Kaplan Biochem Ch 4 Flashcards
stop codon
- UGA (U Go Away)
- UAA (U Are Away)
- UAG (U Are Gone)
start codon; what does it code for?
AUG; codes for methionine
- protein synthesis starts with methionine in eukaryotes and fmet (formylmethionine) in prokaryotes
- therefore the first AA at the amino end (N end) is always Met
How many codons are there?
There are 64 codons, 61 code for AA; so there are 61 tRNAs
most common inherited form of mental retardation
fragile X
Diseases caused by trinucleotide Repeat Expansion
- myotonic dystrophy
- spinobulbar myotonic atrophy aka kennedy syndrome
- Friedrich’s ataxia
A transition mutation
- a point mutation that replaces a purine-pyrimidine base pair with a different purine-pyrimidine base pair.
- ex) an A-T base pair becomes a G-C base pair
silent mutation and effect on protein
- new codon specifies the same amino acid –> no effect on protein
- silent mutation usually in 3rd position: “Wobble effect”
- if you mutate the 3rd nucleic acid in a codon it’s usually a silent mutation
missense mutation and effect on protein and examples
- new codon specifies different amino acid
- effect on protein: possible decrease in function of protein; variable effects
- ex) sickle cell, PKU, Becker’s MD
a transversion mutation
- a point mutation that replaces a purine-pyrimidine base pair with a pyrimidine-purine base pair
- ex) an A-T base pair becomes a T-A or C-G base pair
Nonsense mutation and effect on protein and examples
- new codon is stop codon
- effect on protein: shorter than normal; usually nonfunctional
- ex) DMD (dystrophin), Hemophilia (Factor VIII)
- “Stop the nonsense”
frameshift/in-frame mutation and effect on protein
- addition or deleting of base(s)
- effect on protein: loss of function; shorter than normal or entirely missing
large segment deletion
- cause
- effect on protein
- usually occurs via unequal crossover in meiosis
- effect on protein: variable effects ranging from addition or deletion of a few AA to deletion of an entire exon
triplet repeat expansion
- Expansions in coding regions cause protein product to be longer than normal and unstable
- disease often shows anticipation in pedigree (disease gets worse with each generation)
What will the first 3 AA be in the coding strand?
Coding strand = DNA copy of mRNA except U = T.
- So AUG = start codon –> first 3 AA in DNA will be ATG
purpose of meiosis I
- crossover or recombination between homologous chromosomes is a normal part of meiosis I that generate genetic diversity in reproductive cells (sperm and eggs) with a largely beneficial result.
- normally, homologous maternal and paternal chromosomes exchange equivalent segments so no information is lost from ether one
cause and consequence of alpha-thallasemia
- unequal crossover (in meiosis I) has deleted one or more alpha-globin genes from chromosome 16
Cri-du-chat
- symptoms
- cause
- mental retardation, microcephaly, wide-set eyes, and characteristic kitten-like cry
- results from terminal deletion on the short arm of chromosome 5 (results from unequal crossover in meiosis I)
symptoms of hunting tons
- genetic inheritance
- mean age of onset
- juvenile onset
- AD disorder
- mean age of onset: 43-48
- Sx: mood disturbance, impaired memory, hyperreflexia (are often first signs)
- followed by abnormal gait, chorea (loss of motor control), dystonia, dementia, and dysphagia
- juvenile onset: (
diseases where the expansion of the trinucleotide repeat of the mutant allele is in the coding region
- huntington’s disease
- spinobulbar muscular atrophy
Normal huntington allele has
5 tandom repeats of CAG in the coding region
family members affected with Huntington’s have
30-60 CAG tandem repeats in the coding region
Normal protein vs someone who has Huntington’s
- The normal protein contains 5 adjacent glutamine residues, whereas the proteins encoded by the disease-associated alleles have 30 or more adjacent glutamates
- the long glutamine tract makes the abnormal proteins extremely unstable
diseases where the expansion of the trinucleotide repeat of the mutant allele is in an untranslated region of the gene
- fragile x
- myotonic dystrophy
Amino Acid Activation
- each type of AA is activated by a different aminoacyl tRNA syntheses
- no proofreading during translation to detect if correct AA is bound to correct tRNA
- 2 high-energy bonds from an ATP are required
- the high-energy bond linking the AA to its cognate tRNA will later supply energy to make a peptide bond linking the AA into a protein
peptide bonds occur between
between the carboxyl group of one AA and the amino group of another
During translation, the AA are attached to the ____ ends of their respective ____
During translation, the AA are attached to the 3’ ends of their respective tRNAs
the aminoacyl-tRNAs are situated in the __ and ___ sites of the ribosome.
