Biochemistry Lecture 4/5

Front 1

Amino acids generally have ____ center except for _____.
They are commonly found in their ____ form.

Back 1

A Chiral center
Glycine
L-amino acid form (amino on left) is more commonly found in nature. D-acids maybe found.

Front 2

Proline

Back 2

Differs from other amino acids. Has a secondary amino group and forms rigid ring structure.
Bonds with proline lead to bends in protein shape and interrupts alpha-helix.
Collagen is rich in proline.

Front 3

Nonpolar, aliphatic side chain AA's:

Back 3

Aliphatic -do not contain rings
Alanine (A), Glycine (G) and Proline (P) - cyclic,
Branched:
Valine (V), Leucine (L) and Isoleucine (I)

Front 4

Aromatic Side Chains:

Back 4

Phenylalanine (F) - Non-Polar
Tryptophan (W) - Slight Polar
Tyrosine (Y) - Polar - Has O - more water interaction

Front 5

Sulfur-containg AA's:

Back 5

Methionie (M) and
Cysteine (C):
-constains sulfhydryl groups, 2 cysteine can be used to form disulfide bond.
-uncharged and polar at neutral pH

Front 6

What is responsible for UV light absorbance?

Back 6

Aromaticity and Trp is primary with absorbance at 280 nm that is 4x higher than Tyr.
F does not show much absorbance

Front 7

Polar, uncharged AA

Back 7

Serine (Ser)
Threonine (Thr)
Cysteine (Cys)
Asparagine (Asn)
Glutamine (Gln)

Front 8

Charged AA

Back 8

Acidic - a-AA carboxyl group is negatively charged (pk ~4)
Aspartic Acid (Asp)
Glutamic Acid (Glu)
Negative will want to go to water - act polar.

Basic - amino group of apha-AA positively charged at physiological pH. (pk >10)
Lysine (Lys)
Arginine (Arg)
Histidine (His)

Front 9

Alanine

Back 9

Is non-polar, aliphatic.
Has two ionizable groups giving 2 pka that gives two buffering regions. Can act as either a base or an acid. Most AA are not suitable as physiological pH, to high or low

Front 10

Histidine

Back 10

Is a basic positively charged AA.
Histidine chain has imidazole ring (pka 6) which allows buffering of a possible drop in pH.
-Hemoglobin is rich in histidine.

Front 11

How are biological active amines formed?

Back 11

a-AA are precursors for active amines. Amino group is retained and a-carboxyl group is removed as CO2(decarboxylated)

Front 12

GABA

Back 12

gamma-aminobutyric acid, formed by decarboxylation of a-carboxyl group of glutamate

Front 13

Histamine

Back 13

Formed by decarboxylation of histidine.

Front 14

How is serotonin made?

Back 14

Serotonin is made from Tryptophan which is first hydroxylated to 5-hydroxytryptophan and then decarboxylated.
Serotonin is important in pain perception and regulation of sleep, temperature and blood pressure.

Front 15

Prozac

Back 15

Is an antidepressant drug that blocks serotonin elimination from synaptic clef. Inhibits the re-uptake of serotonin enhancing action of neurotransmitter.

Front 16

Catecholamines

Back 16

Include dopamine, norepinephrine and epinephrine.
Which are formed from tyrosine.
Dopamine and norepinephrine are mainly neurotransmitters. Epi and Norepi may act as hormones.

Front 17

Dopamine

Back 17

Acts as neurotransmitter, or can be used as intermediate for synthesis of norepinephrine or epinephrine.
Tryosine is first hydroxylated to dihydroxy-phenylalanine (L-DOPA) ---> decarboxylated to dopamine (first catecholamine).

Front 18

Important of R groups of proteins

Back 18

Determine how a protein will fold based on charged and polarity. Polar AA cluster on surface of soluble proteins and non-polar cluster on surface of membrane proteins.

Front 19

What determine the 3-D structure of protein?

Back 19

The amino acid sequence( primary structure) will determine the 3-D.
Covalent bonds art the strongest.
Non-covalent bonds are weaker:
H bonds are weaker
Ionic bonds can be strong
VDW (london) bonds are the weakest

Front 20

Bonding of secondary structures?

Back 20

Are stabilized by hydrogen bonds, involving atoms of peptide bonds. C=O and N-H binding.
Beta sheets or a-helix
-3.6 residues per turn
-H bonds are perpendicular (parallel to axis)
-R groups are direct outside of helix

Front 21

What cause interruption of a-helix?

Back 21

Electrostatic repulsion or attraction of AA with charged R-groups. Bulkiness of R-groups and helix disruption by proline and glycine residues.

Front 22

What holds the A and B chains of insulin together?

Back 22

Held by covalent inter-chain disulfide bonds. Bond folds the hormone which is needed for receptor recognition.
C-peptide is needed for proper formation of this bind. Later cleaved and released from insulin into blood.

Front 23

Chaperone function and HsP60

Back 23

Facilitate proper folding - knowing as heat shock proteins (HsP). Hsp60 have barrel shape and required for correct folding of cellular proteins, used to aid folding protein after crossing cellular membrane.

Front 24

How to break hydrogen bonds?

Back 24

Heat and 5-10M urea and salt

Front 25

How to break ionic bonds?

Back 25

Strong acids or bases

Front 26

How to break hydrophobic interactions?

Back 26

1-2% SDS detergent

Front 27

How to reduce disulfide bonds?

Back 27

Use thiol containing compounds?
B-mercapteoethenaol or 2-mercaptoethanol.

Front 28

Function of ubiquitin?

Back 28

Proteins that are misfiled, old or oxidized are tagged by this protein to be degraded in proteasome.
-Alzheimers and Prion disease results in accumulation of these abnormal proteins .

Front 29

TSE - Transmissible Spongiform Encephalopathy - Prion disease

Back 29

Diseased brain develops holes resulting in dementia- leading to death.
-Infectious agent is single protein, named PrP which is normal constituent in brain tissue found on surface of neurons.
-illness occurs from abnormal PrP(sc from scrapie)
-abnormal protein highly infective and not destroyed
-Results from changing the a-helic to b-pleated sheet