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Applied Biochemistry > Protein Synthesis and Protein Function > Flashcards

Protein Synthesis and Protein Function Flashcards

1
Q

what do ribosomes contain?

A

multimeric structure constituting of >50 proteins and one copy of each of 4 rRNAs (18S, 5.8S, 28S, 5S)

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2
Q

ribosomes are assembled in the

A

nucleus within the nucleolus

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3
Q

unlike other organelles, the nucleolus is not a

A

membrane bound structure

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4
Q

Small nucleolar RNAs (snoRNAs) serve as

A

guide

RNAs to direct specific modifications of the rRNAs

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5
Q

these modifications include (2)

A

about 100 methylations of the 2-OH
position on the nucleotide ribose sugar and 100
isomerizations of uridine nucleotides to pseudouridine.

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6
Q

Free ribosomes

A

move anywhere in the cytosol, but not found in the nucleus and
other organelles

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7
Q

membrane bound ribosomes

A

if the protein being made contains an Endoplasmic
Reticulum (ER) targeting sequence, then the ribosome is associated
with the rough ER. These types of proteins are transported to their
destination through a secretory pathway and are usually associated
with the plasma membrane or secreted out of the cell.

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8
Q

mRNA is “read” by the ribosomal machine as a

A

triplet of sequential nucleotides (called a codon)

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9
Q

Translation starts at the — end of the mRNA

A

5’

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10
Q

tRNAs are “charged” by the addition of

A

a specific amino acid that corresponds to that codon

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11
Q

his aminoacyl-tRNA is

created by the action of enzymes called

A

aminoacyl-tRNA

synthetases

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12
Q

Protein translation uses base pairing between the mRNA
codon and a triplet complementary sequence in the tRNA
called the

A

anticodon

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13
Q

steps of translation (4)

A

activation
initiation
elongation
termination

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14
Q

activation

A

formation of aminoacyl-tRNAs

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15
Q

initiation

A

binding of small ribosome to 5’-end
of mRNA and subsequent binding of initiator
Met-tRNA

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16
Q

elongation

A

synthesis of peptide chain

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17
Q

termination

A

synthesis stops and peptide

(protein) is released from the ribosome

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18
Q

The third base in the anticodon triplet (3’ base of the codon)
is the least important for base pairing and some “—” is
tolerated, which means that

A

wobble

if the third base is a U it can pair with A, G or I (Inosine) and if it is a C it can pair with a G or I

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19
Q

Translation starts with an — codon in the mRNA, which in

about 90% of the mRNAs is the first — in the mRNA.

A

AUG

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20
Q

AUG

codes for

A

Methionine

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21
Q

Translation stops when

A

stop codons are encountered in the

mRNA (generally two consecutive stop codons)

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22
Q

translation summary

A
  1. A small ribosomal subunit attaches to the 5’
    end of the mRNA due to recognition of the
    5’cap structure.
  2. This subunit then moves along the mRNA
    until it encounters the first Methionine
    codon (AUG) where the Met-tRNA and the
    large ribosomal subunit bind. Aminoacyl-
    tRNAs bind in the A site (aminoacyl-site) of
    the ribosome.
  3. The ribosome moves 5’to 3’ along the
    mRNA. As the ribosome moves the Met-
    tRNA is simultaneously shifts to the P site
    (peptide site). The A site is now open for
    the next aminoacyl-tRNA corresponding to
    the next codon to bind.
  4. A peptide bond is formed between the Met-tRNA and the new aminoacyl-tRNA in the A site leaving the dipeptide in the A site and an “empty” tRNA in the P site. The ribosome then moves simultaneously discharging the empty tRNA and shifting the peptide into the P site. This process is repeated over and over until a Stop codon is encountered.
  5. Termination of the polypeptide chain involves hydrolysis of the ester bond which releases the protein.
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23
Q

Rifamycin

A

Prevents RNA synthesis

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24
Q

Tetracycline

A

Blocks binding of the aminoacyl-tRNA to the A-site (also binds to
newly forming mineralizing surfaces such as bone and teeth)

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25
Q

Streptomycin

A

Prevents the switch from translation initiation to elongation and
also can cause protein miscoding

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26
Q

Chloramphenicol

A

Blocks the peptidyl transferase reaction so elongation is prevented

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27
Q

Erythromycin

A

Blocks the ribosome exit channel in the ribosome so elongation is
inhibition

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28
Q

how are proteins classified? (2)

A

protein structure

protein function

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29
Q

protein structure (4)

A

– Amino acids and sequences
– Secondary structure
– Tertiary structure
– Quaternary structure

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30
Q

protein function (2)

A

– Motifs

– Domains

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31
Q

primary structure

A

amino acid

sequence

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32
Q

Secondary structure refers to stretches of the

polypeptide chain that form

A

α helices or β sheets

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33
Q

how can beta sheets be arranged (2)

A

anti-parallel beta sheet

parallel beta sheet

34
Q

Changes in Amino Acid Sequence can have a Profound

Effect on

A

Protein Structure and Function

35
Q

Tertiary structure refers to the

A

full 3D

structure of the protein

36
Q

Quaternary structure is a designation used for
proteins that have multiple polypeptide chains
(subunits) and

