Biochem: Exam Chapters 1-4

Front 1

The four key biomolecules of life:

Back 1

proteins
nucleic acids
lipids
carbohydrates

Front 2

_____ allow for dynamic interactions and permit energy and information to move about the cell and organism.

Back 2

Weak bonds

Front 3

_______ form the basis of biochemistry and life itself

Back 3

Transient chemical interactions

Front 4

_____ is the solvent of life

Back 4

Water

Front 5

Our experience of life happens at a distance of _____ angstroms

Back 5

4

Front 6

What is the typical length of a non covalent bond?

Back 6

4 angstroms

Front 7

Weak, reversible but essential interactions

Back 7

transient interactions

Front 8

Describe Brownian Motion:

Back 8

The water and gas molecules of the environment are bouncing randomly about at a rate determined only by the temperature. When molecules collide with pollen granules or dust motes, these molecules then themselves move randomly.

Front 9

How many amino acids are protiens typically made of.

Back 9

50-300

Front 10

what two components of amino acids are hydrogen bonded to form a secondary structure

Back 10

NH
CO

Front 11

what is the highest level of structure that an individual polypeptide can attain

Back 11

tertiary

Front 12

the linkage joining amino acids in a protein is_____

Back 12

peptide bond or amide bond

Front 13

each amino acid unit in a polypeptide is called what

Back 13

residue

Front 14

which terminal is the begging of the amino acid and which is the last

Back 14

N-terminal
C-terminal

Front 15

a polypeptide chain consists of a regularly repeating part called _____

Back 15

Main chain or backbone

Front 16

the variable part of a polypeptide chain is called _____

Back 16

side chain

Front 17

all residues contain these two groups with the exception of _____

Back 17

C==O
N-H
with the exception of proline

Front 18

in a residue which group is a good hydrogen bond acceptor and which is a good hydrogen bond donor

Back 18

the C==O is the good acceptor and the N-H is the good donor

Front 19

Most natural polypeptide chains contain between 50 and 2000 amino acid residues and are commonly referred to as _____

Back 19

Proteins

Front 20

What is the largest protein known and how many amino acids does it contain

Back 20

the muscle protein titian and it consists of 27,000 amino acids

Front 21

peptides made of small numbers of amino acids are called_____

Back 21

oligopeptides or peptides

Front 22

The mean molecular weight of an amino acid residue is ______

Back 22

110g mol-1

Front 23

a dalton is a unit of mass equal to_____

Back 23

a hydrogen atom

Front 24

a protein with a molecular weight of 50,000g mol-1 has a mass equal to

Back 24

50,000 daltons

Front 25

how many kd is 50,000 daltons

Back 25

50

Front 26

The most common cross-links are____

Back 26

disulfide bonds

Front 27

the resulting unit of two linked cysteines is called____

Back 27

cystine

Front 28

what was the first discovery that showed for the first time that a protein has a precisely defined amino acid sequence?

Back 28

the amino acid sequence of insulin

Front 29

in the body are amino acids L amino acids or R amino acids

Back 29

L

Front 30

what is the amino terminus of the tripeptide Gly-Ala-Asp

Back 30

Gly
Glycine

Front 31

What is the approximate molecular weight of a protein composed of 300 amino acids?

Back 31

33,000

Front 32

How many amino acids are in a protein with a molecular weight of 110,000?

Back 32

1,000

Front 33

what determines the 3-D structures of proteins?

Back 33

The amino acid sequence

Front 34

what are two examples of diseases resulting from a change in a single amino acid within a protein

Back 34

sickle-cell anemia
cystic fibrosis

Front 35

what is the geometry of a peptide bond

Back 35

planer

Front 36

for a pair of amino acids linked by a peptide bond how many atoms lie in the same plane? What are they?

Back 36

6 atoms
the alpha-carbon atom and the CO group of the first amino acid and the NH group and the alpha-carbon atom

Front 37

can rotation occur around a peptide bond... Why or Why not?

Back 37

no because the peptide bond has considerable double-bond character because of resonance.

Front 38

the C---N bond distance in a peptide bond is _____?
What is the normal C---N single bond distance?
What is the normal C===N distance?

Back 38

1.32 Angstroms
1.45 Angstroms
1.27 Angstroms

Front 39

are peptide bonds charged or uncharged and why is this important?

Back 39

Uncharged
globular structures are not inhibited by a charge repulsion

Front 40

Give the bond lengths within a peptide unit:
C1alpha - C
C==O
C-N peptide bond
N-H
N-C2alpha

Back 40

C1alpha - C 1.51 Angstroms
C==O 1.24 Angstroms
C-N peptide bond 1.32 Angstroms
N-H 1.0 Angstroms
N-C2alpha 1.45 Angstroms

Front 41

almost all peptide bonds in proteins are______(cis/trans)
Why?

Back 41

Trans
steric hindrance

Front 42

the _________ about two bonds of each amino acid allows proteins to fold in many different ways

Back 42

freedom of rotation

Front 43

in an amino acid backbone, which bond has free rotation?

Back 43

amino group and C2 alpha carbon

Front 44

What is the name of the angles in a peptide chain between the N-Calpha and the C-carboxyl Carbon?

Back 44

torsion angles
N-C alpha phi
C-C carboxyl psi

Front 45

What are the two periodic structures amino acids can fold into?

Back 45

alpha helix
beta pleated shet

Front 46

How is an alpha helix stabilized?

Back 46

hydrogen bonds between the NH and CO groups of the main chain. The CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence.

Front 47

In an alpha helix, how is one residue related to the next? (term)

Back 47

rise or translation

Front 48

what is the rise of one residue to the next in an alpha helix?

Back 48

1.5 Angstroms along the helix axis

Front 49

what is the translation of one residue to the next in an alpha helix?

Back 49

1.5 Angstroms along the helix axis.

Front 50

what is the rotation of one residue in an alpha helix to the next?

Back 50

100 degrees, giving 3.6 per turn

Front 51

How many residues are in a full turn of an alpha helix?

Back 51

3.6 (100 degrees each)

Front 52

Define the pitch of an alpha helix and give the length.

Back 52

The pitch of an alpha helix is the length of one complete turn of the alpha helix and is the product of the translation (1.5 Angstroms) and the number of residues per turn (3.6) = 5.4 Angstroms

Front 53

Essentially, all alpha helices found in proteins are _____ - handed

Back 53

right

Front 54

Which amino acids are not readily accommodated in an alpha helix and why?

Back 54

Branching at the beta carbon atom of valine, threonine, and isoleucine destabilizes alpha helices because of steric hinderance.
Serine, aspartate, and asparagine disrupt alpha helices because their side chains are hydrogen-bond donors or acceptors in close proximity to the main chain where they compete for NH and CO groups
Proline breaks a helix because it's ring structure involves the N which should be a part of the backbone.

Front 55

A beta sheet is composed of two or more polypeptide chains called _____

Back 55

beta strands

Front 56

The distance between adjacent amino acids in a beta chain is _____

Back 56

3.5 Angstroms

Front 57

Do the side chains of a beta sheet point in the same or opposite directions?

Back 57

opposite directions

Front 58

If two adjacent chains in a beta sheet run in opposite directions, it is called _____. If two adjacent chains in a beta sheet run in the same direction, it is called _____

Back 58

antiparallel beta sheet;
parallel beta sheet

Front 59

With antiparallel/parallel beta sheets, which one has the components of one amino acid hydrogen bonding with the components of only one other amino acid?

Back 59

Antiparallel;
parallel: one amino acid hydrogen bonds with two other amino acids

Front 60

Are turns and loops situated on the inside or surface of a beta sheet or alpha helix?

Back 60

surface
they interact with other molecules in solution

Front 61

Are turns and loops are usually composed of amino acids with (hydrophobic/hydrophilic) R groups?

Back 61

Hydrophilic

Front 62

Special types of helices are present in two common fibrous proteins:

Back 62

alpha-keratin;
collagen

Front 63

____ is the primary component of wool and hair

Back 63

alpha-keratin

Front 64

alpha-keratin is composed to two (right/left)-handed alpha helices to create a type of (right/left)-handed superhelix called a _______.

Back 64

right handed;
left handed;
coiled coil protein

Front 65

Intermediate filaments and the muscle proteins myosin and tropomyosin are made of _____

Back 65

coiled coil proteins

Front 66

The two helices in alpha keratin are cross-linked by:

Back 66

van der Waals forces and ionic interactions or by disulfide bonds formed by neighboring cysteine residues

Front 67

What is the most abundant mammalian protein?

Back 67

collagen

Front 68

In what type of helix is glycine every third residue?

Back 68

collagen

Front 69

Every third residue in collagen is _____

Back 69

glycine

Front 70

What is absent in a collagen helix?

Back 70

hydrogen bonds

Front 71

How are the helices in collagen stabilized?

Back 71

steric repulsion of the pyrrolidine rings of the proline residues

Front 72

How many helix strands are in collagen?

Back 72

Three

Front 73

In a superhelical cable of collagen, how are the different strands of helices stabilized?

Back 73

hydrogen bonds between the NH groups of glycine residues and the CO groups of residues on the other chains.

Front 74

In collagen, why does glycine have to appear every third residue?

Back 74

because the center helix is very crowded and glycine is a small amino acid.

Front 75

The only residue that can fit in an interior position of a superhelical cable is ____

Back 75

glycine

Front 76

What is the clinical name of brittle bone disease?

Back 76

osteogenesis imperfecta

Front 77

What is the pathology of osteogenesis imperfect?

