6

Protein Structure Levels. What are the four levels of protein structure?

Answer 6

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Question 7

Protein Structure Levels
Primary structure:

Answer 7

sequence of amino acids.

Question 8

Protein Structure Levels
Secondary structure:

Answer 8

local folding patterns (alpha-helices and beta-sheets).

Question 9

Protein Structure Levels
Tertiary structure:

Answer 9

overall three-dimensional shape.

Question 10

Protein Structure Levels
Quaternary structure:

Answer 10

Arrangement of multiple polypeptide chains.

Question 11

The Central Dogma
What is the central dogma of molecular biology?

Answer 11

The central dogma describes the flow of genetic information from DNA to RNA to protein.

Question 12

Components for Translation
What components are involved in translation?

Answer 12

Ribosomes (made of proteins and rRNAs), mRNA, tRNA, aminoacyl-tRNA synthetases, and various initiation, elongation, and release factors.

Question 13

Ribosome Structure and Function
Describe the structure and function of ribosomes in translation.

Answer 13

Ribosomes consist of large and small subunits that bind mRNA and move along it from 5′ to 3′, reading codons to incorporate the appropriate amino acids into the growing polypeptide chain.

Question 14

The Reading Frame for Codons
How is the reading frame established during translation?

Answer 14

Translation begins with a start codon (AUG), and the reading frame is nonoverlapping, with each codon directing the addition of one amino acid.

Question 15

Ribosome Functional Sites
What are the three functional sites of the ribosome?

Answer 15

A site: accepts aminoacyl-tRNA.
P site: site of peptide bond formation.
E site: exit site for tRNA.

Question 16

Role of tRNA in Translation
What is the role of tRNA in translation?

Answer 16

tRNA molecules base pair within the RNA, forming their structure, and have an anticodon that base pairs with the codon on the mRNA. The appropriate amino acid is added to the tRNA’s 3′ hydroxyl site.

Question 17

Codon–Anticodon Interactions
How do codon–anticodon interactions occur?

Answer 17

The anticodon of tRNA base pairs with the codon on the mRNA in an antiparallel fashion, ensuring correct amino acid incorporation.

Question 18

The Standard Genetic Code
What is the standard genetic code?

Answer 18

The genetic code is redundant, with multiple codons specifying some amino acids. Codons are read 5′‒3′ on the mRNA.

Question 19

Process of Translation
What are the three stages of translation?

Answer 19

Initiation: formation of the initiation complex.
Elongation: addition of amino acids to the growing polypeptide chain.
Termination: release of the polypeptide when a stop codon is encountered.

Question 20

Initiation in Eukaryotes
How does initiation occur in eukaryotic translation?

Answer 20

The initiation complex forms at the 5′ cap of the mRNA, with the small ribosomal subunit and initiation factors scanning for the start codon. The large subunit then binds to begin translation.

Question 21

Elongation: Peptide Bond Formation
Describe the elongation process during translation.

Answer 21

A new tRNA enters the A site, the amino acid in the P site transfers to the A site tRNA, and the ribosome catalyzes peptide bond formation.

Question 22

Termination of Translation What happens during the termination of translation?

Answer 22

When a stop codon is encountered, a release factor enters the A site, releasing the polypeptide from the tRNA in the P site, and the ribosome disassociates.

Question 23

19. Initiation in Prokaryotes
    How does initiation differ in prokaryotic translation?

Answer 23

The initiation complex can form at multiple internal sequences where a Shine–Dalgarno sequence is found. Elongation and termination are similar to those in eukaryotes.

Question 24

Protein Synthesis Regulation
How is protein synthesis regulated in cells?

Answer 24

Not all genes are expressed all the time. There are multiple levels of regulation in the cell to control protein synthesis.

Question 25

Protein Sorting and Transport
How are proteins sorted and transported within the cell?

Answer 25

Translation begins in the cytosol. Proteins with specific amino-terminal signal sequences are transported to the ER. Proteins produced by ribosomes on the RER can end up within the endomembrane system or be secreted out of the cell.

Question 26

22. Evolution of Proteins
    How do proteins evolve?

Answer 26

Proteins evolve through mutations in DNA coding sequences. These mutations can have positive, negative, or neutral effects, with beneficial mutations retained through natural selection.

Question 27

Visual Synthesis of Gene Expression
Summarize the visual synthesis of gene expression.

Answer 27

Nucleotides are the letters of the genetic alphabet, codons are the words in the genetic dictionary, and codons specify which amino acids are added to a polypeptide. Ribosomes translate the language of nucleic acids into the language of proteins.