Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > FINAL MATERIAL > Flashcards

FINAL MATERIAL Flashcards

1
Q

what prefixes refer to how organisms get energy

A
  • photo
  • chemoorgano
  • chemolitho
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what prefixes refer to how organisms synthesize complex organic compounds

A
  • auto

- hetero

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

name the only non-chiral amino acid

A

-glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

which amino acid is often found as a cis-peptide bond?

A

-proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what is the mutation in hemoglobin that leads to sickle cell anemia

A

-glutamic acid to valine

E6V

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Name the branched amino acids. What disease results from defects in the enzyme that catabolizes branched amino acids?

A

Leucine, Isoleucine, and valine

-Maple Syrup Urine Disease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Phenylketonuria (PKU)

A
  • defect in catabolism of phenylalanine
  • extremely painful if untreated
  • severe sequelae similar to MSUD
  • can be controlled by dietary conditions
  • extremely sensitive to artificial sweeteners
  • can lead to mental disabilities, neurological issues, and such
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Tryptophan can be turned to ___

A

serotonin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Lambert-Beer Law

A
  • allows biochemists to measure concentration of protein

- larger side chain means larger UV absorption per mole

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Only ___ forms disulfides

A

cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

The amide amino acids, glutamine and asparagine are sensitive to ___ hydrolyisis

A

acid or base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Name the nonessential amino acids

A

alanine, asparagine, aspartate, glutamate, serine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

name the essential amino acids

A

-Histidine, isoleucine, leucine, lysine, methionine , phenylalanine, threonine, tryptophan, valine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

peptides are simply chains of ____ linked by ____ bonds made by ____ reactions between carboxylic acids and amino groups of amino acids

A
  • amino acids

- amide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

steps of Edman degradation

A
  1. ) label N-terminus with PTC and
  2. ) cleave N-terminal PTC-AA residue and separate it from the remaining peptide
  3. ) identify the PTH-AA by HPLC (high pressure liquid chromatography)
  4. ) repeat reaction with the remaining peptide to determine new N terminal
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

PI of tyrosine

A

5.66

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

pKa of R group of cysteine

A

8.18

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

pKa of R group of Tyrosine

A

10.07

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

pKa of R group of Lysine

A

10.53

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

pKa of R group of Histidine

A

6

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

pKa of R group of arginine

A

12.48

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

pKa of R group of aspartate

A

3.65

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

pKa of R group of glutamate

A

4.25

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Pyruvate dehydrogenase complex is made of _ enzymes

A

3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

E1 of pyruvate dehydrogenase complex.

Protein and function

A

pyruvate dehydrogenase:

  • decarboxylates pyruvate via TPP
  • oxidizes active acetylaldehyde
  • transfers 2 electrons and acetyl to lipoic acid on E2
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

E2 of PDH. protein and function

A
  • dihydrolipoyl transacetylase

- transfers acetyl-group to CoA to make acetyl-CoA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

E3 of PDH. Protein and function

A
  • dihydrolipoyl dehydrogenase

- reduces oxidized lipoic acid on E2 transfers 2 electrons via FADH2 to NAD+—> NADH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

what reaction did we learn that utilized substrate channeling

A

PDH complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

what compounds inhibit PDH complex?

A

ATP, acetyl-CoA, NADH, fatty acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

what activates the PDH complex?

A

-AMP, CoA, NAD+, Ca2+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

what enzymes are under regulation in the citric acid cycle?

A
  • citrate synthase
  • isocitrate dehydrogenase
  • a-ketoglutarate dehydrogenase complex
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

synthase

A

-condensation reactions occur without NTP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

synthetase

A

-condensation reactions requiring NTP (may also be known as ligases)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

phosphorylase

A

-breaks bonds using phosphate as a nucleophile

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

hydrolase

A

-breaks bonds using water as nucleophile

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

kinase

A

-transfers phosphoryl from NTP to acceptor

37
Q

phosphatase

A

-removes phosphoryl by hydrolysis

38
Q

amino acids can be joined together via ___ reactions to form ___

A

condensation reactions

polypeptides

39
Q

polypeptides can be cleaved to yield monomers via a ____ reaction

A

-hydrolysis

40
Q

when we talk about peptide groups, we are refering to ___ atoms

A

6 atoms

Ca1-CO-NH-Ca2

41
Q

Describe the unique characteristics of the peptide bonds

A
  • no free rotation around them because of partial double-bond character (thanks to resonance)
  • the peptide bond (C-O and C-N bonds) fall between a single and a double bond length
42
Q

a torsional angle, aka omega, refers to the __ bond, is usually ___, and means the molecule is in the __ configuration

