ch 9 proteins and their synthesis

Question 1

r group properties

Answer 1

• charged
• hydrophilic
• hydrophobic
• aromatic

Question 2

primary structure

Answer 2

linear sequence of amino acids

Question 3

secondary structure

Answer 3

arises from interaction btw neighboring amino acids
- alpha helix or pleated sheet

Question 4

tertiary structure

Answer 4

interactions btw more distant amino acids or cofactors
- 3d

Question 5

quaternary structure

Answer 5

interactions btw multiple polypeptides
- dimer, trimer, tetramer
- homo - identical polypeptides
- hetero - different polypeptides

Question 6

polypeptide

Answer 6

chain of amino acids linked by peptide bonds

Question 7

3d structure of tertiary structure stabilized by

Answer 7

• hydrophobic interactions
• ionic interactions
• h-bonding
• van de waals forces

Question 8

2 major protein classes

Answer 8

• structural (myosin, actin, collagen)
• active (PEP carboxylase, endonuclease)

Question 9

sanger sequencing

Answer 9

determining amino acid sequence
- proteolytic enzymes cut btw specific amino acids to produce specific fragments
- movement through electrophoretic field depends on size and charge of fragments

Question 10

unambigous

Answer 10

1 codon, 1 amino acid

Question 11

degernate

Answer 11

1 amino acid, >1 codon

Question 12

3 features of the genetic code

Answer 12

1. each amino acid is specified by a group of three nucleotides, a codon, in the mRNA
2. the genetic code is non-overlapping
3. of the 64 possible codons, 61 encode individual amino acids. therefore most amino acids are specified by more than one codon

Question 13

5 components required for translation

Answer 13

mRNA - template for protein synthesis
amino acids - protein building blocks
tRNAs - carry aa to the ribosome, decode mRNA info
ribosome - RNP complex, catalyzes peptide bond formation
protein factors - IF, EF, RF

Question 14

tRNA

Answer 14

• adapter molecule for protein synthesis
• base-pairing btw tRNA and an mRNA codon specifies the aa to be inserted
• a cell must contain at least 20 different tRNA (one for each aa)
• aa are covalently attached to tRNA = charging

Question 15

aminoacyl-tRNA synthetase

Answer 15

charging accuracy is crucial for translation
- binds only one amino acid
- binds only the appropriate tRNA

Question 16

how does the cellular tRNA set relate to degeneracy

Answer 16

1. more than one tRNA species can be charged with the same amino acid — isoacceptors - most organisms contain at least 3 different tRNAs that are charged with serine
2. a single tRNA species can recognize more than one codon — wobble

Question 17

wobble

Answer 17

the ability of the 3rd nucleotide of the anticodon (5’ end) to pair imprecisely, allowing the anticodon to align with different codons
G-C or G-U pair
U-A pr U-G pair

Question 18

ribosome function

Answer 18

brings all components together
catalyzes peptide bond formation

Question 19

two subunits of ribosomes

Answer 19

small subunit - binds mRNA, decoding site
large subunit - catalyzes peptide bond formation

Question 20

APE

Answer 20

key site of interaction on the ribosome
A - amino acyl site - incoming tRNA binds
P - peptidyl site - tRNA temporarily carrying the elongating pp chain
E - exit site - empty tRNA leaves

Question 21

3 steps of translation

Answer 21

1. initiation
2. elongation
3. termination

Question 22

initiation (prokaryotes)

Answer 22

SSU binds to mRNA - start codon is positioned at P site
fMet-tRNA binds to the start codon - IF1 and IF2 ensure correct positioning
16S aligns with shine-dalgarno sequence to position the start codon at the P site
the large subunit recognizes the 30S initiation complex and binds - IF1 and IF2 are released

Question 23

shine-dalgarno sequence

Answer 23

ribosome binding site (RBS)
base-paring btw the shine-dalgarno sequence and the 16S rRNA aligns the start codon in the P site

Question 24

initiation (eukaryotes)

Answer 24

small subunit recognizes the 5’ cap and binds - i-tRNA and IF associated
mRNA is scanned processively for the 1st AUG (start codon)
large subunit binds - IF release, i-tRNA in P site

Question 25

elongation

Answer 25

continuing cycle of peptide bond catalysis

Question 26

termination

Answer 26

stop codon recognized by a RF RF binds in the A site hydrolysis breaks the bond btw the tRNA (P site and the PP chain ribosome subunits dissociated from each other and mRNA

Question 27

nonsense mutation

Answer 27

introduction of a stop codon leading to premature termination of translation - generally biologically inactive - may be toxic

Question 28

3 types of post-translational processing

Answer 28

protein folding covalent additions of chemical groups or peptides to defined positions/sequences protein sorting and trageting

Question 29

post-translational processing

Answer 29

chaperonin complexes aid protein folding

Question 30

chemical modifications

Answer 30

- addition of chemical groups - addition of polypeptides - addition of complex molecules - cleavage - amino acid modification

Question 31

phosphorylation regulates:

Answer 31

enzyme activity protein-protein interactions protein-nucleic acid interactions cellular localization

Question 32

protein degradation

Answer 32

tagging a protein with ubiquitin targets a protein for destruction - small peptide attached to lysine side chains

Question 33

signal sequence

Answer 33

the amino-terminal sequence of a secreted protein which is required for the export of the protein from the cell

Question 34

nuclear localization sequence (nls)

Answer 34

the sequence of a protein required for its transport from the cytoplasm to the nucleus