Back 77

The inner glycine residue is replaced by other amino acids

Front 78

The accumulation of defective collagen results in _____

Back 78

cell death

Front 79

Vitmin C is required for the formation of stable collagen fibers because it assists in the formation of _____ from _____ in the (1st, 2nd proline)

Back 79

hydroxyproline; proline; 2nd

Front 80

What are the symptoms of scurvy? What causes it?

Back 80

skin lesions, blood-vessel fragility
Caused by less stable collagen due to a lack of hydroxyproline due to lack of vitamin C

Front 81

_____ refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds.

Back 81

tertiary structure

Front 82

Tertiary structure is the result of interactions between _____

Back 82

R groups of the polypeptide chain

Front 83

Are globular proteins water soluble or lipid soluble?

Back 83

Water soluble

Front 84

How many amino acids are in myoglobin?

Back 84

153 amino acids

Front 85

What protein performs most of the chemical transactions in the cell?

Back 85

globular proteins

Front 86

Where is myoglobulin found?

Back 86

predominantly in the heart and skeletal muscle

Front 87

What does moglobulin do?

Back 87

It is an oxygen-ginding protein and it appears to facilitate the diffusion of oxygen from the blood to the mitochondria, the primary site of oxygen utilization in the cell.

Front 88

What is heme?

Back 88

a prosthetic (helper) group containing an iron atom

Front 89

Is myoglobin an extremely compact molecule?

Back 89

yes

Front 90

What are the overall dimensions of a myoglobin protein??

Back 90

45 x 35 x 25 Angstroms

Front 91

how many alpha helices does myoglobin have?

Back 91

8

Front 92

What are the only polar residues on the interior of a myoglobin protein?

Back 92

Two histidine residues

Front 93

What do the two histidine amino acids on the interior of a myoglobin protein do?

Back 93

Play critical roles in binding the heme iron and oxygen.

Front 94

Does the outside of a myoglobin consist of only polar, only nonpolar, or both types of residues?

Back 94

both, which can render the molecule water soluble

Front 95

Certain combinations of secondary structure are present in many proteins and frequently exhibit similar functions. These combinations are called _____

Back 95

motifs or supersecondary structures

Front 96

What motif is this?

Back 96

helix-turn-helix

Front 97

______ refers to the arrangement of subunits and the nature of their interactions.

Back 97

Quaternary structure

Front 98

What is the simplest sort of quaternary structure?

Back 98

dimers

Front 99

What is a dimer?

Back 99

the simplest form of quaternary structure consisting of two identical subunits.

Front 100

How many alpha and how many beta subunits does human hemoglobin have?

Back 100

2 alpha
2 beta

Front 101

Human hemoglobin exists as ______ tetramer

Back 101

alpha2beta2 tetramer

Front 102

the enormous difference between calculated and actual folding times in a protein is called _____

Back 102

Levinthal's paradox

Front 103

What are IUP's?

Back 103

Intrinsically Unstructured Proteins

Front 104

IUP's are important in _____ and _____

Back 104

Signaling and regulatory pathways

Front 105

What is the general name for diseases that occur due to protein aggregate formation from misfolded proteins?

Back 105

Amyloidoses

Front 106

Which amino acids are hydrophobic?

Back 106

(9)
Glycine (Gly, G)
Alanine (Ala, A)
Valine (val, V)
Leucine (Leu, L)
Isoleucine (Ile, I
Methionine (Met, M)
Proline (Pro, P)
Phenylalanine (Phe, F)
Tryptophan (Trp, W)

Front 107

Which amino acids are polar but not charged?

Back 107

(6)
Serine (Ser, S)
Threonine (Thr, T)
Tyrosine (Tyr, Y)
Cysteine (Cys, C)
Asparagine (Asn, N)
Glutamine (Gln, Q)

Front 108

Which three amino acids contain hydroxyl (OH-) groups?

Back 108

Serine (Ser, S), threonine (Thr, T), tyrosine (tyr, Y)

Front 109

This is a version of alanine (Ala, A) with a hydroxyl group attached to it:

Back 109

Serine (Ser, S)

Front 110

These two amino acids are similar but one contains a sulfhydryl and one replaces the sulfhydryl with a hydroxy group.

Back 110

Cysteine (sulfhydryl) Cys, C
Serine (hydroxyl) Ser, S

Front 111

Which two amino acids are polar and contain a carboxylamino group?

Back 111

Asparagine (Asn, N) and Glutamine (Gln, Q)

Front 112

Positively charged amino acids are (hydrophobic/hydrophilic)

Back 112

Hydrophilic

Front 113

What are the hydrophilic amino acids?

Back 113

(3)
Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)

Front 114

These two amino acids have long side chains that are positively charged at the end

Back 114

Lysine (Lys, K)
Arginine (Arg, R)

Front 115

This amino acid contains an imidazole group.

Back 115

Histidine (His, H)

Front 116

What amino acids are negatively charged?

Back 116

Aspartate (Asp, D)
Glutamate (Glu, E)