Biology: Protein Synthesis Fundamentals

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Questions and Answers

Which method is used to determine the structural information of proteins?

Electrophoresis

Mass Spectrometry

X–ray Crystallography (correct)

Fluorescence Microscopy

What does a PDB ID represent?

A unique identification number for PDB entries (correct)

A classification code for molecular structures

A version control number for protein databases

A numerical identifier for protein interactions

Which tool is specifically designed for real-time visualization of molecular structures?

Chem3D

RasMol

PyMOL (correct)

Scaffolds

What type of data can be found in a PDB file?

Molecule name, secondary structure, and atomic coordinates Signup and view all the answers

Which database focuses specifically on the evolutionary classification of protein structures?

CATH Signup and view all the answers

Which type of protein is typically round and associated with metabolic functions?

Globular proteins Signup and view all the answers

What is the main function of fibrous proteins?

Stabilization of cellular structures Signup and view all the answers

Which protein function is primarily associated with hemoglobin?

Transport protein Signup and view all the answers

Which statement accurately describes enzymes?

They increase reaction rates significantly. Signup and view all the answers

What structural characteristic differentiates globular proteins from fibrous proteins?

Fibrous proteins have a long and narrow shape. Signup and view all the answers

Which type of protein acts as a biochemical catalyst in reactions?

Enzymes Signup and view all the answers

What role do antibodies play in the body?

They protect against pathogens. Signup and view all the answers

Which subunit arrangement characterizes quaternary protein structures?

Multiple polypeptide subunits Signup and view all the answers

Which type of protein is primarily involved in muscle contraction?

Myosin Signup and view all the answers

Which protein is responsible for iron storage in a non-toxic form?

Ferritin Signup and view all the answers

What is the primary structure of a protein composed of?

Peptide bonds linking amino acids Signup and view all the answers

Which of the following correctly identifies simple proteins?

Proteins yielding only amino acids upon hydrolysis Signup and view all the answers

What type of structure is characterized by a coiled strand and hydrogen bonds forming between certain amino acids?

Secondary Structure Signup and view all the answers

Which interactions are primarily responsible for forming the tertiary structure of a protein?

Hydrophobic interactions and electrostatic interactions Signup and view all the answers

What defines conjugated proteins?

Proteins combined with a non-protein moiety Signup and view all the answers

What is the role of derived proteins?

They are degradation products of simple and conjugated proteins. Signup and view all the answers

Which of the following statements is true regarding the quaternary structure of proteins?

It involves the interaction of multiple subunits. Signup and view all the answers

Which type of proteins includes examples like keratin and collagen?

Fibrous Proteins Signup and view all the answers

What is the most common type of secondary structure in proteins?

Alpha Helix Signup and view all the answers

Which end of a polypeptide chain is referred to as the N-terminus?

The end with a free amino group Signup and view all the answers

What type of beta-pleated sheet occurs when beta-strands run in the same direction?

Parallel Beta-sheet Signup and view all the answers

What classification of diseases involves changes in the secondary structure of proteins, specifically misfolding into beta sheets?

Spongiform Encephalopathy and Amyloidosis Signup and view all the answers

What is the main purpose of the Protein Data Bank (PDB)?

To serve as an international repository for protein structure data Signup and view all the answers

Which structural database contains information specifically about nucleic acids?

NDB Signup and view all the answers

What can extreme conditions cause proteins to undergo?

Denaturation Signup and view all the answers

Which characteristic is true for beta strands in antiparallel beta-pleated sheets?

They run in opposing directions Signup and view all the answers

Where was the Protein Data Bank (PDB) initially established?

Brookhaven National Laboratory Signup and view all the answers

What role do proteins play in energy storage compared to adipose tissue?

They are second only to adipose tissue Signup and view all the answers

What is the primary role of messenger RNA (mRNA) in protein synthesis?

To carry genetic information from DNA to the ribosome Signup and view all the answers

What is the function of transfer RNA (tRNA) during protein synthesis?

To deliver amino acids to the ribosome for protein synthesis Signup and view all the answers

Which of the following statements correctly describes ribosomes in the context of protein synthesis?

Ribosomes translate the mRNA sequence into a polypeptide chain Signup and view all the answers

What signifies the termination of protein synthesis?

The ribosome encounters a stop codon on the mRNA Signup and view all the answers

During the initiation process of protein synthesis, what happens first?

The ribosome assembles around the start codon on the mRNA Signup and view all the answers

What is the significance of codons during protein synthesis?

Codons determine the sequence of amino acids in proteins Signup and view all the answers

Which macromolecule directly decodes the message carried by mRNA?

Transfer RNA (tRNA) Signup and view all the answers

In eukaryotic cells, what must occur to mRNA before it can be translated?

