Chapter 12.2 Translation Flashcards
What are proteins?
Proteins are the final product of the decoding of instructions carried by mRNA, which were originally encoded in the DNA
Translation: The resulting mRNA is a single-stranded copy of the gene, which next must be translated into a protein molecule. During translation, the mRNA is “read” according to the genetic code, which relates the DNA sequence to the amino acid sequence in proteins. Each group of three bases in mRNA constitutes a codon, and each codon specifies a particular amino acid. The mRNA sequence is thus used as a template to assemble—in order—the chain of amino acids that form a protein
Protein Synthesis: Protein synthesis is accomplished through a process called translation. After DNA is transcribed into a messenger RNA (mRNA) molecule during transcription, the mRNA must be translated to produce a protein. In translation, mRNA along with transfer RNA (tRNA) and ribosomes work together to produce proteins
Describe how amino acids are joined to form a polypeptide and distinguish between a polypeptide and a protein
Amino acids are joined together to form a polypeptide through a process known as peptide bond formation. This occurs when the amino group of one amino acid performs a nucleophilic attack on the electrophilic carbonyl carbon of the carboxyl group of another amino acid. The carboxyl group of the amino acid must first be activated to provide a better leaving group than OH-. The resulting link between the amino acids is an amide link, which biochemists call a peptide bond. This reaction is associated with the release of a water molecule
Now, let’s distinguish between a polypeptide and a protein:
- Polypeptide: A polypeptide is a chain of amino acids linked together by peptide bonds. It’s a long unbranched chain made out of amino acids. Polypeptides are shorter and simpler than proteins and may function as hormones, enzymes, or structural components in the body
- Protein: A protein is a complex molecule made up of one or more polypeptide chains. Therefore, all proteins are polypeptides, but not all polypeptides are proteins. Proteins are more complex and usually larger than polypeptides. They play many critical roles in the body, including catalyzing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another
Explain the four levels of protein structure
- Primary Structure: the unique order in which amino acids are linked together to form a protein. Proteins are constructed from a set of 20 amino acids. The amino acid sequence of a protein is determined by the information found in the cellular genetic code. The order of amino acids in a polypeptide unique and specific to a particular protein. Altering a single amino acid causes a gene mutation, which most often results in a non-functioning protein
- Secondary Structure: the coiling or folding of a polypeptide chain that gives the protein its 3D shape. there are two types of secondary structures observed in proteins. One type is the alpha helix structure, which resembles a coiled spring and is secured by hydrogen bonding in the polypeptide chain. The second type is the beta pleated sheet. This structure appears to be folded or pleated and is held together by hydrogen bonding between polypeptide units of the folded or pleated and is held together by hydrogen bonding between polypeptide units of the folded chain that lie adjacent to one another
- Tertiary Structure: This refers to the comprehensive 3D structure of the polypeptide chain of a protein. there are several types of bonded and forces that hold a protein in its tertiary structure. Hydrophobic interactions greatly contribute to the folding and shaping of a protein
- Quaternary Structure: this level of structure is relevant when a protein consists of more than one polypeptide chain. It refers to the structure formed by several protein molecules (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex
Outline the factors that determine protein shape and function
The shape and function of a protein are determined by several factors:
Amino Acid Sequence: The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration synthesis
Chemical Properties of Amino Acids: The structure of a protein is caused by the chemical properties of its amino acids, which is coded by a DNA sequence (a gene). For example, a strand of amino acids folds on itself, creating a unique shape in the tertiary structure of the protein
Protein Folding: Protein folding is a process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from a random coil
Interactions Among Amino Acids: Interactions among the amino acids within the protein contribute to the protein’s final shape. These interactions can include hydrogen bonds, ionic bonds, and disulfide bridges
Environmental Conditions: Factors such as temperature, pH, and the presence of other molecules can influence the shape and function of a protein
Explain how the genetic code specifies the relationship between the sequence of codons in mRNA and the amino acid sequence of a polypeptide
The genetic code specifies the relationship between the sequence of codons in mRNA and the amino acid sequence of a polypeptide in the following way:
- Codons: Cells decode mRNAs by reading their nucleotides in groups of three, called codons. Each codon specifies a particular amino acid
- Start and Stop Codons: The codon AUG serves as the start codon where translation begins. It also encodes the amino acid methionine. There are also three “stop” codons that mark the end of a protein