A

refers to the complete

structure of all subunits

37
Q

Protein motifs are shared sequences of amino

acids that can be used to identify

A

potential

members of a protein family

38
Q

Shared motifs

generally equate to

A

similar functions

39
Q

Protein domains are structural entities that

A

function essentially independently within a
protein and can be built from a specific motif or
set of motifs

40
Q

A single protein can have multiple (2)

A

motifs and

domains

41
Q

examples of protein sequence motifs (5)

A 
• Proteolytic enzyme cleavage sites
• Phosphorylation sites
• Binding motifs (e.g. RGD sequence, heparin 
binding site, etc)
• Transmembrane spanning sequences
• Protein secretion leader sequences
42
Q

Many proteins have a “—”

structure, which also appears in other proteins

A

supersecondary

43
Q

These structural motifs are formed
by the 3D arrangement of amino acids and do
not necessarily

A

predict a biological function

44
Q

in addition there are also sequence motifs

that can be found in both (2)

A

proteins and DNA

45
Q

These sequence motifs generally have

A

biological significance

46
Q

Helix-loop-helix

A

common in transcription
factors and consists of α helices bound by a
looping stretch of amino acids

47
Q

Helix-turn-helix

A

DNA binding motif consisting
of two α helices joined by a short stretch of
amino acids

48
Q

Zinc finger

A

DNA binding motif consisting of

two β strands

49
Q

DNA sequence motifs (2)

A

DNA promoter and TF binding sites

DNA sequence repeat elements

50
Q

100s of programs and dozens of databases

currently that catalog all of the known (2)

A

promoter

and transcription factor binding sequences in DNA

51
Q

Amelogenin

A

stabilizes the amorphous Ca-P phase, control of apatite crystal
morphology and organization, control of enamel thickness.
Amelogenins have the ability to self-assemble into nanosperes and
thereby guide HAP crystal formation/growth.

52
Q

Ameloblastin

A

Cell adhesion protein, controls cell differentiation, maintains rod
integrity

53
Q

Enamelin

A

Cooperates with amelogenin to control mineral nucleation and
elongated growth

54
Q

Kallikrin 4

A

Digests enamel proteins during maturation stage facilitating their
removal and hardening the final layer of enamel

55
Q

Mmp-20

A

Cleaves amelogenin, ameloblastin and enamelin at the secretory stage
to produce stable intermediates with defined functions.

56
Q

enamel is formed by

A

ameloblasts

57
Q

what is enamel composed of?

A

90% amelogenin and 10% enamelin

58
Q

as apatite crystals grow — is removed

A

amelogenin

59
Q

Amelogenin is high in (4), but contains no (2)

A

proline, leucine, histidine and glutamine

hydroxyproline or cystine

60
Q

Two genes for amelogenin, one on the X (AMELX) and the other on the Y (AMELY) chromosome, which results in minor differences in the — between males and females

A

enamel

61
Q

dentin formation occurs before

A

formation of enamel (Reciprocal Induction)

62
Q

— differentiate from cells in the dental papilla

A

Odontoblasts

63
Q

odontoblasts secrete their organic matrix around the area that is directly
adjacent to the

A

inner enamel epithelium

64
Q

Odontoblasts move towards center of tooth forming the

— —

A

odontoblast process

65
Q

Odontoblast process secretes hydroxyapatite crystals and

mineralizes matrix forming the — —

A

mantle dentin

66
Q

(2) dentin form through different process

A

Primary and secondary

67
Q

major component of dentin

A

type 1 collagen (`90%)

68
Q

Dentin Sialophosphoproteins (DSPP)

A

Immediately cleaved after secretion into DSP,

DGP and DPP

69
Q

Dentin Matrix Protein 1 (DMP1)

A

Produced by odontoblasts and early-stage

osteocytes

70
Q

Bone Sialoprotein

A

Role in biomineralization

71
Q

Osteopontin

A

HA binding and contains an RGD motif,

mineralization inhibitor

72
Q

MEPE

A

Matrix Extracellular Phosphogylcoprotein,
contains an RDG motif and in bone appears to be
an inhibitor of mineralization

73
Q

cementoblasts (2)

A

acellular cementum

cellular cementum

74
Q

Cellular cementum

A

cementoblasts arising from

adjacent area of bone

75
Q

Acellular cementum

A

arising from dental follicle

76
Q

Acellular cementum

A

arising from dental follicle

77
Q

— cementum forms first

A

Acellular

78
Q

Acellular cementum

A

arising from dental follicle

79
Q

cementum contains (3)

A

cementoblasts
collagen
osteopontin, osteocalcin, osetonectin (SPARC), BSP, BAG75, others

80
Q

what is the PDL formed from?

A

fibroblast cells from the central follicle

81
Q

cells secrete collagen, which interacts with

A

fibers on the surface of adjacent bone and cementum

Applied Biochemistry (52 decks)

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