- the aminoacyl-tRNAs are situated in the P and A sites of the ribosome.
- P stands for Peptide site
- A stands for acceptor site
Aminoacyl-tRNA synthetase
- class of enzyme that recognizes and pairs specific tRNA with their corresponding AA
- each AA is activated by a different aminoacyl-tRNA synthetase
- aa-tRNA synthetase transfers the activated AA to the 3’ end of the correct tRNA
- have self-checking functions to prevent incorrectly paired aa-tRNAs from forming. If, however, one does release an incorrectly paired product, there is no mechanism during translation to detect the error and an incorrect AA will be introduced into some protein!
the peptide bond forms between the ____ of the amino acid (or growing peptide) in the __ site and the ___ of the next amino acid at the __ site
- the peptide bond forms between the carboxyl group of the amino acid (or growing peptide) in the P site and the amino group of the next amino acid at the A site
- this reaction gives off h20
Proteins are synthesized from the ___ to the _____
proteins are synthesized from the amino to the carboxy terminus
translation occurs in the ____ of ____
translation occurs in the cytoplasm of both prokaryotic and eukaryotic cells
in ______, ribosomes can begin translation the mRNA even before RNA polymerase completes its transcripton
- in Prokaryotes, ribosomes can begin translation the mRNA even before RNA polymerase completes its transcripton
- in eukaryotes, translation and transcription are completely separated in time and space with transcription in the nucleus and translation in the cytoplasm
streptomycin inhibits
initiation of protein synthesis (TRANSLATION)
Steps involved in elongation of protein synthesis
- aminoacyl-tRNA binds to A site of the ribosome
- this is inhibited by shiga toxin (cuts 28S rRNA)
- tetracycline also inhibits step 1 - peptide bond forms. this requires 2 high energy bonds per activation
- Peptidyl transferase is an enzyme that is part of the large subunit
- chloramphenicol inhibits peptidyl transferase - translation of ribosome 3 nucleotides along the mRNA
- requires GTP
- pseudomonas and diphtheria toxin inhibit ADP-ribosylation
In initiation of protein synthesis the ____ ribosomal subunit binds to the mRNA
In initiation of protein synthesis the small ribosomal subunit binds to the mRNA
in Prokaryotes, the ___ rRNA of the _____ subunit binds to the _______ in the 5’ untranslated region of the mRNA
in Prokaryotes, the 16S rRNA of the small subunit binds to the Shine-Dalgarno in the 5’ untranslated region of the mRNA
in ____, translation and transcription are completely separated in time and space with transcription in the _____ and translation in the _____
in eukaryotes, translation and transcription are completely separated in time and space with transcription in the nucleus and translation in the cytoplasm
Shiga toxin inhibits
step 1 of elongation of protein synthesis (TRANSLATION): aminoacyl-tRNA binding to A site of the ribosome
- cuts an adenine residue from 28S rRNA in the 60S subunit
chloramphenicol inhibits
chloramphenicol inhibits peptidyl transferase: step 2 of elongation of protein synthesis (TRANSLATION)
The initiator tRNA in eukaryotes carries ___
- Elongation is a 3-step cycle that is repeated for each AA added to the protein after the initiator methionine
- The initiator tRNA in eukaryotes carries met
Translation of protein synthesis ends when the stop codon reaches the ___
- what enzyme is involved?
- Translation of protein synthesis ends when the stop codon reaches the A site of the ribosome
- peptidyl transferase (with the help of release factor) hydrolyzes the completed protein from the final tRNA in the P site.
