lecture 6

Question 1

what are proteins made up of?

Answer 1

proteins are made up of alpha amino acid monomers that are linked to peptide bonds

Question 2

what is the polymer of protein?

Answer 2

dipeptides and polypeptides with three or more amino acids linked together by peptide bonds

Question 3

what determines the functions of proteins?

Answer 3

the shape and amino acid sequence

proteins are in almost every cellular function

Question 4

what is the monomer of proteins?

Answer 4

amino acids

Question 5

what is the structure of amino acids?

Answer 5

alpha carbon attached to an amino group and a carboxyl group

Question 6

what types of forms can amino acids occur in?

Answer 6

a,b,y forms

alpha, beta, y=third carbon

Question 7

what is GABA?

Answer 7

gamma-aminobutyric acid

y-amino acid that functions as a neurotransmitter that is responsible for neuron firing ( helps you relax )

Question 8

What are D and L isomers of amino acids?

Answer 8

enantiomers

Question 9

which isomers ( D or L ) of amino acids is used as building blocks of proteins?

Answer 9

L isomers

Question 10

True or false

Amino acids are great biological buffers?

Answer 10

true
-they maintain the pH range of cells

Question 11

what do amino acids do at a low pH?

Answer 11

the carboxyl and amino group accept a proton and becomes protonated

-NH3+

Question 12

what do amino acids do at a high pH?

Answer 12

the carboxyl and amino group donates a proton and becomes dissociated

-COO-

Question 13

what are zwitterions?

Answer 13

the term for when amino acids are present in their dipolar ionic state

Question 14

what do the chemical and physical properties of the R group in amino acids do?

Answer 14

it determines the unique characteristics of a particular amino acid.

Question 15

Are the R groups polar or non polar?

Answer 15

non polar

Question 16

Are the R groups polar/electrically charged or non polar?

Answer 16

polar/electrically charged

look for positive charge (+) or look for carboxyl or hydroxyl

Question 17

the structural and functional diversity of proteins is based on what?

Answer 17

based on the different arrangements of amino acids.

Question 18

proteins predominantly made of leucine would be hydrophobic or hydrophilic?

Answer 18

hydrophobic ( non polar )

Question 19

proteins predominantly made of Serine would be hydrophobic or hydrophilic?

Answer 19

hydrophilic ( polar )

Question 20

what is the polypeptide backbone of proteins?

Answer 20

the repeating structure of atoms with side chains coming out like charms on a bracelet

Question 21

what is the N-terminus of polypeptides?

Answer 21

the free amino end

Question 22

what is the C-terminus of polypeptides?

Answer 22

the free carboxyl end

Question 23

where does the energy go when forming a bond and when a breaking a bond?

Answer 23

forming a bond= energy in
breaking a bond = energy out

Question 24

what are the four levels of protein structure?

Answer 24

1) primary structure: amino acid sequence
2) secondary structure: coiling and folding in the polypeptide chain
3) tertiary structure: overall 3D shape that is determined by the amino acid side chains
4) Quaternary structure: association of multiple polypeptide chains

Question 25

In the primary structure, what determines the sequence of the amino acid chain?

Answer 25

the nucleotide sequence of the gene that encodes the protein

Question 26

what are these bonds called?

Answer 26

peptide bonds

Question 27

what occurs in sickle-cell anemia?

Answer 27

the negatively charged amino acid is replaced by a nonpolar one resulting in altered protein folding ( affecting the secondary and tertiary structure of protein ) -> this occurs in the primary structure

Question 28

what are the two types of forms created during the secondary structure of proteins?

Answer 28

1) alpha helix ( coiled - holds helix cells in shape) 2) Beta pleated sheet ( folded - hold neighboring strands of sheet together ) ## Footnote alpha helix = fibrous proteins of wool, skin, nails beta pleated sheet = globular proteins, fibroin, silk protein produced by spiders

Question 29

at which level of protein stucture is the protein given its final shape?

Answer 29

tertiary stucture= given a 3D shape of the folded polypeptide chain

Question 30

what are the four possible interactions in the tertiary structure?