- Reading Frame: mRNA codons are read during translation, beginning with a start codon and continuing until a stop codon is reached. mRNA codons are read from 5’ to 3’, and they specify the order of amino acids in a protein from N-terminus (methionine) to C-terminus
- Genetic Code Table: The full set of relationships between codons and amino acids (or stop signals) is called the genetic code. The genetic code table shows that many amino acids are represented by more than one codon
Discuss the redundancy of the genetic code
redundancy/degeneracy refers to when the multiple three-base pair codon combinations can specify the same amino acid. This redundancy is a result of there being more codons (64 possible combinations) than there are amino acids to encode (20 amino acids), leading to some amino acids being encoded by more than one codon
This redundancy in the genetic code has several implications:
- Fault Tolerance: The redundancy of the genetic code makes it more fault-tolerant for point mutations. For example, fourfold degenerate codons can tolerate any point mutation at the third position
Translational Pausing: The redundancy of the genetic code also enables translational pausing. This additional layer of information purposely slows or speeds up the translation-decoding process within the ribosome, helping to prescribe the functional folding of the nascent protein
Protection Against Mutations: The redundancy in the genetic code has the effect of making genes less susceptible to mutation. When a mutation changes a codon so it codes for the wrong amino acid, the proteins made from that gene may lose their function
Describe the structure and function of tRNA
Structure:
- tRNAs are usually short molecules, between 70-90 nucleotides in length
- The two most important parts of a tRNA are its anticodon and the terminal 3’ hydroxyl group, which can form an ester linkage with an amino acid
- The last three bases on the 3’ end of tRNA are always CCA – two cytosines followed by one adenine base
- The anticodon loop, which pairs with mRNA, determines which amino acid is attached to the acceptor stem
Function:
- tRNAs act as temporary carriers of amino acids, bringing the appropriate amino acids to the ribosome based on the messenger RNA (mRNA) nucleotide sequence
- They pair with mRNA in a complementary and antiparallel manner, and each tRNA can base pair with a stretch of three nucleotides on mRNA
- These sets of three nucleotides on the mRNA are called codons and the corresponding sequence on the tRNA is called the anticodon
- On one end of the tRNA, an appropriate amino acid is attached to its 3’ hydroxyl group based on the anticodon and the ribosome catalyzes the formation of a peptide bond between this amino acid and the elongating polypeptide chain
Explain how aminoacyl-tRNA synthetases attach amino acids to tRNAs
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that attach the appropriate amino acid onto its corresponding tRNA. This process is also known as “charging” or “loading” the tRNA with an amino acid. Here’s how it works:
- Amino Acid Activation: The synthetase first binds ATP and the corresponding amino acid (or its precursor) to form an aminoacyl-adenylate, releasing inorganic pyrophosphate (PPi)
- tRNA Binding: The adenylate-aaRS complex then binds the appropriate tRNA molecule’s D arm
- Amino Acid Transfer: The amino acid is transferred from the aa-AMP to either the 2’- or the 3’-OH of the last tRNA nucleotide (A76) at the 3’-end
- Aminoacyl-tRNA Formation: The overall reaction can be summarized as follows: Amino Acid + tRNA + ATP → Aminoacyl-tRNA + AMP + PPi
- Editing Reaction: Some synthetases also mediate an editing reaction to ensure high fidelity of tRNA charging. If the incorrect tRNA is added (i.e., the tRNA is found to be improperly charged), the aminoacyl-tRNA bond is hydrolyzed
Discuss the structure and function of ribosomes
Structure:
- Ribosomes are composed of two subunits – smaller and larger. The smaller subunit is where the mRNA binds and is decoded, and in the larger subunit, the amino acids get added
- Both of the subunits contain both protein and ribonucleic acid components
- Ribosomes can be found floating within the cytoplasm or attached to the endoplasmic reticulum
- Prokaryotes have 70S ribosomes while eukaryotes have 80S ribosomes
Function:
- The primary function of a ribosome in any cell is to produce proteins. Proteins are used in almost all cellular functions; as catalysts they speed the time of reactions, as fibers they provide support, and many proteins function in specific tasks, like contracting muscle cells
- Ribosomes recognize the structure of the mRNA bound to a tRNA, the two subunits of the ribosome can combine to start synthesizing protein from the mRNA strand
- The ribosome acts as a large catalyst, forming peptide bonds between amino acids
- The used tRNA is released back into the cytosol so it can bind to another amino acid
- Eventually, the mRNA will present a codon to the ribosome that means “stop”. Special proteins will detach the string of amino acids from the last tRNA, and the protein will be released
Apply the genetic code by translating a mature, eukaryotic mRNA sequence
5’-AUGGUGCUGAAUAA-3’
This sequence can be translated into a polypeptide using the genetic code. The mRNA is read in groups of three nucleotides, known as codons, from the 5’ end to the 3’ end. Each codon corresponds to a specific amino acid.
Here’s the translation:
AUG: Methionine (Met)
GUG: Valine (Val)
CUG: Leucine (Leu)
AAU: Asparagine (Asn)
AA: Stop
So, the polypeptide sequence would be: Met-Val-Leu-Asn
Please note that the actual mRNA sequences in eukaryotes are usually much longer, and this is a simplified example for illustrative purposes. Also, the ‘Stop’ does not correspond to an amino acid but signals the end of translation. The resulting polypeptide would therefore consist of the four amino acids: Methionine, Valine, Leucine, and Asparagine.
Describe the three stages of translation
- Initiation: The ribosome assembles around the target mRNA. The start codon (usually AUG) is recognized and the first tRNA molecule, carrying the amino acid methionine, attaches to the P site of the ribosome
- Elongation: During this stage, amino acids are brought to the ribosome by tRNAs and linked together to form a growing polypeptide chain. Each tRNA has an anticodon that is complementary to the codon of the mRNA. The ribosome shifts one codon along the mRNA, allowing another tRNA molecule to attach
- Termination: This stage occurs when a stop codon is encountered on the mRNA. The completed polypeptide chain is released, and the ribosome disassembles
Summarize the similarities and differences between the translation in bacteria and eukaryotes
Similarities:
- Both processes occur in the cytoplasm
- Both use mRNA as a template to synthesize proteins
- Both processes involve the use of ribosomes, tRNA, and various other factors
- The basic plan of translation is similar in both, involving initiation, elongation, and termination stages
Differences:
- Timing: In bacteria, translation occurs simultaneously with transcription, while in eukaryotes, these two processes are separated
- mRNA Processing: Bacterial mRNA is generally ready for translation once it’s transcribed. In contrast, eukaryotic mRNA undergoes post-transcriptional modifications like splicing, 5’ capping, and 3’ polyadenylation before it’s ready for translation
- Initiation: Bacteria use a Shine-Dalgarno sequence for ribosome binding, while eukaryotes use a 5’ cap
- First Amino Acid: The first amino acid in the polypeptide chain is formylmethionine in bacteria and methionine in eukaryotes
- Ribosome Size: Bacterial ribosomes are 70S (composed of 50S and 30S subunits), while eukaryotic ribosomes are 80S (composed of 60S and 40S subunits)
Outline the process of eukaryotic alternative splicing and explain how it increases protein diversity
Pre-mRNA Processing: When an RNA transcript is first made in a eukaryotic cell, it is considered a pre-mRNA and must be processed into a messenger RNA (mRNA). This includes the addition of a 5’ cap to the beginning of the RNA, a 3’ poly-A tail to the end, and the removal of “junk” sequences called introns
Splicing: In splicing, some sections of the RNA transcript (introns) are removed, and the remaining sections (exons) are stuck back together
Alternative Splicing: Some genes can be alternatively spliced, leading to the production of different mature mRNA molecules from the same initial transcript. This process allows for the production of multiple proteins (protein isoforms) from a single gene coding
Protein Diversity: Alternative splicing greatly expands the diversity of the proteins that can be made from a single gene. This is important because multicellular organisms make so many different types of cells that compose the diverse tissue types of their body. But each cell only has the same genetic code
α (alpha) carbon
The alpha (α) carbon in an amino acid plays a significant role in protein translation. Here’s how it functions:
Core Structure: Each amino acid has the same core structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and a hydrogen atom
Peptide Bond Formation: A peptide bond is formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid. This reaction is catalyzed by ribosomes and generates one water molecule
Polypeptide Chain Formation: The formation of peptide bonds leads to the creation of a polypeptide chain. Amino acids are covalently strung together by peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000
R Group Attachment: In addition to the amine and the carboxylic acid, the alpha carbon is also attached to a hydrogen and one additional group that can vary in size and length. In the diagram, this group is designated as an R-group. Within living organisms, there are 20 amino acids used as protein building blocks. They differ from one another only at the R-group position