- the mRNA, ribosome, tRNA and factors can all be reused for additional protein synthesis
in Eukaryotes, the ____ subunit, binds to the ____ and slides down the message to the first AUG
in Eukaryotes, the small subunit, binds to the 5’ cap structure and slides down the message to the first AUG
tetracycline inhibits
tetracycline inhibits step 1 of elongation of protein synthesis: aminoacyl-tRNA binding to A site of the ribosome
The charged initiation tRNA becomes bound to the AUG start codon on the message through _____
- the initiatior tRNA in prokaryotes carries ___
- the initiator tRNA in eukaryotes carries ___
The charged initiation tRNA becomes bound to the AUG start codon on the message through base pairing with its anticodon.
the initiatior tRNA in prokaryotes carries ___
- Elongation is a 3-step cycle that is repeated for each AA added to the protein after the initiator methionine
- The initiatior tRNA in prokaryotes carries fmet
pseudomonas and diphtheria toxin inhibit
in Eukaryotic cells, elongation factor 2 (eEF-2) used in translocation is inactivated through ADP-ribosylation by Pseudomonas and Diphtheria toxins
the P site is the site on the ribosome where ____ initially binds
- the P site is the site on the ribosome where (f) met initially binds.
- After formation of the first peptide bond, the P site is a binding site for the growing peptide chain
the aminoacyl site (A site) binds ??
the aminoacyl site (A site) binds each new incoming tRNA molecule carrying an activated AA
Elongation is a 3-step cycle that is repeated for each AA added to the protein after the initiator methionine
- Each cycle uses ?? high-energy bonds
Elongation is a 3-step cycle that is repeated for each AA added to the protein after the initiator methionine
- Each cycle uses 4 high-energy bonds:
- 2 from the ATP used in AA activation to charge the tRNA, and 2 from GTP
During elongation, the ribosome moves in the _____ direction along the mRNA, synthesizing the protein from ___ to _____ terminus.
During elongation, the ribosome moves in the 5’ to 3’ direction along the mRNA, synthesizing the protein from amino to carboxy terminus.
Peptidyl Transferase
- what is it and action
- an enzyme that is part of the large subunit, forms the peptide bond between the new AA and the carboxy end of the growing peptide chain
- The bond linking the growing peptide to the tRNA in the P site is broken, and the growing peptide attaches to the tRNA located in the A site.
This is step 2 of protein elongation
What occurs in the translocation step of protein synthesis
aka the 3rd step in the elongation step of translocation
- the ribosome moves exactly 3 nucleotides (one codon) along the message.
- This moves the growing peptidyl-tRNA into the P site and aligns the next codon to be translated with the empty A site.
in Eukaryotic cells, ____ used in translocation is inactivated through _____ by Pseudomonas and Diphtheria toxins
in Eukaryotic cells, elongation factor 2 (eEF-2) used in translocation is inactivated through ADP-ribosylation by Pseudomonas and Diphtheria toxins
Shiga and Shiga-like toxins clip an ____ residue from the ___ in the ___ subunit stopping protein synthesis in Eukaryotic cells
Shiga and Shiga-like toxins clip an adenine residue from the 28S rRNA in the 60S subunit stopping protein synthesis in Eukaryotic cells
Some well-known inhibitors of prokaryotic translocation include:
Some well-known inhibitors of prokaryotic translocation include:
- streptomycin
- erythromycin
- tetracycline
- chloramphenicol
Some well-known inhibitors of eukaryotic translocation include:
Some well-known inhibitors of eukaryotic translocation include:
- cycloheximide
- diptheria toxin
- pseudomonas toxin
Chloramphenicol inhibits ______ but not ______
Chloramphenicol inhibits mitochondrial protein synthesis but not cytoplasmic protein synthesis, because mitochondrial ribosomes are similar to prokaryotic ribosomes
Examples of eukaryotic proteins that are translated on ribosomes associated with the RER
- secreted proteins
- proteins inserted into the cell membrane
- lysosomal enzymes
Proteins translated on free cytoplasmic ribosomes include:
- cytoplasmic proteins
- mitochondrial proteins (encoded by nuclear genes)
the N-terminal hydrophobic signal sequence is used to ensure ____
the N-terminal hydrophobic signal sequence is used to ensure translation on the RER
- involves the signal recognition particle (SRP)
- crosses ER membrane (that’s why it’s hydrophobic, aka lipid soluble)
- translation begins in cytoplasm. Signal sequence causes ribosomes to attach to ER.