It must receive a poly-A tail and guanine cap Signup and view all the answers

How many different amino acids are there that can be linked together during protein synthesis?

20 Signup and view all the answers

Which molecule is primarily responsible for linking amino acids together during protein synthesis?

Peptide bonds Signup and view all the answers

Study Notes

Protein Synthesis

Protein synthesis is the process of producing polypeptide chains (proteins).
It occurs in two phases: transcription and translation.
In eukaryotes, mRNA must be processed before it leaves the nucleus.

Three Types of RNA

Messenger RNA (mRNA) carries genetic information to ribosomes, acting as a blueprint for protein construction.
Ribosomal RNA (rRNA), along with protein, forms ribosomes, the sites where protein synthesis occurs.
Transfer RNA (tRNA) transports amino acids to ribosomes for protein synthesis; it acts like a "truck" delivering the correct amino acid.

Genes & Proteins

Proteins are made of amino acids linked by peptide bonds.
There are 20 different amino acids.
Amino acid chains are called polypeptides.
Segments of DNA that code for amino acid sequences are called genes.
DNA contains a triplet code.
Every three bases on DNA represent one amino acid.
Each three-letter unit on mRNA is called a codon.
Most amino acids have more than one codon.
The genetic code is nearly universal.

Overview of Transcription

During transcription, a segment of DNA unwinds and unzips.
DNA serves as a template for mRNA formation.
RNA polymerase joins RNA nucleotides to create mRNA codons that are complementary to the DNA triplet code in a complementary manner.
mRNA is created using only one DNA strand as a template.
Transcription begins at a promoter DNA region (e.g., TATA box).
Transcription ends at a terminator region.
Pre-mRNA is released after transcription is complete.

RNA Polymerase

An enzyme located in the nucleus, RNA Polymerase separates the two DNA strands and links RNA nucleotides together.

Processing Pre-mRNA

Occurs in the nucleus.
Pre-mRNA comprises introns and exons.
Introns do not code for proteins, whereas exons do.
Introns are spliced out by spliceosome enzymes.
Exons are rejoined to create mature mRNA.
The mature mRNA leaves the nucleus and enters the cytoplasm.

Messenger RNA (mRNA)

Carries the information to synthesize a specific protein.
Typically 500 to 1000 nucleotides long.
A sequence of 3 bases forms a codon.
AUG is the start codon, and UAA, UAG, and UGA are stop codons.

Transfer RNA (tRNA)

75 to 80 nucleotides long.
Picks up the appropriate amino acid from the cytoplasm.
Transports amino acids to mRNA on ribosomes.
Contains anticodons that are complementary to mRNA codons.
Bonds to mRNA through hydrogen bonds using appropriate codons.
Four ATP's are required for each amino acid added to the polypeptide chain : Two to "charge" the tRNA, one to carry the charged tRNA to the ribosome and one to move the ribosome to the next codon.

Ribosomal RNA (rRNA)

100 to 3000 nucleotides long.
Found inside the cell nucleus.
Forms ribosomes with proteins.

Ribosomes

Composed of large and small subunits.
Consist of rRNA and proteins.
Two sites, P and A, are involved in protein synthesis
Ribonucleoproteins

Peptide Synthesis

Incoming tRNA carries the amino acid bound to it into the ribosome A site.
Formation of peptide bond between the two amino acids.
Empty tRNA exits from the P site.
Ribosome moves over one codon.

Translation

Synthesis of proteins in the cytoplasm.
Involves mRNA, tRNA, ribosomes, and amino acids.
Three steps: initiation, elongation, and termination.
Initiation starts with the start codon AUG.
Elongation involves linking amino acids.
Termination occurs with the stop codon (UAG, UAA, or UGA).

mRNA Codons Join the Ribosome

mRNA codons align with ribosome sites (P and A sites).

Initiation

First tRNA binds to the start codon in the P site.
Second tRNA binds to the next codon in the A site.
Peptide bond forms between the two amino acids.

Elongation

Peptide bond forms between amino acids in the A and P site.
Ribosome moves over one codon.
Empty tRNA leaves the P site.

Ribosomes move over one codon

The ribosome moves over one codon, shifting the next codon into the A site. The first empty tRNA leaves.

Termination

Stop codon (UAG, UAA, or UGA) enters the A site.
Release factor binds to the stop codon.
The polypeptide chain is released.
Ribosome subunits detach.

End Product - The Protein

The end product of protein synthesis is a primary structure of a protein.
A sequence of amino acids bonded by peptide bonds.