Amino group
Peptide Bond Formation: A peptide bond is formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid. This reaction is catalyzed by ribosomes and generates one water molecule
Polypeptide Chain Formation: The formation of peptide bonds leads to the creation of a polypeptide chain. Amino acids are covalently strung together by peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000
Transfer RNA
tRNA Interaction: In translation, the codons of an mRNA are read in order (from the 5’ end to the 3’ end) by molecules called transfer RNAs, or tRNAs. Each tRNA has an anticodon, a set of three nucleotides that binds to a matching mRNA codon through base pairing. The other end of the tRNA carries the amino acid that’s specified by the codon
Carboxyl group
Peptide Bond Formation: A peptide bond is formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid. This reaction is catalyzed by ribosomes and generates one water molecule
Polypeptide Chain Formation: The formation of peptide bonds leads to the creation of a polypeptide chain. Amino acids are covalently strung together by peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000
Activation: The carboxyl group of amino acids takes part in activation. The enzyme aminoacyl tRNA synthetase catalyzes the reactions. The activation occurs in two steps; the formation of aminoacyl adenylate and the formation of aminoacyl tRNA
In summary, the carboxyl group of an amino acid plays a crucial role in protein translation, contributing to the formation of peptide bonds that link amino acids together in the protein chain
R Group/Side Chain
known as the side chain
The R group determines the identity of the amino acid
During translation, the sequence of codons in the mRNA determines the sequence of amino acids in the protein. Each codon corresponds to a specific amino acid, and by extension, a specific R group
The properties of the R group influence the behavior of the amino acid within the protein structure. For instance, R groups can be nonpolar, polar, or charged, and this can affect how the amino acid interacts with other amino acids in the protein, as well as with the environment
In the tertiary structure of a protein, interactions between R groups contribute significantly. These interactions can include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces
In summary, the R group of an amino acid plays a crucial role in protein translation, influencing the identity of the amino acid, the interactions within the protein structure, and ultimately, the function of the protein
Peptide bond
A peptide bond plays a crucial role in the process of translation, which is the synthesis of proteins from amino acids. Here’s how it functions:
Formation: A peptide bond is formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid. This reaction is catalyzed by ribosomes and generates one water molecule
Polypeptide Chain: The formation of peptide bonds leads to the creation of a polypeptide chain. Amino acids are covalently strung together by peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000
Elongation: During the elongation phase of translation, the nascent polypeptide chain extends by one amino acid residue during each elongation cycle. A peptide bond is formed between the incoming amino acid (carried by a tRNA in the A site) and the growing polypeptide chain (attached to the tRNA in the P site)
Translocation: Once the peptide bond is formed, the mRNA is pulled onward through the ribosome by exactly one codon. This shift allows the first, empty tRNA to drift out via the E (“exit”) site. It also exposes a new codon in the A site, so the whole cycle can repeat
Amino end
The amino end, also known as the N-terminus, is the start of a protein or polypeptide referring to the free amine group (-NH2). During protein synthesis, or translation, the amino end of the protein is the first part that is translated
The process of translation synthesizes a protein from the N-terminus to the C-terminus2. The mRNA is read in order from the 5’ end to the 3’ end, and each codon specifies a particular amino acid. These amino acids are linked together by peptide bonds to form a polypeptide chain
Carboxyl end
In summary, the carboxyl end plays a crucial role in the formation of polypeptides during translation, contributing to the formation of peptide bonds that link amino acids together in the protein chain.