- a signal peptidase remove the signal sequence because its only function is entrance to the ER lumen.
- translation continues on RER.
- this only happens to proteins that leave the cytoplasm. i.e., go to lysosome, go to cell membrane, or are secreted
Phosphorylation of mannose residues is important for ___
Phosphorylation of mannose residues is important for directing an enzyme to a lysosome.
Ehlers-Danlos Syndromes represent a collection of defects in the _______
- like Osteogenesis Imperfecta, these syndromes are a result of _____ in which defects in several different genes (loci) can result in similar symptoms
Ehlers-Danlos Syndromes represent a collection of defects in the normal synthesis and processing of collagen
- defect = mutations in collagen genes and lysyl hydroxylase gene
- like Osteogenesis Imperfecta, these syndromes are a result of locus heterogeneity in which defects in several different genes (loci) can result in similar symptoms
- EDS type IV, the ____ type, is an autosomal ____ disease caused by mutations in the gene for _____
- Characteristic features include:
- EDS type IV, the vascular type, is an autosomal dominant disease caused by mutations in the gene for type 3 procollagen.
- Characteristic features include:
- thin, translucent skin
- arterial, intestinal or uterine rupture,
- and easy bruising
Scurvy is a disease with
Scurvy is a disease with deficient hydroxylation secondary to ascorbate deficiency
Major symptoms of Scurvy
petechiae, ecchymoses, loose teeth, bleeding gums, poor wound healing, poor bone development
- Osteogenesis imperfecta is a disease resulting in mutations in ______
- major symptoms:
- Osteogenesis imperfecta is a disease resulting in mutations in collagen genes.
- major symptoms: skeletal deformities, fractures, blue sclera
Major symptoms of EDS
hyperextensible, fragile skin, hypermobile joints, dislocations, varicose veins, ecchymoses, arterial, intestinal ruptures
the ____ signal sequence is used to ensure translation on the RER
the N-terminal hydrophobic signal sequence is used to ensure translation on the RER
Menkes Disease results in ____
- cause:
- type of diasese
- specific mutation:
Menkes Disease results in deficient cross-linking secondary to functional copper deficiency
- aka EDS type IX (Kinky hair syndrome)
- X-linked recessive disease
- incidence of 1/100,000 newborns
- mutation in gene ATP7A, which encodes an ATP-dependent copper efflux protein in the intestine
_______ is important for directing and enzyme to a lysosome.
Phosphorylation of mannose residues is important for directing and enzyme to a lysosome.
Major symptoms of Menkes Disease
depigmented (steely) hair, arterial tortuosity and rupture, cerebral degeneration, osteoporosis, anemia
- aka EDS type IX (Kinky hair syndrome)
- symptoms (in part) due to weak collagen
The domains of the IgG molecule are examples of ___ structure
The domains of the IgG molecule are examples of tertiary structure:
- the positioning of 2ndary structures in relation to each other to generate 3D shapes
- Tertiary structure also includes the shape of the protein as a whole (globular, fibrous)
- Mutation causing Menkes Disease
- result
- mutation in gene ATP7A, which encodes an ATP-dependent copper efflux protein in the intestine
- Copper can be absorbed into the mucosal cell, but cannot be transported into the bloodstream
- Consequently, an affected individual will have SEVERE copper deficiency and all copper-requiring enzymes will be adversely affected
- Lysyl oxidase requires copper and plays a direct role in collagen formation by catalyzing the cross-linking of collagen fibrils.
- deficiency in the activity of this enzyme and other copper-dependent enzymes would be responsible for symptoms
Is Collagen extracellular or intracellular?
Collagen is Extracellular!
