Translation and Protein Structure

Question 1

amino acid

Answer 1

made up of an alpha carbon, an amino group, a carboxyl group, a hydrogen atom, and a R group

Question 2

hydrophobic amino acids

Answer 2

do not readily interact with water or form H-bonds; nonpolar R groups composed of hydrocarbon chains or uncharged carbon rings ten to aggregate with each other → stabablized via van der Waals forces; R groups are typically buried in the interior of folded proteins

Question 3

polar R group amino acids

Answer 3

permanent charge sensation; hydrophilic → tend to form H-bonds with each other or with water molecules; located on the outside surface of a folded protein

Question 4

R groups of basic and acidic amino acids

Answer 4

typically charged → stronly polar; located on the outside surface of folded proeteins; can form ionic bonds; basic amino acids → R group gains a protion (+ charged); acidid amino acids → R group loses a proton (- charged)

Question 5

glycine

Answer 5

R group = hydrogen; symmetric, nonpolar, and small; allows for free rotation around the C-N bond → increasing flexibility of polypeptide backbone

Question 6

proline

Answer 6

R group = linked to amino group; creates a kink in the polypeptide chain → restricting the rotation of C-N bond and putting contraints on protein folding

Question 7

cysteine

Answer 7

SH group; forms S-S bond; covalently joins R groups

Question 8

peptide bond

Answer 8

bond fomred between two amino acids; carboxyl group of one reacts with the amino group of the next → releases H2O (condensation reaction)

Question 9

polypeptide (protein)

Answer 9

polymer of amino acids connected by peptide ponds; one amino and one carboxyl end

Question 10

amino acid residues

Answer 10

amino acids that are incorperated into a protein

Question 11

primary structure

Answer 11

sequence of amino acids in a protein whcih determins how the protein will fold

Question 12

secondary structure

Answer 12

interactions between stretches of amino acids in a protein; stabalized by hydrogen bonds in the polypeptide backbone

Question 13

tertiary structre

Answer 13

longer-range interactions between secondary strcuctures; forms the 3D shape of protein

Question 14

quaternary structure

Answer 14

protein made up of multiple polypeptides that interact with each other

Question 15

alpha helix

Answer 15

right-handed coil; R group projects outwards

Question 16

beta sheet

Answer 16

folds back and forth on itself; R groups project alternatively above and below the plane; can be parallel or aniparallel

Question 17

denatured

Answer 17

unfolded protein

Question 18

translation

Answer 18

sequence of bases in mRNA specifies order of sucessive amino acids that are added to a newly senthesized polypeptide chain

Question 19

ribosomes

Answer 19

structures of RNA and protein that bind with mRNA; the site of translocation; located in the cytoplasm; contains the A, P and E site

Question 20

codon

Answer 20

each non-overlapping group of three adjacent nucleotides; each codon in mRNA codes for a single amino acid in the polypeptide chain

Question 21

tRNA

Answer 21

matches amino acids to mRNA codons; carries out the translation (links the proper amino acid to the proper codon); always has CCA at its 3’ end

Question 22

aminoacyl tRNA synthase

Answer 22

connects specific amino acids to specific tRNA molecules; riectly responible for translating codon sequence in nucleic acid to a specific amino acid in a polypeptide chain (links proper amino acid to proper tRNA)

Question 23

anticodon

Answer 23

pairs with the complimentary codon in mRNA; made up of three bases in anticodon loop

Question 24

genetic code

Answer 24

most codons specify an amino acid according to a genetic code

Question 25

initiation codon

Answer 25

codon at whcih translation begins; doed by AUG which specifies Met; polypeptide synthesis starts from amino and goes to the carboxyl end

Question 26

stop codons

Answer 26

UAA, UAG, UGA

Question 27

initiation

Answer 27

initiator AUG codon is recognized → Met is established at the first amino acid in the new polypeptide chain

Question 28

elongation

Answer 28

sucessive amino acids are added one by one to the growin chain

Question 29

termination

Answer 29

the addition of amino acids stops → completed polypeptide chain is released from the ribosome

Question 30

initiation factors

Answer 30

(in eukaryotes) one group of initiation factors binds to the 5’ cap that is added to the mRNA durring processing → factors recruit a small subunit of the ribosome while other factors bring up a transfer RNA charged with Met → the initiation complex moves along the mRNA until it encounters its first AUG triplet

Question 31

elongation factors

Answer 31

bound to GTP molecules → break their high-energy bonds to provide energy for elongation of polypeptide

Question 32

release factor

Answer 32

ribosome encounters a stop codon → protein release factor binds to its A site → bond connecting the polypeptide to tRNA breaks → creates carbonyl terminus of polupeptide completing the chain → small and large ribosomal subinits dissociate from mRNA and from each other

Question 33

polycistronic mRNA

Answer 33

formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA; allows for the coding of more than one protein

Question 34

operon

Answer 34

group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter

Question 35

protein family

Answer 35

a group of proteins that are structurally and functionally related as a result of shared evolutionary history

Question 36

mutation and selection

Answer 36

sequences of amino acids can be altered by mutations → affects the protein functions

Question 37

folding domains

Answer 37

form → function; genes that gain new folding domains gain additonal functions provided by said folding domain