Answer 30

1) hydrogen bonds 2) hydrophobic interactions 3) disulfide bridges 4) ionic bonds

Question 31

what are the two forms of tertiary structure?

Answer 31

1) globular ( combinations of a-helices and b-sheets, roughly spherical) 2) Fibrous ( consisting of a-helices )

Question 32

what is hemoglobin?

Answer 32

a globular protein with four polypeptide subunits in the quaternary structure.

Question 33

what is collagen?

Answer 33

a fibrous protein consisting of three helical polypeptides coiled together

Question 34

what is protein folding?

Answer 34

when a cell synthesizes polypeptides they must fold into their correct shape or conformation

Question 35

what are chaperonins?

Answer 35

protein complexes which separate new polypeptides from the potentiallly disruptive chemical conditions within the cytoplasm.

Question 36

what are monomeric proteins?

Answer 36

proteins made of single polypeptide chain (no quaternary structure )

Question 37

what are oligomeric proteins?

Answer 37

proteins that consist of two or more polypeptide chains

Question 38

what is a conjugated protein?

Answer 38

protein that contains amino acids and some other chemical group, a prosthetic group

Question 39

what is a simple protein?

Answer 39

a protein only made up of amino acids ## Footnote doesn't combine with other macromolecules

Question 40

what is protein denaturation?

Answer 40

the process by which involves the disruption and possible destruction of both the secondary and tertiary and sometimes quaternary structures. ## Footnote causes the coilage of a random shape

Question 41

what can cause protein denaturation?

Answer 41

- heat ( frying an egg, boiling milk ) - alcohol ( causes H-bonds to form between the new alcohol molecule and the protein side chains instead of normal H-bonds) - change in pH

Question 42

Give an example of denaturation in disease.

Answer 42

- mutations - Alzheimer's diease -AD (presence of protein plaques and neurofilbrillary tangles in the brain) - cancer ( caused by misfolding of proteins that function as tumor-suppressor agents )

Question 43

what are prions?

Answer 43

misfolded proteins that become an infectious agent - can affect the structure of the brain or neural tissue causing untreatable fatal damage

Question 44

Why is prion dieases collectively called **spongiform encephalopathies**?

Answer 44

because they cause sponge-like vacuoles in the brain. ## Footnote i.e. mad cow disease

Question 45

what are the two forms that prions exist as?

Answer 45

1) version consisting of three alpha helical regions and two short beta sheets 2) misfolded form made of beta sheets (infectious agent)

Question 46

what is happening in this image?

Answer 46

Prion proteins are attaching to normal proteins and infecting them causing them to become a prion and affect other prions.

Question 47

what are the 8 protein functions?

Answer 47

1) enzymatic proteins 2) storage proteins 3) chemical messenger proteins 4) contractile and motor proteins 5) defensive proteins 6) transport proteins 7) receptor proteins 8) structural proteins

Question 48

what is the role of enzymatic proteins?

Answer 48

function is to accelerate chemical reactions

Question 49

what is the role of storage proteins?

Answer 49

function is to provide a source of amino acids for developing embryos or developinh infants (milk)

Question 50

what is the role of chemical messengers?

Answer 50

its role is to coordinate an organism's activities such as hormones ( endocrine system ) and neurotransmitters ( nervous system ) | ex: insulin , acetylcholine ( ACh)

Question 51

what is the role of contractile proteins?

Answer 51

function in movement | muscle movement, undulations of cilia and flagella

Question 52

what is the role of defensive proteins?

Answer 52

function as defensive substances within the body | parasite, bacteria, virus

Question 53

what is the role of transport proteins?

Answer 53

function is to move substances within the body or in and out of cells | hemoglobin

Question 54

what is the role of receptor proteins?

Answer 54

function is to regulate the response of the cell to chemical stimuli

Question 55

what is the role of structural proteins?

Answer 55

function is to provide support. They function in the cell membrane, muscle tissue, tendons and ligaments | collagen and elastin = fibrous proteins