- very HY! Found in bones, BM, tendons
- when see hydroxyproline think collagen (= AA unique to collagen)
- collagen is a triple repeat tripeptide (Gly-X-Y) with 3 strands and every 3rd AA is glycine
- Gly-X-Y
Examples of N-linked glycoproteins
- blood clotting factors
- immunoglobulins
- receptors
- transporters
- blood groups
Synthesis of secretory, membrane, and lysosomal proteins
- this only happens to proteins that leave the cytoplasm. i.e., go to lysosome, go to cell membrane, or are secreted
- translation begins in cytoplasm on free ribosomes, but after translation of the signal sequence…
- signal sequence causes ribosomes to attach to ER
- translation continues on RER
- During translation, the nascent protein is fed through the membrane of the RER and captured in the lumen.
- signal peptidase removes the signal sequence (bc its only function is entrance to ER lumen)
- then the protein passes into the Golgi for further modification and sorting. In transit through the ER and golgi, the proteins acquire oligosaccharide side chains commonly attached at SERINE and THREONINE residues (if O-linked) or at ASPARAGINE residues (if N-linked) - N-linked glycosylation (in ER) requires participation of a special lipid called dolichol phosphate
- proper folding is required in ER for transfer of protein to Golgi
- phosphorylation of mannose by phosphotransferase signals to lysosome
- from lysosome proteins go to cell membrane for secretion (or to be part of membrane)
- O-linked glycosylation
- examples of things that are O-glycosylated
- Occurs in the golgi
- i.e. serine or threonine
- Examples: cOllagen is O-glycosylated
- proteoclycans, hyaluronic acid (lubricants), chrondroitin, mucins
Lysyl Oxidase
Lysyl oxidase requires copper and plays a direct role in collagen formation by catalyzing the cross-linking of collagen fibrils.
collagen is a triple repeat tripeptide with 3 strands and every ___ AA is ____
collagen is a triple repeat tripeptide with 3 strands and every 3rd AA is glycine
Examples of proteins that are NOT glycosylated
- albumin
- insulin
- glucagon
This sequence is found on proteins that are destined to be secreted (ex insulin), placed in the cell membrane (i.e. Na+-K+ ATPase), or ultimately directed to the lysosome (i.e. sphingomyelinase)
the N-Terminal hydrophobic signal sequence
- 4mo who fails to grow and appears mentally retarded, with kinky, hypopigmented hair. What else do you expect to see on further examination?
- diagnosis?
- gene mutated?
- result?
- Expect to see elongation and tortuosity of the major arteries on arteriogram
- additional tests may reveal bladder diverticula and subdural hematomas
- blood test will show low serum ceruloplasmin and only 10% normal copper levels
- Diagnosis: Menkes Disease
- disease caused by mutations in the gene ATP7A, which encodes the ATP-dependent copper efflux protein in the intestine.
- result: Severe copper deficiency bc copper can be absorbed into the mucosal cell but can’t be transported into the bloodstream.
in O-linked glycosylation the oligosaccharide side chains are attached at ____ and ____ residues
In transit through the ER and golgi, the proteins acquire oligosaccharide side chains commonly attached at SERINE and THREONINE residues (if O-linked)
Lysosomal enzymes are glycosylated and modified in a characteristic way. Most importantly, when they arrive in the Golgi, specific _____ residues in their oligosaccharide chains are _________
Lysosomal enzymes are glycosylated and modified in a characteristic way. Most importantly, when they arrive in the Golgi, specific MANNOSE residues in their oligosaccharide chains are PHOSPHORYLATED by N-ACETYLGLUCOSAMINE-1 PHOSPHOTRANSFERASE
- this phosphorylation is the critical event that removes them from the secretion pathway and direct them to lysosomes
Genetic defects affecting the phosphorylation of lysosomal enzymes produces I-cell disease in which ___
Genetic defects affecting the phosphorylation of lysosomal enzymes produces I-cell disease in which lysosomal enzymes are released into the extracellular space and inclusion bodies accumulate in the cell, compromising its function
Major function of lysosomes and how do they do that?
