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

Protein Synthesis & Protein Function (Exam III) Flashcards

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
Q

The third base in the anticodon triplet (3’ base of the codon) is the lease important for base pairing and generates:

A

The wobble position

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26
Q

Translation starts with the AUG codon in mRNA which in about 90% of cases is the _______ in the mRNA

A

First AUG

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27
Q

AUG codes for

A

Methionine

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28
Q

Generally speaking how many stop codons is necessary to termination translation

A

2

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29
Q

A small ribosomal subunit attaches to the 5’ end of mRNA due to recognition of the:

A

5’ cap structure

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30
Q

The small ribosomal subunit moves along the mRNA until it encounters the first methionine codone where the _____ will bind

A

Met-tRNA and the large ribosomal subunit

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31
Q

Aminoacyl-tRNAs bind in the ______ site of the ribosome

A

A site (aminoacyl-site)

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32
Q

The ribosome move 5’ to 3’ along the mRNA. As the ribosome moves, the Met-tRNA is simultaneously shifted to the _____ site

A

P site (peptide site)

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33
Q

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

A site

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34
Q

The process of translation largely uses what form of energy

A

GTP

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35
Q

Type of bond formed between the Met-tRNA and the new aminoacyl-tRNA in the A site

A

Peptide bond

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36
Q

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

A

Dipeptide
Empty

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37
Q

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:

A

P site

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38
Q

Once a stop codon is encountered, termination of the polypeptide chain involved _____ of the ester bond which releases the protein

A

Hydrolysis

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39
Q

Many antibiotics target

A

Transcription or translation

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40
Q

Antibiotic that prevents RNA synthesis

A

Rifamycin

41
Q

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

A

Tetracycline

42
Q

Antibiotic that prevents the switch from translation initiation to elongation and also can cause protein miscoding

A

Streptomycin

43
Q

Antibiotic that blocks the peptide look transferase reaction so elongation is prevented

A

Chloramphenicol

44
Q

Antibiotic that blocks the ribosome exit channel in the ribosome so elongation is inhibited

A

Erythromycin

45
Q

Which antibiotics effect elongation

A

Streptomycin
Chloramphenicol
Erythromycin

46
Q

Linear sequence of amino acids

A

Primary structure

47
Q

Stretches of the polypeptide chain that form alpha-helices or beta-sheets

A

Secondary structure

48
Q

What are the two forms of the beta-sheet structure

A

1- anti-parallel Beta sheet
2- parallel Beta sheet

49
Q

Changes in _______ can have a profound effect on protein structure and function

A

Amino acid sequence

50
Q

The 3D structure of a single polypeptide chain

A

Tertiary structure

51
Q

Designation used for proteins that have multiple polypeptide chains (subunits) and refers to the complete structure of all subunits

A

Quaternary structure

52
Q

Shared sequences of amino acids that can be used to identify potential members of a protein family

A

Protein motifs

53
Q

Shared protein motifs general equate to

A

Similar functions

54
Q

Structure entities that function essentially independently within a protein

A

Protein domain

55
Q

Protein domains can be built from a specific _____ or a set of _____

A

Specific motif
Set of motif

56
Q

A single protein can have multiple

A

Motifs and domains

57
Q

A proteolytic enzyme cleavage site and phosphorylation sites are examples of

A

Protein sequence motifs

58
Q

RGD sequence and heparin binding sites are examples of

A

Binding motifs

59
Q

Transmembrane spanning sequences and protein secretion leader sequences are examples of

A

Protein sequence motifs

60
Q

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

A

Supersecondary

61
Q

What can be found in both proteins and DNA and generally have biological significance

A

Protein motifs

62
Q

Common in transcription factors and consist of alpha-helices bound by a looping stretch of amino acids

A

Helix-loop-helix motif

63
Q

DNA binding motif consisting of two alpha-helices joined by short stretch of amino acids

A

Helix-turn-helix motif

64
Q

DNA binding motif consisting of two beta-strands

A

Zinc finger

65
Q

Alu, DNA transposons, LINE, SINE, SSR, etc. are all examples of

A

DNA sequence repeat elements

66
Q

What cells arise from dental papilla (2)

A

Odontoblasts
Undifferentiated mesenchymal cell fibroblasts

67
Q

What cells are derived from the dental follicle

A

Cementoblasts
Fibroblasts
Osteoblasts

68
Q

Odontoblasts give rise to

A

Dentin

69
Q

Undifferentiated mesenchymal cell fibroblasts give rise to

A

Pulp

70
Q

Cementoblasts give rise to

A

Cementum

71
Q

Fibroblasts give rise to

A

Periodontal ligament

72
Q

Osteoblasts give rise to

A

alveolar bone

73
Q

What cells are derived from inner dental epithelium

A

Ameloblasts

74
Q

Ameloblasts give rise to

A

Enamel

75
Q

Major protein of enamel that stabilizes the amorphous calcium-phosphate phase, control of apatite crystal morphology and organization and controls enamel thickness

A

Amelogenin

76
Q

Amelogenins have the ability to _______ into nanosperes and thereby guide HAP crystal formation/growth

A

Self-assemble

77
Q

Major protein of enamel cell adhesion protein, controls cells differentiation and maintains rod integrity

A

Ameloblastin

78
Q

Major protein of enamel that cooperates with amelogenin to control mineral nucleation and elongated growth

A

Enamelin

79
Q

Major protein of enamel that digests enamel proteins during maturation stage facilitation their removal and hardening the final layer of enamel

A

Kalikrin 4

80
Q

Major protein of enamel that cleaves a amelogenin, amelobalstin and Enamelin at the secretory stage to produce stable intermediates with defined functions

A

MMP-20

81
Q

What is formed by ameloblasts and contains 90% amelogenin and 10% Enamelin

A

Enamel

82
Q

In enamel as apatite crystals grow _____ is removed

A

Amelogenin

83
Q

High in proline, leucine, histidine and glutamine but contains no hydroxyproline or cysteine

A

Amelogenin

84
Q

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 ____

A

AMELX
AMELY

85
Q

The self assembly of amelogenin is dependent upon:

A

Hydrophilic C-terminus

86
Q

Occurs before the formation of enamel (reciprocal induction)

A

Dentin formation

87
Q

Odontoblasts differentiate from cells in the

A

Dental papilla

88
Q

Secrete their organic matrix around the area that is directly adjacent to the inner enamel epithelium

A

Odontoblasts

89
Q

When odontoblasts movie toward center of tooth they form

A

Odontoblast process

90
Q

Odontoblasts secrete ________ and mineralize matrix forming the mantle dentin

A

Hydroxyapatite crystals

91
Q

What is the major component found in dentin

A

Type I collagen

92
Q

The small integrin-binding N-linked glycoproteins

A

SIBLING family proteins

93
Q

Immediately cleaved after secretion into DSP, DGP and DPP

A

DSPP

94
Q

Produced by odontoblasts in early-stage osteocytes

A

DMP1

95
Q

Plays a role in biomineralization

A

Bone sialoprotein

96
Q

HA binding and contains an RGF motif, mineralization inhibitor

A

Osteoponin

97
Q

Matrix extracellular phosphoglycoprotein that contains RGD motif and in bone appears to be an inhibitor of mineralization

A

MEPE

98
Q

Accelular cementum forms before _____

A

Cellular cementum

99
Q

Formed by fibroblast cells from the dental follicle

A

Periodontal ligament

Applied Biochemistry (18 decks)

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