Proteins

Question 1

Proteins

Answer 1

Biopolymers of amino acids joined by peptide bonds

Question 2

Amino acids

Answer 2

molecules containing an amine group, carboxylic acid group, and a side chain that varies

Question 3

proteinogenic

Answer 3

natural amino acids; 22 amino acids that are used in polypeptides

Question 4

non-proteinogenic

Answer 4

amino acids that are not used for making proteins or amino acids that are produced indirectly (e.g. hydroxyproline)

Question 5

Unusual amino acids

Answer 5

expansions of the genetic code

Question 6

pyrrolysine and selenocysteine are only made when what is present?

Answer 6

selenium

Question 7

Amber

Answer 7

UAG stop codon

Question 8

Opal

Answer 8

UGA stop codon

Question 9

making a prokaryote timeline

Answer 9

minutes to hours

Question 10

making a eukaryote timeline (human cells)

Answer 10

hours to days

Question 11

why is translation in eukaryotes slower?

Answer 11

more complex, extra time needed for post-translational modification

Question 12

why are prokaryotes faster?

Answer 12

transcription and translation are coupled

Question 13

membrane bound ribosomes

Answer 13

On rough ER, proteins targeted for release

Question 14

free ribosomes

Answer 14

in cytosol, proteins used within the cell

Question 15

Ribosomes

Answer 15

2 subunits and are named according to rate of sedimentation (Svedberg is 10^-13 seconds)

Question 16

polysomes (polyribosomes)

Answer 16

translational parallel processing. More than 1 ribosome can be attached to single mRNA at a time

Question 17

polysomes were originally called what?

Answer 17

ergosomes

Question 18

Tetracyclin

Answer 18

antibiotic compounds isolated from dirt from graveyards; developed into aureomycin (which is a tetracycline). Tetracyclines bind reversible to the 30s subunit and prevents the binding of aminoacyl-t-RNA to the mRNA complex, PREVENTING BACTERIA FROM TRANSLATING NEW PROTEINS

Question 19

primary

Answer 19

sequence

Question 20

secondary

Answer 20

folding and coiling

Question 21

tertiary

Answer 21

interactions between side chains (R groups)

Question 22

quaternary

Answer 22

interactions between polypeptides

Question 23

N-terminus (amide)

Answer 23

targeting, survival. (First AA determines half life, post-translationally modified for further processing)

Question 24

N end rule

Answer 24

identity of N termal AA determines how long the peptide can last before it degrades

Question 25

C-terminus (carboxyl)

Answer 25

retention, sorting. KDEL most common sequence for ER retentions; post-translationally modified for further processing. Contains signals for later protein sorting.

Question 26

KDEL

Answer 26

most common amino acid sequence

Question 27

Polar Side Chains

Answer 27

AA side chains tend to gather on outside of the protein; can interact with water

Question 28

Non-polar side chains

Answer 28

AA side chains are buried on the inside of tight packed structure

Question 29

Secondary structure shapes are formed by what?

Answer 29

hydrogen bonds

Question 30

tertiary structure

Answer 30

3D protein structure, created by interaction between the side chains. Mostly determined by the primary structure

Question 31

dimer

Answer 31

two identical peptide chains bind together

Question 32

dimer

Answer 32

two identical peptide chains bind together

Question 33

heterodimer

Answer 33

two different peptide chains bind together

Question 34

N-linked glycosylation

Answer 34

sugar group is added covalently to the N terminus (it becomes a glycoprotein)

Question 35

Glycosylation occurs in what?

Answer 35

all eukaryotes but not prokaryotes

Question 36

If proteins accumulate in CYTOSOL

Answer 36

chaperone proteins are activated or produced to help re-fold misfiled proteins

Question 37

Unfolded protein response (UPR)

Answer 37

occurs when proteins occur in the ENDOPLASMIC RETICULUM

Question 38

what degrades misfiled proteins?

Answer 38

enzymes

Question 39

what refold misfiled proteins?

Answer 39

chaperones

Question 40

apoptosis

Answer 40

cell gives up/ death by cell

Question 41

Prions

Answer 41

Creutzfeldt-Jacob Disease/Mad Cow disease/bovine spongiform encephalothapy

Question 42

Prions

Answer 42

misshapen PrP protein capable of changing the shape of other proteins

Question 43

Sequencing: Edman degradation

Answer 43

Break off N-terminal AA one by one and run on gen to identify (labour intensive, similar to Sanger sequencing)

Question 44

Mass spectroscopy

Answer 44

measure mass to charge ration.

Question 45

BLAST

Answer 45

search tool you can put sequence into to see what the corresponding sequence/ gene is for (Basic Logical Alignment Search Tool

Question 46

Southern Blots

Answer 46

DNA

Question 47

Northern Blots

Answer 47

RNA

Question 48

Immunoblotthing: Western Blotting

Answer 48

rapid and sensitive assay for the detection and characterization of proteins that works by exploiting the specificity inherent in antigen-antibody recognition

Question 48

Immunoblotthing: Western Blotting

Answer 48

rapid and sensitive assay for the detection and characterization of proteins that works by exploiting the specificity inherent in antigen-antibody recognition

Question 49

Immunohistochemistry

Answer 49

using antibodies to specific proteins to identify their presence and location in tissue samples. let anatomy decide location.

Question 50

ELISA (Enzyme Linked ImmunoSorbent Assay)

Answer 50

detects presence of proteins in a sample. Inverse of western. (Antibody to substrate first, then add sample to see if it sticks to antibody)