Chem 7

Front 1

What are the worker molecules that caryr out the processes of life encoded by the genome

Back 1

proteins

Front 2

What four groups are covalently bonded with the alpha carbon of an amino acid?

Back 2

1) amino group 2) carboxylic acid group 3) hydrogen atom 4) r-group

Front 3

At a pH of 7, are most amino acids ionized?

Back 3

Yes, but have no net charge (COO-, NH3+)

Front 4

Name the hydrophobic groups

Back 4

Alanine, valine, isoleucine, leucine, methionine, phenyulalanine, tyrosine, tryptophan

Front 5

Where do hydrophilic AAs tend to be located?

Back 5

On the outside of the protein where they make it water soluble

Front 6

What kinds of AAs tend to be hydrophilic

Back 6

Acidic, basic, polar

Front 7

Name the basic AAs

Back 7

Lysine, Arginine, Histidine

Front 8

Name the acidic AAs

Back 8

Aspartic acid, glutamic acid

Front 9

Name the polar AAs

Back 9

Serine, theronine, aspargine, glutamine

Front 10

Describe glycine

Back 10

Simplest AA, R=H

Front 11

Describe proline

Back 11

imino acid -> R has N in ring. This forms a kink that limits the folding of the chain.

Front 12

Describe cysteine

Back 12

Has a sulfhydryl moiety in R group -> can form disulfide bridges

Front 13

How are all natural AAs oriented?

Back 13

L-stereoisomers

Front 14

Describe the formation of peptide bonds

Back 14

It is a dehydration b/t CO[OH] and [H]NH -> CONH

Front 15

What forms the backbone of polypeptides?

Back 15

alpha carbons of AAs

Front 16

Name six functions of proteins

Back 16

1) enzymes 2) structural 3) transport 4) regulatory 5) signaling 6) motor

Front 17

What is collagen found in?

Back 17

Bone matrix, tendoms, ligaments, cartilage

Front 18

Name some protective proteins

Back 18

fibrinogen and thrombin

Front 19

Name some transport proteins

Back 19

hemoglobin, myoglobin, serum proteins [albumin -fatty acid transport, lipoprotins-lipoprotein transport], membrane carriers [facilitated diffusion, active transport], storage proteins [e.g. ferritin], docking proteins

Front 20

Name some regulatory proteins

Back 20

Transcription proteins, chaperon proteins, toxins [e.g. snake venom]

Front 21

Name some signaling proteins

Back 21

hormones, receptors [hormones/neurotransmitters], transducers (e.g. G-proteins), Connecons, Synapsisns, Channel proteins, Protective proteins (e.g. antibodies)

Front 22

Name two motor proteins

Back 22

Actin and Myosin

Front 23

Describe the difference between a simple and conjugated protein

Back 23

Simple is just polypeptides

Front 24

Describe the difference between a fibrous and globular protein

Back 24

Fibrous are rope-shaped strands, water insoluble, used for structures. Globular are globe-shaped, water soluble w/ mobile/dynamic function.

Front 25

Describe the difference between monomeric and oligomeric proteins

Back 25

Oligomeric proteins are composed of multiple polypeptides (protomers), which may or may not be covalently bonded

Front 26

What is primary protein structure?

Back 26

linear arangement of AAs

Front 27

What is secondary protein structure?

Back 27

The helical or zigzag conformation d/t hydrogen bonding within the peptide backbone (a-helix, b-sheet)

Front 28

Where do you start numbering polypepides from?

Back 28

The NH end

Front 29

What is a peptide?

Back 29

Short (<20-30)

Front 30

What is a polypeptide?

Back 30

Long (up to 4000 residues)

Front 31

What is a protein

Back 31

A polypeptide or complex of polypeptides with a well-defined three-dimensional structure

Front 32

What is protein conformation?

Back 32

The higher levels of structure beyond primary struture

Front 33

What dictates a protein's three-dimensional structure?

Back 33

Weak bonds w/in and b/t polypeptide chains

Front 34

Describe A-helix

Back 34

The H of the imino group bonds to the o on the carbynl group of the fourth amino acid behind it. It forms a right-handed helix. This forms a rod from which R-groups protrude.

Front 35

Describe B-sheet

Back 35

Two or more polypeptide chains or two regions of one chain are tied together by h-bonds. 5-8 residue segments. R-groups protrude from upper and lower surfaces of the sheet. Often forms floor of binding pocket or hydrophobic core of proteins. (H of imino group bonds w/ o of carbynl group)

Front 36

Describe B-sheet turns

Back 36

3-4 residues at the surface form a bend which redirects chain toward the interior of the protein and allows tight folding/compact shape. Often contain proline or glycine.

