Ls 3 Lecture 3

Front 1

The alpha helix

Back 1

many membrane proteins

h bonds for stability

not all amino acids will allow you to form alpha helix

Front 2

Myoglobin

Back 2

primary mode of alpha helixes in 3-D shape. gets shape by "chaperones" which allow the protein to fold

has a heme group

Front 3

heme group

Back 3

allows iron to bind, and hence O to bind

Front 4

Histidine

Back 4

can accept or donate an O

pH of solutions in cells are usually around 7 which means 1/2 of histidine is charged, half if uncharged. means it can change charge easily

found in a lot of active sites

Front 5

How do you determine the pK?

Back 5

you look at what pH do you pull a charge on or off

pKa of amino acids far away from 7 don't readily change their charge

Front 6

Which amino acids have hydroxyls and you can easily add a phosphate?

Back 6

serine and threonine

Front 7

Why are all active sites like a vacuum?

Back 7

because the electrical force is very strong

-water shield electric force and reduces charge

Front 8

What is the only covalent bond?

Back 8

the primary chain of amino acids

Front 9

Non template strand

Back 9

the strand that is from the gene

Front 10

template strand

Back 10

the copy of the gene that is used in transcription and codes for the mRNA

Front 11

Proteins are _____ made up of amino acids.

Back 11

polymers

Front 12

a protein of n amino acids can form ___ # of proteins.

Back 12

20^n proteins

Front 13

tertiary structure

Back 13

domain folding

ex. immunoglobin (globular domain)

Front 14

Quarternary structure

Back 14

subunit mix

Front 15

Acidic Amino Acids

Back 15

R groups donate H readily in aqueous environment and have a negative charge

Front 16

Basic Amino Acids

Back 16

acquire a H readily in aqueous environments and have a positive charge

Front 17

Why is pK important?

Back 17

the side chains determine the characteristic properties of each amino acid within a protein

amino acids have different pK's that determines their net ionic charge

(determines wether it will have a net charge at a given pH)

Front 18

What is the only amino acid that can donate a proton at neutral pH

Back 18

Histidine

Front 19

Polar amino acids that are uncharged but able to form H bonds

Back 19

serine
threonine
asparagine
glutamine

Front 20

aromatic amino acids

Back 20

phenylalanine
tyrosine
tryptophan

Front 21

hydrophobic amino acids

Back 21

alanine
valine
isoleucine
leucine
methionine
phenylalanine
tyrosine
tryptophan

strings of these are prevalent in membrane proteins

Front 22

What amino acid makes S-S disulfide bonds?

Back 22

cysteine

Front 23

What amino acid is put at bends?

Back 23

glycine

Front 24

What amino acid is put at kinks?

Back 24

proline

Front 25

Why are proteins linear polymers of amino acids?

Back 25

proteins usually have 100 to 2000 amino acids

amino acids are joined by peptide bonds

chemical structure of the peptide bond is key in defining the stable 3D structures of proteins

Front 26

What does peptide bond formation do?

Back 26

removes water

Front 27

Why is the peptide unit planar?

Back 27

because the carbon-nitrogen bond has partial double bond character due to resonance

(double bonds cannot move back and forth)

Front 28

At neutral pH, the backbone of proteins is uncharged except _____

Back 28

for the N terminus and the C terminus

(NH and CO in backbone are available for H-bonding)

Front 29

What is the role of bonds in the 3D structure of proteins?

Back 29

covalent bonds hold the chain of a.a. together

non covalent bonds are responsible for the 3D structure

H-bonds: C=o --H-N

Ionic bonds: Co2- --NH3 +

Van Der Waals interactions and hydrophobic bonds: CH3 --CH3

Front 30

Globular domain is what shape?

Back 30

round

Front 31

fibrous domain has what characteristic?

Back 31

strong helices

Front 32

What is the viral membrane?

Back 32

place that will hook onto cells

Front 33

What are protein motifs?

Back 33

specific combinations of secondary structures that have a particular topology and are organized into characteristic 3D structure

ex. coiled coil
ex. dimer formation by hydrophobic amino acids

Front 34

How do proteins work?

Back 34

binding to other molecules

catalyzing chemical reactions

Front 35

protease

Back 35

degrade protein

Front 36

kinase

Back 36

add phosphate to a protein

has a pocket for ATP so it's an ATP binding protein

Front 37

phosphatase

Back 37

remove phosphate

Front 38

RNA polymerase

Back 38

synthesize RNA

Front 39

Ribuonuclease

Back 39

RNase-degrades RNA

Front 40

What can protein function be measured by?

Back 40

affinity (binding strength), specificity (binding preference), and velocity (speed of reactions)

Front 41

How do enzymes catalyze chemical reactions?

Back 41

by bringing the substrate to its transition state to make the reaction go faster.

transition state= position things have to be in, in order to react.

brings two substrates together at the right orientation, changes charge of substrate

induces strains in chemical bonds of the substrate molecule

Front 42

Antibodies (immunoglobins Ig)

Back 42

produced in response to foreign molecules

highly specific, can tell proteins that differ by a single a.a.

inducing agent = antigen

region of antibody that binds to antigen = complementarity determining regions (CDR).

Front 43

Epitope

Back 43

region of an antigen that the antibody recognizes. part of the antigen that will actually bind the antibody

Front 44

HbS mutation (Dr. Frederick Sanger)

Back 44

compared hemoglobin from normal and anemia patient

-used peptide fingerprinting and peptide sequencing methods

-found single amino acids changes from glutamate to valine in the HbS mutations

-proteins usually have charges, so he ran the test to recognize abnormal spots

changing the hydro phobic for a hydro phillic amino acid
-can be very serious

Front 45

Feedback Inhibition

Back 45

the amount of the end product is high it inhibits an enzyme that functions early in the reaction pathway

+ feedback is destabilizing (explosion)

- feedback is stabilizing (doesn't waste metabolic energy)

common in biosynthesis such as amino acid pathways because you only make what you need

Front 46

Competition of feedback

Back 46

the inhibitor can fit into the active site but cannot leave
-competes with real substrate from getting in

-comp. inhibitor usually has similar chemical structure as the substrate
-inhibitor are usually the product of the reaction

Front 47

Allosteric Regulation

Back 47

allosteric refers to shape

changes of protein conformation and activity upon binding to a ligand (activator, inhibitor, substrate)

ex. hemoglobin, binds to O, lowers the km of other subunits which = higher affinity of protein to O

Front 48

What is an example of an allosteric regulation?

Back 48

ligand induced activation

binds to a non-substrate ligand.
cAMP and GTP are common regulatory ligands that modify protein activity
(g proteins have high binding affinity and short lifetime which is good for the system)

Front 49

What does kinase have the ability to do?

Back 49

phosphorylate proteins

Front 50

Chemical Modification (of protein function)

Back 50

can either activate or inhibit protein activity

ex. reversible modification like phosphorylation (using ATP to phos. proteins)

Front 51

What function does phosphorylation serve?

Back 51

it provides a lot of enzymatic activity in cells

-works with cAMP

Front 52

What is bacteriorhodopsin?

Back 52

a membrane protein

rhodopsin converts light

majority of integral proteins are made of alpha helices

Front 53

Protein Synthesis

Back 53

transcription (DNA --> mRNA) and translation (mRNA --> proteins) are the most important regulation of protein level

Front 54

Protein Degradation

Back 54

level of proteins are precisely regulated by ubiquitination and proteosome degradation

Front 55

What is "RNA"

Back 55

the enzyme that allows for protein synthesis