- to digest materials that the cell has ingested by endocytosis
- lysosomes contain multiple enzymes that collectively, digest carbohydrates (glycosylases), lipids (lipases), and proteins (proteases)
- when a lysosomal enzyme is missing the undigested substance accumulates in the cell and can lead to serious consequences
Lysosomes are especially prominent in which cells
lysosomes are especially prominent in neutrophils and macrophages
- In N-linked glycosylation proteins acquire oligosaccharide side chains commonly attached at _____ residues
- N-linked glycosylation requires participation of ____
- In N-linked glycosylation proteins acquire oligosaccharide side chains commonly attached at ASPARAGINE residues
- N-linked glycosylation (in ER) requires participation of a special lipid called dolichol phosphate
Major symptoms of I-cell disease
- coarse facial features, gingival hyperplasia, macroglossia
- craniofacial abnormalities, joint immobility, clubfoot, claw-hand, scoliosis
- psychomotor retardation, growth retardation
- cardiorespiratory failure, death in first decade
- bone fracture and deformities (i.e. can be born with dislocated hips, etc)
- mitral valve defect (heart murmur)
- secretion of active lysosomal enzymes into blood and extracellular fluid
- hepatosplenomegaly
- suffer from repeated URT infections
- examination of fibroblasts from skin biopsy shows presence of numerous intracellular inclusions (can see large lysosomes on ECM)
- biochemical analysis shows decreased levels of lysosomal hydrolase beta-glucuronidase within the fibroblasts, but elevated levels of this enzyme within the culture medium
glycosylation
addition of oligosaccharide as proteins pass through the ER and Golgi apparatus
proteolysis
cleavage of peptide bonds to remodel proteins and activate them
- ie proinsulin, trypsinogen, prothrombin
gamma carboxylation produces
produces Ca2+ binding sites
prenylation
addition of frankly or geranylgeranyl lipid groups to certain membrane-associated proteins
hydroxyproline
- AA unique to collagen
- produced by hydroxylation of proudly residues at the Y positions in pro collagen chains as they pass through the RER
post translational modifications of collagen (9 steps)
- prepro-alpha chains containing hydrophobic signal sequence are synthesized by ribosomes attached to the RER
- the hydrophobic signal sequence is removed by signal peptidase in the RER to form pro-alpha chains
- selected prolines and lysine are hydroxylated by prolyl and lysyl hydroxylases. These enzymes (located in the RER) require ascorbate (Vit C). Def of Vit C = scurvy
- Selected hydroxylysines are glycosylated
- Three pro-alpha chains assemble to form a triple helical structure (procollagen) which can now be transferred to the Golgi. Modification of oligosaccharide continues in the golgi
- Procollagen is secreted from the cell
- the pro peptides are cleaved from the ends of pro collagen by proteases to form collagen molecules (also called tropocollagen)
- collagen molecules assemble into fibrils. Cross-linking involves lysyl oxidase, an enzyme that requires O2 and copper
- fibrils aggregate and cross-link to form collagen fibers
Type 1 Collagen:
- Characteristics
- tissue distribution
- associated diseases
- Characteristics: bundles of fibers, high tensile strength
- tissue distribution: bone, skin, tendons
- associated diseases: OI, EDS
This enzyme cross-links collagen molecules to assemble them into fibrils. It requires what?
collagen molecules assemble into fibrils. Cross-linking involves lysyl oxidase, an enzyme that requires O2 and copper
Type 2 Collagen:
- Characteristics
- tissue distribution
- associated diseases
- Characteristics: thin fibrils, structural
- tissue distribution: cartilage, vitreous humor
- associated diseases: none
Type 3 Collagen:
- Characteristics
- tissue distribution
- associated diseases
- Characteristics: thin fibrils, pliable
- tissue distribution: blood vessels, granulation tissue
- associated diseases: EDS Type 4, keloid formation
These enzymes (located in the RER) require ascorbate (Vit C).
- prolyl and lysyl hydroxylases
- these hydroxylate selected proline and lysine residues in collagen
Type 4 Collagen:
- Characteristics
- tissue distribution
- associated diseases
- Characteristics: amorphous
- tissue distribution: basement membrane
- associated diseases: goodpasture syndrome, alport disease, epidermylosis bullies