Front 37

What AAs break a-helix?

Back 37

proline and hydroxyproline

Front 38

What is tertiary structure?

Back 38

The overall form or three-dimensional arangement of AA residues of a polypeptide chain.

Front 39

What interactions (5) produce tertiary structure?

Back 39

1) H-bonding b/t hydrophilic R-groups and water 2) ionic bonds b/t oppositely charged acidic and basic R-groups 3) hydrophobic interactions b/t hydrophobic r-groups 4) intrachain disulfide bonds 5) presence of imino acides (*proline can't H-bond -> H is removed in peptide dehydration)

Front 40

Is tertiary structure rigid?

Back 40

No, it undergoes minute fluctuations d/t weakness of stabalizing bonds

Front 41

What are motifs?

Back 41

particular combinations of secondary structures - "signatures for specific functions"

Front 42

What is the helix-loop-helix motif?

Back 42

Found in calcium-binding proteins and DNA-regulating proteins

Front 43

What is the zinc finger motif?

Back 43

Zn ion is bound by histidine residues of an alpha helix and cystein residures in a pair of antiparellel beta strands. Found in DNA or RNA-binding transcription proteins.

Front 44

What is the coiled coil motif?

Back 44

Amphipathic a-helices created by hydrophobic R-groups on one side and hydrophillic R-groups on the other side of the helix. Allows fibrous proteins to self-assemble into oligomers.

Front 45

What are domains?

Back 45

Parts of proteins with specific functions. Large proteins tend to be mosaics of different domains and thus perform different functions simultaneously.

Front 46

What is quartenary structure?

Back 46

The manner in which protomers of an oligomeric/multimeric protein are associated.

Front 47

What holds together polypeptides?

Back 47

Numerous weak bonds, sometimes disulfide bridges

Front 48

What are multimeric proteins?

Back 48

Enzymes in a pathway may be associated as subunits in a multimeric protein -> increased efficiency

Front 49

What is quininary structure?

Back 49

The manner in which a protein must be associated with some other large molecule(s) or membrane components in order to function (e.g. the membrane/macromolecular assemblies)

Front 50

What level of structure do molecular machines represent?

Back 50

Quintinary

Front 51

What are homologous proteins?

Back 51

Proteins w/ similar AA sequences/3d structures. Common evulationary ancestor. (e.g. monomeric O2-binding protein is ancestor of hemoglobin, myoglobin, plant leghemoglobins.

Front 52

What is the native state?

Back 52

The most stable conformation of a protein.

Front 53

What is denaturation?

Back 53

The loss of native state d/t the breaking of weak bonds in the molecule.

Front 54

What bonds are not affected by denaturation?

Back 54

The peptide bonds (primary structure)

Front 55

What configuration do denaturated proteins assume?

Back 55

Random coil

Front 56

What causes denaturation?

Back 56

changes in temperature or pH

Front 57

Is denaturation reversible?

Back 57

In some cases if the temp or pH is reversed, but it takes a while (minutes)

Front 58

What do chaperones do?

Back 58

They increase the efficiency of proper protein folding. Found in all organisms. Molecular chaperones bind to proteins as they are synthesized in the ribosomes and prevent aggregation and degradation.

Front 59

What are chaperonins?

Back 59

Huge cyllindrical hollow proteins that protect proteins from interference while binding.

Front 60

How many types of AAs may be present in proteins?

Back 60

Initially formed w/ only 20 AAs; they wind up being composed of > 100 AAs d/t chemical modifications

Front 61

What is acetylation?

Back 61

Addition of acetyl to N-terminus; 80% of proteins; prevents degradation.

Front 62

What marks cystolic proteins for degreadation?

Back 62

Ubiquitin. It marks the protein for degradation in a proteasome.

Front 63

How are misfolded proteins recognized?

Back 63

Misfolding exposes normally hidden hydrophobic residues, which are identified and ubiquified.

Front 64

How are viral proteins identified?

Back 64

They are ubiquitinated and degrades, and their peptide fragments are transported to the ER where they bind w/ MHC, which is then expressed on the cell surface -> attack by cytotoxic T-cells.

Front 65

What can misfolded proteins cause?

Back 65

Slowly-developing degenerative diseases. As the proteins are broken down, insoluble plaques of peptide fragments build up (e.g. Alzheimers, Parkinsons)