The carboxyl end, also known as the C-terminus, is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus
In the process of protein synthesis, polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid. This reaction is catalyzed by ribosomes and generates one water molecule. A peptide bond links the carboxyl end of one amino acid with the amino end of another, expelling one water molecule
polypeptide
A polypeptide is a long, continuous, and unbranched peptide chain. It’s essentially a protein, with the technical difference being that some large proteins are made up of several polypeptide chains
In the process of translation, a cell reads information from a molecule called a messenger RNA (mRNA) and uses this information to build a polypeptide, or chain of amino acids. The mRNA sequence is decoded to build a polypeptide that extends by one amino acid residue during each elongation cycle. Various elongation factors facilitate this process
protein, residues
In the process of translation, a protein is synthesized from amino acids according to the sequence of codons in the messenger RNA (mRNA). Each amino acid added to the growing polypeptide chain during this process is often referred to as a residue
The term “residue” is used because, during the formation of the peptide bond that links amino acids together in the protein chain, each amino acid loses one water molecule (H2O). Hence, what is left and incorporated into the protein is called a residue
The sequence of residues in a protein, its primary structure, is determined by the sequence of nucleotides in the corresponding gene. This sequence of residues determines how the protein folds into its unique three-dimensional structure, which in turn determines its function
primary structure
The primary structure of a protein refers to the sequence of amino acids that make up the protein. This sequence is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation
Secondary structures
The secondary structure of a protein refers to the local spatial arrangement of the polypeptide backbone. The two most common types of secondary structures are alpha-helices and beta-sheets
In the context of translation, the formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure. These structures are known to fold rapidly because they are stabilized by intramolecular hydrogen bonds
Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. For instance, a secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination
Tertiary structures
The tertiary structure of a protein is the complete three-dimensional structure of the arrangements of atoms found within a single polypeptide chain. This structure is formed as a result of various types of bonding interactions, including hydrogen bonding, disulfide bridges, hydrophobic interactions, and ionic bonding
In the context of translation, the tertiary structure is crucial for the function of the protein. The process of translation synthesizes a linear sequence of amino acids. This linear sequence then folds into a three-dimensional shape, or tertiary structure, which is often necessary for the protein’s function
Quaternary structure
The quaternary structure is the highest level of protein structure and refers to the structure of proteins which are themselves composed of two or more smaller protein chains, also referred to as subunits. This structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits
Alpha helix and Beta sheet
Alpha-helices and beta-sheets are the two most common secondary structure motifs in proteins. They are the first major steps in the folding of a polypeptide chain, and they establish important topological motifs that dictate subsequent tertiary structure and the ultimate function of the protein
Alpha-Helix: The alpha helix is formed when the polypeptide chains twist into a spiral. This allows all amino acids in the chain to form hydrogen bonds with each other. The most common type of secondary structure of a protein is the alpha-helix. In the alpha-helix protein, a hydrogen bond is formed between the N−H group to the C=O group of the amino acid
Beta-Sheet: The beta pleated sheet is polypeptide chains running alongside each other. It is called the pleated sheet because of the wave-like appearance. The second essential type of secondary structure of a protein is the Beta-Pleated Sheets of Protein. It consists of various beta strands linked by hydrogen bonds between adjacent strands
Denatured
When a protein is denatured, there is a change in its three-dimensional structure that renders it incapable of performing its assigned function. This means that a denatured protein cannot do its job
Proteins can denature due to various factors such as changes in temperature, pH, or exposure to certain chemicals. When a protein denatures, it unfolds and becomes almost linear. This change in structure can lead to the loss of biological activity, as the function of a protein is highly dependent on its structure
In the context of translation, if a newly synthesized protein were to become denatured, it would not be able to perform its intended function within the cell. This could have various impacts depending on the specific role of the protein. For example, if an enzyme were denatured, it could disrupt a metabolic pathway within the cell
