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Applied Biochemistry > Protein Synthesis & Protein Function (Exam III) > Flashcards

Protein Synthesis & Protein Function (Exam III) Flashcards

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1
Q

Eukaryotic translation is driven by

A

Ribosomes

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2
Q

What type of structures are ribosomes

A

Multimeric

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3
Q

What rRNAs are involved in eukaryotic translation (4)

A

28S, 18S, 5.8S, 5S

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4
Q

Ribosomal machinery is assembled within the

A

nucleolus (inside the nucelus)

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5
Q

What is unique about the nucleolus

A

Not a membrane-bound structure

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6
Q

Serves as guide RNAs to direct specific modifications of the rRNAs

A

SnoRNAs (small nucleolar RNAs)

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7
Q

In eukaryotic translation the modifications on the 2-OH positions on the nucleotide ribose sugar include:

A

Around 100 methylations of the 2-OH position

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8
Q

In eukaryotic translation, what modification occurs to uridine nucleotides creating pseudouridine

A

Around 100 isomerizations

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9
Q

Ribosomes found moving anywhere in the cytosol - not fond in nucleus and other organelles

A

Free ribosomes

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10
Q

If the protein being made contains an endoplasmic reticulum targeting sequence, then the ribosome is associated with the:

A

Rough ER

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11
Q

Ribosomes associated with the rough ER are considered

A

Membrane-bound ribosomes

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12
Q

There is a very specific ______ pathway associated with proteins made in the ribosomes of the RER

A

Secretory

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13
Q

Read by the ribosomal machine as a triplet of sequential nucleotides (codon)

A

Messenger RNA

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14
Q

Where does translation start?

A

5’ end of the mRNA

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15
Q

In order for a protein to be made we need a tRNA that has a ________ that basepairs with the codons of mRNA

A

Anticodon

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16
Q

TRNAs are “charged” by the addition of a specific ______ that corresponds to that codon

A

amino acid

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17
Q

The aminoacyl tRNA is created by the action of enzymes called

A

Aminoacyl-tRNA synthetases

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18
Q

Protein translation uses base pairing between:

A

The codon (in mRNA) and the anticodon (in tRNA)

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19
Q

There is _____ for each codon-anticodon pair

A

TRNA

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20
Q

Steps of translation (4)

A

1- activation
2- initiation
3- elongation
4- termination

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21
Q

Step of translation: formation of aminoacyl-tRNAs

A

activation

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22
Q

Step of translation: binding of ribosome to 5’ end of mRNA and subsequent binding of initiator Met-tRNA

A

Initiation

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23
Q

Step of translation: synthesis of the peptide chain

A

Elongation

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24
Q

Step of translation: synthesis stops and peptide (protein) is released from the ribosome

