Biochemistry Ch 1 - AA, Peptides, Proteins

Question 1

Central Dogma

Answer 1

DNA -> RNA -> Protein

Question 2

Replication

Answer 2

DNA copies itself

Question 3

Transcription

Answer 3

DNA copied into RNA

Script for using nucleic acids

Question 4

Translation

Answer 4

RNA translated into protein

Translating nucleic acids into amino acids

Question 5

Reverse Transcription

Answer 5

Reverse Transcriptase makes RNA into complementary cDNA

Retroviruses (HIV)

Question 6

ncRNA

Answer 6

Noncoding RNA, function as tRNA or rRNA within the cell

Skips the last step of translation into protein

Question 7

Epigenetics

Answer 7

Changes of gene activity

DNA sequence modified resulting in different phenotype but original DNA sequence stays the same

All DNA the same in different cells (muscle vs epithelial) yet they don’t look or act the same

Question 8

Amino Acid Structure

Answer 8

Carboxyl acid group (HOOC)
Amino group (NH3)
H atom 
R group - different in every AA
Alpha carbon - center

Question 9

Enantiomers

Answer 9

Pair of AA that have mirror image of each other.

L-aa (left amino group) (the ones made in humans)
D-aa (right amino group)

Question 10

Isoelectric point of AA (pI)

Answer 10

Iso=equal. Neither pos or neg charge

Net charges change when H ions are added or removed. Changing pH

Low pH = inc H+ = amine +1 charge (POS AA)

High path = inc OH- = carb group -1 charge (NEG AA)

(pKa1 (amino) + pKa2 (carb)) / 2 = pI

Question 11

Zwitterion

Answer 11

Hybrid

AA that has a net zero charge

Because NH3 is (+) and COOH is (-) charged

Question 12

Peptide bond

Answer 12

Connects 2 AAs

COOH looses OH and NH2 looses H creating H2O

N=C

Double bond so can’t move

Question 13

α - helix (secondary structure)

Answer 13

AA helix where C=O group form a hydrogen bond with N-H group 4 AAs does the spiral.

R groups just stick out

Question 14

β - pleated sheet (secondary structure)

Answer 14

Antiparallel sheet: AA starts with Carboxyl group and the second AA below starts with Amino group
Symmetrical hydrogen bonds: 1AA + 1 AA

Parallel sheet: both AA start with Carboxyl group.
Unsymmetrical hydrogen bonds: 1 AA binds with 2 AA

N-H + O=C

Question 15

Tertiary structure

Answer 15

Secondary structures coming together where AA side chains interact with each other

H bonds, ionic bonds, disulfide bonds

Question 16

Hydrolysis

Answer 16

Breaking the peptide bond

Question 17

Acid Hydrolysis

Answer 17

Strong acid + heat to break peptide bond

Question 18

Proteolysis

Answer 18

Protease breaks the peptide bond

Specific - choose which AA to break

Question 19

Trypsin

Answer 19

Protease that breaks carboxyl side like Arginine or Lysine

Produced by pancreas to digest food

Question 20

Histidine

Answer 20

-pKa 6.5 which is close to physiological pH 7.4

Can exist as protonated (+) and deprotonated (-) forms

Can stabilize and destabilize a substrate

Question 21

Protonated

Answer 21

Protonated

Question 22

Deprotonated

Answer 22

pH > pKa of AA = negative charge

Question 23

Proline

Answer 23

Has a secondary alpha amino group

The side chain forms a second bond with the alpha Nitrogen

Alpha helix breaker = adds a kink to the α helix

Question 24

Glycine

Answer 24

Side chain is just one H atom

No chiral carbon = optical activity under polarized light

Very flexible

Alpha helix breaker = adds a kink to the α helix

Question 25

Cysteine

Answer 25

Side chain has a thiol group = sulfur and hydrogen (-SH) Can form a disulfide bond if close to another Cystine

Question 26

Disulfide Bridge

Answer 26

Redox reaction: OIL RIG Oxidation is Loss Reduction is Gain When 2 Cystines are next to each other they are in reducing form (have 2 extra H) 2 H float away (oxidation) creating a bond between the Sulfides in the EXTRACELLULAR space

Question 27

Cysteine vs Cystine

Answer 27

e (for electron) lost during disulfide bond formation It was oxidized (H fell off)

Question 28

Amino Group

Answer 28

NH3. H+ acceptor Basic. The Nitrogen is happy making it Pos (+) pKa ~ 9

Question 29

Carboxylic Acid Group

Answer 29

COOH H+ donor Acidic Neg (-) charge pKa ~ 2

Question 30

pK

Answer 30

Negative log of acid dissociation constant

Question 31

Non-polar, Hydrophobic AA

Answer 31

H2O Haterz Alkyl (7) - CH? Aromatic (2) -

Question 32

Polar, Hydrophilic AA

Answer 32

H2O lovers Contain an O or Sulfur atom Neutral (6) - Acidic (2) - have COOH acid Basic (3) - have N (very positive)

Question 33

Alkyl Group

Answer 33

Non polar, hydrophobic Contain 1 to 4 carbons Glycine - has only H for the R group Alanine - Methionine - has but methyl makes it nonpolar Isoleucine - Valine - Leucine - Proline-cyclic. Connects to amino group from α-Carbonsbbmn

Question 34

Aromatic Group

Answer 34

Non polar, hydrophobic Phenylalanine - benzyl side chain Tryptophan - lg. Double ring with N

Question 35

Neutral Group

Answer 35

Polar, hydrophilic Have —OH group (amide) ``` Serine Threonine Asparagine Glutamine Cysteine -> cystine Tyrosine ```

Question 36

Acidic Group

Answer 36

Polar, hydrophilic Have —COOH- group (carboxylate) Aspartic Acid -> aspartate Glutamic Acid -> glutamate Donate their hydrogen and left in anion form

Question 37

Basic Group

Answer 37

Polar, hydrophilic Have pos charged N atoms Histidine Lysine Arginine

Question 38

Conformational Structure

Answer 38

Proper 1°, 2°, 3°, 4° Structures completing the final protein Active 3D structure

Question 39

Temp Denaturation

Answer 39

Breaks the bonds of 2°, 3°, 4° 1° structure ok

Question 40

pH Denaturation

Answer 40

Breaks ionic bonds in 3° abs 4° 1° and 2° structures are ok Like vinegar (H+)

Question 41

Chemical Denaturation

Answer 41

Break hydrogen bonds in 2°, 3° and 4° 1° structure ok

Question 42

Enzyme Denaturation

Answer 42

All bonds broken in 1°, 2°, 3°, and 4° structures