Chapter 13: Translation and Proteins Flashcards
Biological polymerization of
amino acids into polypeptide chains.
Translation
This class of molecules adapts specific triplet codons in mRNA to their correct amino acids. (Adaptor hypothesis)
transfer RNA
Three consecutive ribonucleotides complementary to the
codon of the mRNA.
Anticodon
True or False. Electron microcopy reveals that the bacterial ribosome is about 40 nm at its largest dimension and consists of two subunits, one large and one small.
True
Composition of ribosome subunit.
- one or more molecules of RNA
2. ribosomal proteins
When the two subunits are associated with each other in a single ribosome, the structure is sometimes called?
Monosome
Reflection of the density, mass, and shape of ribosome subunits (RNA components and ribosomal proteins).
Svedberg coefficient (S)
Size of prokaryotic monosome.
70S particle (50S large subunit and 30S small subunit)
Size of eukaryotic monosome.
80S (60S large subunit and 40S small subunit)
True or False. Sedimentation coefficients, which reflect the variable rate of migration of different-sized particles and molecules, are additive.
False
Are part of the moderately repetitive DNA fraction and are present in clusters at various chromosomal sites. Part of the DNA that transcribes RNA.
rRNA gene (rDNA)
True or False. In humans, these gene (rDNA)
clusters have been localized near the ends of chromosomes
13, 14, 15, 21, and 22.
True
True or False. In humans, a gene cluster encoding 5S rRNA has been located on chromosome 1.
True
True or False. In pro and eukaryotic organisms, tRNAs are transcribed as larger precursors, which are cleaved into mature 4S tRNA molecules.
True
A number of nucleotides are unique to tRNA. These bases are called?
Modified base
True or False. Modified structures of tRNA are created after transcription of tRNA. (posttranscriptional modification)
True
True or False. The presence of modified bases enhances hydrogen bonding efficiency during translation.
True
This arrangement created a series of paired stems and unpaired loops resembling the shape of a clover-
leaf.
cloverleaf model of tRNA
The end of the tRNA molecule where the
amino acid is covalently joined to the terminal adenosine residue. All tRNA molecules possess this sequence.
CCA-3’
True or False. Shapes of the intervening loops may be recognized by the specific enzymes responsible for adding amino acids to tRNAs.
True
The tRNA molecules must be chemically linked to their respective amino acids. This process of called?
Charging
Charging of amino acid to the tRNA is mediated by what enzyme?
Aminoacyl tRNA synthetases.
True or False. Because of the ability of the third member of a triplet code to “wobble,” it is now thought that there are only 31 different tRNAs.
True
True or False. It is also believed that there are only
20 synthetases, one for each amino acid, regardless of the greater number of corresponding tRNAs.
True
The subset of tRNA molecules that recognize a common amino acid is called?
Isoaccepting tRNAs
True or False. Synthetases are highly specific thus, there are only 20 types of synthetases corresponding to the 20 different amino acids.
True
True or False. Most ribosomes, when they are not involved in translation, are dissociated into their large and small subunits.
True
Upon initiation of translation, these molecules enhance the binding affinity of the various translational components.
Initiation factors (IFs)
In prokaryotes, the initiation codon, AUG calls for the modified amino acid called?
formylmethionine (fmet)
This sequence is composed of six ribonucleotides precedes the initial AUG start codon. This is also where the IF1-small ribosomal small subunit complex bind before translation proceeds.
Shine–Dalgarno sequence
True or False. Shine–Dalgarno sequence contains only pyrimidines.
False.
In the initiation phase, this molecule serves to inhibit the small subunit from associating with the large subunit.
Initiation factor 3 (IF3)
In the initiation phase, this molecule primarily blocks the A site from being bound to a tRNA
Initiation factor 1 (IF1)
In step 2 of the initiation phase of translation, this molecule serves as a GTPase and interacts with the mRNA and the charged tRNA, stabilizing them in the P site.
Initiation factor 2 (IF2)
The aggregate, upon release of IF3, then combines with the large ribosomal subunit forming what molecule in bacteria?
70S initiation complex
The first phase of translation is?
Initiation
The second phase of translation is?
Elongation
In step 1 of elongation, Charged tRNAs are transported into the ribosome complex by one of the elongation factors called?
EF-Tu
True of False. EF-Tu is a GTPase and is bound by a GTP, the hydrolysis of which provides energy for the process.
True
Lengthening of the growing polypeptide chain by one amino acid is called?