A

Termination

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25
The third base in the anticodon triplet (3’ base of the codon) is the lease important for base pairing and generates:
The wobble position
26
Translation starts with the AUG codon in mRNA which in about 90% of cases is the _______ in the mRNA
First AUG
27
AUG codes for
Methionine
28
Generally speaking how many stop codons is necessary to termination translation
2
29
A small ribosomal subunit attaches to the 5’ end of mRNA due to recognition of the:
5’ cap structure
30
The small ribosomal subunit moves along the mRNA until it encounters the first methionine codone where the _____ will bind
Met-tRNA and the large ribosomal subunit
31
Aminoacyl-tRNAs bind in the ______ site of the ribosome
A site (aminoacyl-site)
32
The ribosome move 5’ to 3’ along the mRNA. As the ribosome moves, the Met-tRNA is simultaneously shifted to the _____ site
P site (peptide site)
33
After the Met-tRNA is shifted to the P site, the _____ is now open for the next aminoacul-tRNA corresponding to the next codon to bind
A site
34
The process of translation largely uses what form of energy
GTP
35
Type of bond formed between the Met-tRNA and the new aminoacyl-tRNA in the A site
Peptide bond
36
When the peptide bond is formed between the Met-tRNA and the aminoacyl-tRNA this forms a ______ in the A site and a ______ tRNA in the P site
Dipeptide Empty
37
Once the dipeptide is formed, leaving an empty tRNA in the P site, the ribosome then moves simultaneously discharging the empty tRNA and shifting the peptide into the:
P site
38
Once a stop codon is encountered, termination of the polypeptide chain involved _____ of the ester bond which releases the protein
Hydrolysis
39
Many antibiotics target
Transcription or translation
40
Antibiotic that prevents RNA synthesis
Rifamycin
41
Antibiotic that blocks the binding of the aminoacyl-tRNA to the A-site (also binds to newly forming mineralizing surfaces such as bone and teeth
Tetracycline
42
Antibiotic that prevents the switch from translation initiation to elongation and also can cause protein miscoding
Streptomycin
43
Antibiotic that blocks the peptide look transferase reaction so elongation is prevented
Chloramphenicol
44
Antibiotic that blocks the ribosome exit channel in the ribosome so elongation is inhibited
Erythromycin
45
Which antibiotics effect elongation
Streptomycin Chloramphenicol Erythromycin
46
Linear sequence of amino acids
Primary structure
47
Stretches of the polypeptide chain that form alpha-helices or beta-sheets
Secondary structure
48
What are the two forms of the beta-sheet structure
1- anti-parallel Beta sheet 2- parallel Beta sheet
49
Changes in _______ can have a profound effect on protein structure and function
Amino acid sequence
50
The 3D structure of a single polypeptide chain
Tertiary structure
51
Designation used for proteins that have multiple polypeptide chains (subunits) and refers to the complete structure of all subunits
Quaternary structure
52
Shared sequences of amino acids that can be used to identify potential members of a protein family
Protein motifs
53
Shared protein motifs general equate to
Similar functions
54
Structure entities that function essentially independently within a protein
Protein domain
55
Protein domains can be built from a specific _____ or a set of _____
Specific motif Set of motif
56
A single protein can have multiple
Motifs and domains
57
A proteolytic enzyme cleavage site and phosphorylation sites are examples of
Protein sequence motifs
58
RGD sequence and heparin binding sites are examples of
Binding motifs
59
Transmembrane spanning sequences and protein secretion leader sequences are examples of
Protein sequence motifs
60
Many proteins have a ______ structure, which also appears in other proteins. These structural motifs are formed by the 3D arrangement of amino acids and do not necessarily predict a biological function
Supersecondary
61
What can be found in both proteins and DNA and generally have biological significance
Protein motifs
62
Common in transcription factors and consist of alpha-helices bound by a looping stretch of amino acids
Helix-loop-helix motif
63
DNA binding motif consisting of two alpha-helices joined by short stretch of amino acids
Helix-turn-helix motif
64
DNA binding motif consisting of two beta-strands
Zinc finger
65
Alu, DNA transposons, LINE, SINE, SSR, etc. are all examples of
DNA sequence repeat elements
66
What cells arise from dental papilla (2)
Odontoblasts Undifferentiated mesenchymal cell fibroblasts
67
What cells are derived from the dental follicle
Cementoblasts Fibroblasts Osteoblasts
68
Odontoblasts give rise to
Dentin
69
Undifferentiated mesenchymal cell fibroblasts give rise to
Pulp
70
Cementoblasts give rise to
Cementum
71
Fibroblasts give rise to
Periodontal ligament
72
Osteoblasts give rise to
alveolar bone
73
What cells are derived from inner dental epithelium
Ameloblasts
74
Ameloblasts give rise to
Enamel
75
Major protein of enamel that stabilizes the amorphous calcium-phosphate phase, control of apatite crystal morphology and organization and controls enamel thickness
Amelogenin
76
Amelogenins have the ability to _______ into nanosperes and thereby guide HAP crystal formation/growth
Self-assemble
77
Major protein of enamel cell adhesion protein, controls cells differentiation and maintains rod integrity
Ameloblastin
78
Major protein of enamel that cooperates with amelogenin to control mineral nucleation and elongated growth
Enamelin
79
Major protein of enamel that digests enamel proteins during maturation stage facilitation their removal and hardening the final layer of enamel
Kalikrin 4
80
Major protein of enamel that cleaves a amelogenin, amelobalstin and Enamelin at the secretory stage to produce stable intermediates with defined functions
MMP-20
81
What is formed by ameloblasts and contains 90% amelogenin and 10% Enamelin
Enamel
82
In enamel as apatite crystals grow _____ is removed
Amelogenin
83
High in proline, leucine, histidine and glutamine but contains no hydroxyproline or cysteine
Amelogenin
84
There are two genes for amelogenin, one on the X and the other on the Y which results in minor differences in the enamel between males and females. The gene on the X is _____ while the gene on the Y is ____
AMELX AMELY
85
The self assembly of amelogenin is dependent upon:
Hydrophilic C-terminus
86
Occurs before the formation of enamel (reciprocal induction)
Dentin formation
87
Odontoblasts differentiate from cells in the
Dental papilla
88
Secrete their organic matrix around the area that is directly adjacent to the inner enamel epithelium
Odontoblasts
89
When odontoblasts movie toward center of tooth they form
Odontoblast process
90
Odontoblasts secrete ________ and mineralize matrix forming the mantle dentin
Hydroxyapatite crystals
91
What is the major component found in dentin
Type I collagen
92
The small integrin-binding N-linked glycoproteins
SIBLING family proteins
93
Immediately cleaved after secretion into DSP, DGP and DPP
DSPP
94
Produced by odontoblasts in early-stage osteocytes
DMP1
95
Plays a role in biomineralization
Bone sialoprotein
96
HA binding and contains an RGF motif, mineralization inhibitor
Osteoponin
97
Matrix extracellular phosphoglycoprotein that contains RGD motif and in bone appears to be an inhibitor of mineralization
MEPE
98
Accelular cementum forms before _____
Cellular cementum
99
Formed by fibroblast cells from the dental follicle
Periodontal ligament

Applied Biochemistry (18 decks)

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