Classification of Proteins

Simple proteins- formed of only amino acids. Hydrolyzed into amino acids.
Further divided into fibrous proteins(Keratin, Elastin, Collagen) and globular proteins (Albumin, Globulin, Glutelin, Histones).
Conjugated proteins- combined with non-protein moiety
Derived proteins- derivatives or degraded products of simple and conjugated proteins. (e.g., proteans, metaproteins, proteoses, peptones, and pepides).)

Structure of a protein

Primary structure- amino acid sequence.
Secondary structure- alpha helix and beta sheet.
Tertiary structure- overall 3D conformation.
Quaternary structure- arrangement of multiple polypeptide chains.

Classes of Protein Structure

Globular proteins- usually round and ball-shaped; involved in metabolic functions (enzymes, antibodies, hemoglobin).
Fibrous proteins- long and narrow; involved in structural functions (collagen, keratin).

Functional Classification of Proteins

Enzymes- biochemical catalysts.
Transport proteins- transport molecules (e.g., hemoglobin).
Storage proteins- store substances (e.g., ferritin).
Mechanical support- stabilize structures (e.g., keratin, collagen).
Movement- involved in muscle contraction (e.g., myosin).
Nerve transmission- involved in nerve signals; receptor for acetylcholine
Hormones- regulatory functions; insulin.
Protection- antibodies protect against harmful agents.
Storage of energy- proteins act as energy stores (amino acids)
Prolonged fasting may make protein essential.

Secondary structure of a protein

Alpha-helix: The most common type. Fingernails and toenails, etc.
Beta sheets: Form the core of globular proteins.
N-terminus: The end with the free amino group.
C-terminus: The end with the free carboxyl group
Parallel: beta-strands run in the same direction
Antiparallel: beta-strands run in opposite directions

Alpha Helix Versus Beta Sheet

Alpha-helix: Right-handed, rod-like structure with hydrogen bonds within the polypeptide chain. R groups are generally outside the helix.
Beta sheet: Sheet-like structure with hydrogen bonds between amino acid residues in different sections of the chain. R groups are directed both inside and outside the sheet.. Can be parallel or antiparallel, based on chain directions

Clinical Implications of Secondary Structure of Proteins

Secondary structure can be altered by mutations or extreme conditions.
Spongiform encephalopathy and amyloidosis are diseases related to misfolding and beta sheet formation of proteins.
Misfolding and beta sheet formation may lead to tissue damage.

Structural Databases

Important in solving molecular biology problems.
Protein Databank (PDB) is the international repository for macromolecular structure data (e.g. amino acid sequences and structures).
Moved to Research Collaboratory for Structural Bioinformatics (RCSB)

NDB: Nucleic Acid Structure Database

Contains information about experimentally determined nucleic acids and assemblies.
Used for searching based on annotations relating to sequence, structure, function, and for downloads, analysis.

PDB- Protein Structure database

Contains information about the 3D structures of proteins.
PDB files hold experimentally determined structures of biological macromolecules.
Structural information is determined by X-ray crystallography or NMR spectroscopy.
PDB structure information offers a broad range of features and search parameters. Includes molecule name, primary and secondary structure, ligand, coordinates, and crystallographic information.

Protein visualizing tools Uses

Display structural information from the PDB in 3D.
Image manipulation for various perspectives.

RasMol/RasTop

A molecular graphics program for visualizing proteins, nucleic acids, and small molecules.
Reads molecule coordinate files and interactively displays the molecule with different color schemes.
Enables different molecule representations (e.g., depth cued wireframes, sticks, space-filling, ball and stick, ribbons, etc.).

Pymol

A molecular graphics system with an embedded Python interpreter.
Designed for real-time visualization and high-quality image and animation generation.
Features for creating movies, measuring bond distances, and reassembly.

Online Visualizer

Allows for interactive viewing of PDB structures.
Uses an online viewer, often associated with NCBI.

Secondary structure prediction algorithm

Ab initio methods: Use single-sequence information.
Homology-based methods: Use multiple-sequence alignment information.

Ab Initio-Based Methods

Measure relative propensity of amino acids to occur in secondary structure elements.
Use known crystal structures to determine propensity scores.
Chou-Fasman and Garnier-Osguthorpe-Robson (GOR) algorithms are examples.

Homology-Based Methods

Combine ab initio prediction and multiple-sequence alignments.
Improve prediction accuracy by 10%.
PHD is an example.

PHD - neural network algorithm for secondary structure prediction

PHD predicts secondary structure based on hydrogen bonds information from multiple sequence alignments.

How good are the methods?

Accuracy ranges from 50% for single sequence/single residue methods to 71% for multiple sequence methods.

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Description

Explore the intricate processes of protein synthesis through transcription and translation. This quiz delves into the roles of various types of RNA and the relationship between genes and proteins, guiding you through the essential concepts of molecular biology.