Elongation
This molecule is embeded in the large ribosome subunit and is responsible for creating the peptide bonds linking one amino acid to the next as well as the hydrolysis of covalent bond between the preceeding tRNA and its cognate amino acid.
23S rRNA of the ribosome large subunit (an example of ribozyme, an RNA capable o of catalyzing a reaction). This function is formerly thought to be performed by peptidyl transferase.
Third site on the ribosome where uncharged tRNA exits the ribosome large subunit.
E (exit) site
The entire mRNA–tRNA–aa2–aa1 complex then shifts in the direction of the P site by a distance of three nucleotides. This process is called?
Translocation
True or False. The energy produced by the hydrolysis of GTP is utilized to lock the proper structures in place during each step of elongation.
True
True or False. the role of the small subunit during elongation is one of “decoding” the triplets present in mRNA, whereas the role of the large subunit is peptide bond synthesis.
True
Third phase of translation.
Termination
These codons do not specify an amino acid, nor do they call for a tRNA in the A site. They signal the termination of the translation process.
Stop codons, termination codons, nonsense codons
What are the stop codons.
UAG, UAA, UGA
The action of this enzymes is signaled by the termination codon. These enzymes cleave the polypeptide chain from the terminal tRNA, releasing it from the translation complex.
GTP-dependent release factors
As elongation proceeds and the initial portion of mRNA has passed through the ribosome, the mRNA is free to associate with another small subunit to form a second initiation complex. This process results to?
Polyribosomes or polysomes
About one-third of the 16S RNA is responsible for producing a flat projection called?
Platform
Modulates movement of the mRNA–tRNA complex during translocation.
Platform
True or False. The interface between the two subunits, considered to be the location in the ribosome where polymerization of amino acids occurs, is composed almost exclusively of RNA. In contrast, the numerous ribosomal proteins are found mostly on the periphery of the ribosome.
True
Prokaryotic and Eukaryotic rRNA share the same structure called?
Core sequence
The addition of this sequence impart addition function to the core sequence in eukaryotic rRNA.
Expansion sequence
True or False. Transcription and translation are coupled in prokaryotes, in eukaryotes these two processes are separated both spatially and temporally.
True
True or False. In eukaryotic cells, transcription occurs in the nucleus and translation in the cytoplasm.
True
Significance of the temporal and spatial separation of transcription and translation in eukaryotes.
This separation provides multiple opportunities for regulation of genetic expression in eukaryotic cells.
Its presence in eukaryotes is considered to increase the efficiency of translation by interacting with the initiator tRNA.
Kozak sequence
Three key differences between eukaryotic and prokaryotic mRNA.
- 5′-end of mRNA is capped with a 7-methylguanosine (7-mG)
- Many mRNAs contain a purine (A or G) three bases upstream from the AUG initiator codon, which is followed by a G (A/GNN -AUG-G). This sequence is called the Kozak sequence.
- Eukaryotic mRNAs require the posttranscrip-
tional addition of a poly-A tail on their 3′-end (polyadenylated)
Kozak sequence is considered analogous to what sequence found in the upstream region of prokaryotic mRNAs.
Shine–Dalgarno sequence
In the absence of this sequence, mRNA potential messages are rapidly degraded in the cytoplasm.
Poly-A
True or False. In eukaryotes the amino acid formylmethionine is not required as it is in prokaryotes. However, the AUG triplet, which encodes methionine, is essential to the formation of the translational complex, and a unique transfer RNA (tRNA-Met) is used during initiation.
True
Individuals afflicted with this disorder have an important metabolic pathway blocked. As a result, they cannot metabolize the alkapton 2,5- dihydroxyphenylacetic acid, also known as homogentisic acid.
Alkaptonuria
True or False. Parents who are so related have a higher probability than unrelated parents of producing offspring that express recessive traits because such parents are both more likely to be heterozygous for some of the same recessive traits.
True
The confirmation about mutant genes that alter the eye color of fruit flies could be linked to biochemical errors that, in all likelihood, involved the loss of enzyme function led to what hypothesis?
one-gene:one-enzyme hypothesis (later modified into one-gene:one-polypeptide chain hypothesis)
True or False. Nearly all enzymes are proteins, not
all proteins are enzymes.
True
Individuals affected by this disease have erythrocytes that, under low oxygen tension, become elongated and curved because of the polymerization of hemoglobin.
Sickle cell anemia
True or False. Polypeptides and proteins. Both are molecules composed of amino acids. They differ, however, in their state of assembly and functional capacity.
True
This aspect of a protein is essential to the function of the molecule.
3-D conformation
Building blocks of proteins.
Amino acid (there are 20 of these)
True or False. When released from the ribosome following translation, a polypeptide folds up and assumes a higher order of structure. When this occurs, a three-dimensional conformation emerges. In many cases, several polypeptides interact to produce this conformation. When the final conformation is achieved, the molecule is now fully functional and is appropriately called a protein.
True
Gross structure of an amino acid.
Each amino acid has:
- a carboxyl group
- an amino group
- an R (radical) group (a side
chain) bound covalently to a central carbon (C) atom
What amino acid component gives its chemical identity?
R (radical) group aka the side chain
Chemical identity of an amino acid as identified by its r (radical) group may be:
- nonpolar (hydrophobic)
- polar (hydrophilic)
- positively charged
- negatively charged
Amino group of one amino acid reacts with the carboxyl group of another amino acid during a dehydration reaction, releasing a molecule of H2O. The resulting covalent bond is called?
peptide bond
The free amino group at one end of a polypeptide chain is called?
N-terminus
The free hydroxyl group at one end of a polypeptide chain is called?
C-terminus
Four levels of protein structure are recognized. These are?
- Primary
- Secondary
- Tertiary
- Quaternary
The sequence of amino acids in the linear backbone of the polypeptide is called?
Primary structure
Certain regular or repeating configurations in space assumed by amino acids lying close to one another in the polypeptide chain.
Secondary structure
One type of a secondary structure composed of a spiral chain of amino acids stabilized by hydrogen bonds.
Alpha helix
One type of a secondary structure characterized by a single-polypeptide chain folding back on itself, or several chains running in either parallel or antiparallel fashion next to one another.
Beta-pleated sheet
Defines the three-dimensional conformation of the entire chain in space. Each protein twists and turns and loops around itself in a very particular fashion, characteristic of the specific protein.
Tertiary structure
Applies to those proteins composed of more than one polypeptide chain and indicates the position of the various chains in relation to one another.
Quaternary structure
A spontaneous process whereby a linear molecule exiting the ribosome achieved a three-dimensional, thermodynamically stable conformation based solely on the combined chemical properties inherent in the amino acid sequence.
Protein folding
Proteins that function by mediating the folding process by excluding the formation of alternative, incorrect patterns.
Chaperons (molecular chaperons or chaperonins)
As misfolded proteins are transported out of the endoplasmic reticulum to the cytoplasm, they are “tagged” by another class of small proteins called?
Ubiquitins
The protein–ubiquitin complex moves to a cellular structure called _____, within which the ubiquitin is released and the misfolded proteins are degraded by proteases.
Proteasome
These are aggregates of misfolded protein that causes scrapie in sheep, bovine form encephalopahty (mad cow disease) in cattle, and Creutzfeldt–Jakob disease.
Prions
The misfolded protein (called PrPSc ) is
an altered version of a normal cellular protein called?
PrP^c
True or False. The difference between PrP^c and PrP^Sc lies in their secondary protein structures. Normal, noninfectious PrP^c folds into a beta-pleated sheet , whereas infectious PrP^Sc folds into an alpha-helix.
False. Normal, noninfectious PrP^c folds into an alpha-helix. Infectious PrP^Sc folds into a beta-pleated sheet.
Respiratory pigments that transport oxygen, which is essential for cellular metabolism.
Hemoglobin and myoglobin
Are structural proteins associated with the skin,
connective tissue, and hair of organisms.
Collagen and keratin
Are contractile proteins, found in abundance in muscle tissue.
Actin and myosin
The basis of the function of microtubules in mitotic and meiotic spindles.
Tubulin
Proteins that function in the immune system of vertebrates.
immunoglobulins
Proteins involved in the movement of molecules across membranes; some of the hormones and their receptors, which regulate various types of chemical activity.
Transport protein
Proteins that binds DNA in eukaryotic organisms
Histone
Protein that regulate gene expression.
Transcription factors
Sequences, usually between 50 and 300 amino acids, and represent modular portions of the protein that fold into stable, unique conformations independently of the rest of the molecule.
Protein domain
True or False. Different domains impart different functional capabilities. Some proteins contain only a single domain, while others contain two or more.
True
The significance of domains resides in the tertiary structures of proteins. Each domain can contain a mixture of secondary structures, including alpha-helices and beta-pleated sheets. The unique conformation of a given domain imparts a specific function to the protein.
True