A

Ca-C-N-Ca bond

  • is usually 180 degrees
  • 180 degrees refers to the trans configuration
43
Q

the Phi bond refers to the bond between

A

N and Calpha

44
Q

steric interference prohibits phi and psi angles of certain magnitudes like ____

A

0,0 or 180, 90

45
Q

ramachandran plots

A

show backbone angles for all of AAs in a protein, or all of the backbon angles for a specific AA in a variety of protein

46
Q

ramachandran plots

A

Visual display of φ & ψ angle sets showing sterically allowed conformations

47
Q

1° structure

A

covalent arrangement of all amino acids in protein sequence plus disulfides
(plus non-amino acid stuff like prosthetic groups & glycosylations & fatty acids etc etc etc)

48
Q

secondary structure

A

local spatial arrangements of groups of amino acids
Some stable, recurring arrangements with regular (or unchanging) φ & ψ angles for each residue in
some 2° structures are named, examples: α-helix, β-conformation (or β-strand) & β-turn

49
Q

in an alpha helix protein, Hydrogen bonding occurs between:

A

the carbonyl oxygen of one peptide bond and the N-H group of the 4th amino acid away

50
Q

there are approximately __ residues per turn in a polypeptides alpha helix

A

3.6 residues (5.4 Angstroms)

51
Q

amphipathic

A

hydrophilic parts as well as hydrophobic

52
Q

Levinthal’s paradox

A

➔ Protein folding cannot possibly operate as a random trial & error process
-if protein folding was a random process then: •If one assumes that each conformation requires ≥10-13 seconds to explore,
(since t = 10-13 seconds for single molecular vibrations)
then ≈10^(77) years required for small polypeptides to fold by random process

53
Q

Application of Lambert-Beer Law:

A
  • summarizes the light absorbing properties of the aromatic molecules
  • is Abs=(path length)(concentration)(extinction coefficient)
  • is used in then laboratory to quantify the protein concentration of samples
54
Q

Keq provides information on ___, but not reaction ____

A
  • thermodynamics (if Keq is positive number than products are thermodynamically favorable over reactants
  • does not provide information on reaction rate
55
Q

predict the net charge on peptide:

K-L-A-E-H-S-D at pH 1, 7, and 14

A

+3, -1, -3

56
Q

when molecular oxygen binds to a heme-containing protein like myoglobin, the two open-coordination bonds of Fe2+ are occupied by

A

-one O2 molecule and one amino acid R-group

57
Q

the psi bond refers to

A

-C alpha and C

58
Q

the omega bond refers to

A

-C-N bond

59
Q

the structure and dynamics of a single domain (22 kDa) of a protein would be investigated using ___:
NMR, electron microscopy, or x-ray crystallography

A

-Nuclear Magnetic Resonance (NMR)

60
Q

The structure of an 80 kDa enzyme bound to an inhibitor would best be investigated using ____:
NMR, electron microscopy, or x-ray crystallography

A

x-ray crystallagraphy

61
Q

the structure of a large viral capsid (4 Mega Dalton) sample would best be investigated using ____:
NMR, electron microscopy, or x-ray crystallography

A

-electron microscopy

62
Q

put the one letter amino acid code for:

two amide R-groups that never carry any net charge at neutral pH

A

-N and Q

63
Q

put the one letter amino acid code for:

ionizable R group that often forms polypeptide crosslinks

A

-C

64
Q

put the one letter amino acid code for:

two acid R-groups that carry negative charges at neutral pH

A

-D and E

65
Q

put the one letter amino acid code for:

Heterocyclic R-group that can act as a general base in enzyme catalytics

A

-H

66
Q

put the one letter amino acid code for:

amino acid serving as the initiator for the biological protein synthesis

A

-M

67
Q

put the one letter amino acid code for:

largest R group with the most absorbance of UV light at 280 nm

A

W

68
Q

put the one letter amino acid code for:

three R-groups that can readily be phosphorylated

A

S, T, Y

69
Q

put the one letter amino acid code for:

-only secondary amine R-group and often located in B-turns

A

-P

70
Q

put the one letter amino acid code for:

two basic r groups that carry full positive charges at neutrall pH

A

K and R

71
Q

smallest R group and often located in B-turns

A

G

72
Q

Two isomeric aliphatic R-groups, one with a second chiral center

A

-I and L

73
Q

put the one letter amino acid code for:

a large aromatic R-group with almost no polar character whatsoever

A

F

74
Q

put the one letter amino acid code for:

smallest branched-chain R-group with virtually no polar character

A

V

75
Q

smallest chiral R group that prefers to fold as in alpha helix

A

A

76
Q

Mass Spectrometry

A
  • Molecules first must be ionized in a vacuum (MALDI*, ESIˇ)
  • Molecules introduced into an electric plus magnetic field
  • Then molecules follow path through the field as a function of their mass-to-charge ratio = m / z
  • Easily automated ! now often analyze peptides derived from proteins
  • MS can be used to confirm the identity of your purified protein
  • MS can even identify chemically modified versions of your protein
77
Q

is lactose a reducing sugar?

A
  • Lactose and maltose are two examples of reducing sugars, but sucrose is not.
  • to be a reducing sugar the anomeric carbon must be FREE!!!
  • The reducing end of a disaccharide is the monosaccharide with a free anomeric carbon that is not involved in a glycosidic bond and is thus capable of converting to the open-chain form
78
Q

chymotrypsin and trypsin cleave with different specificities. What feature gives chymotrypsin its substrate specificity?

A

-chymotrypsin’s hydrophobic pocket has the perfect space and geometry to fit aromatic R groups

79
Q

chymotrypsin and trypsin cleave with different specificities. What feature gives trypsin its substrate specificity?

A
  • Trypsin favors basic residues like lysine and arginine
  • An important difference is that residue 189 is a negatively charged Asp in trypsin
  • The aspartate residue (Asp 189) located in the catalytic pocket (S1) of trypsin is responsible for attracting and stabilizing positively charged lysine and/or arginine, and is, thus, responsible for the specificity of the enzyme. This means that trypsin predominantly cleaves proteins at the carboxyl side (or “C-terminal side”) of the amino acids lysine and arginine
80
Q

Simple diffusion:

-describe and define and identify a solute transported by each mechanism

A

simple diffusion is how O2 gets into tissues. It does not require energy nor is a channel needed. The substance just goes down its concentration gradient

81
Q

Facilitated diffusion

-describe and define and identify a solute transported by each mechanism

A
  • Facilitated diffusion is the process of spontaneous passive transport of molecules or ions across a cell’s membrane via specific transmembrane integral proteins.
  • this is how glucose enters cells
82
Q

Primary Active transport

-describe and define and identify a solute transported by each mechanism

A
  • requires energy-usually in the form of ATP

- this channel requires energy to pump ions or substrates against their concentration gradient like in the Na-K+ ATPase

83
Q

Secondary active transport

-describe and define and identify a solute transported by each mechanism

A

-Secondary active transport uses electrochemical gradients established to move certain solutes against their concentration gradients. Like the Na+-Glut transporter in the small intestines. Na+ flows down its concentration gradient and glucose goes along for the ride

84
Q

Identify 3 traits that distinguish channels from carriers

A
  • • Solutes diffuse through the pore of channel proteins, whereas career proteins bind solutes on one side of membrane and release it on the other side
  • channels are not saturable, but carriers can be
  • Carrier proteins can transport molecules or ions against the concentration gradient, while channel protein cannot.
  • • Carrier proteins move across the membrane, whereas channel proteins do not move while transporting molecules or ions.
85
Q

Lineweaver-Burk Equation

A

= (Km/Vmax)(1/[S] + 1/Vmax

86
Q

Scatchard plot equation

A

[Bound]/[Free] = 1/Kd * (Bmax - [RL])

87
Q

epinephrine and glucagon are ___

A

-kinda similar

88
Q

PFK 2 is active when ____ and makes

A
  • dephosphorylated

- fructose 2,6 phosphate

Biochemistry (7 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions