Brainscape's Knowledge GenomeTM

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


See full index

Biochemistry > Semester 1: Midterm 1 > Flashcards

Semester 1: Midterm 1 Flashcards

1
Q

What are stereoisomer?

A

Molecules with the same molecular formula and sequence of bonded atoms. Differs only in 3D orientations of their atoms in space

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

Diastereomers

A

When 2 or more stereoisomers have diff. configuration at 1 or more (not all) stereocenters
(non-superimposable mirror images)

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

Enantiomers

A

Stereoisomers with a non-superimposable mirror image

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

How is a peptide bond formed?

A

Condensation reaction between alpha carboxylic group and alpha amino group (-> elimination of H2O)

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

Where can we usually find non-polar AAs?

A

Buried within the hydrophobic core of the protein, or within the lipid portion of the membrane

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

Where do we usually find polar AAs?

A

On the protein surface

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

AAs with nonpolar side chain?

A

Aliphatic: Gly, Ala, Val, Leu, Ile, Pro, Met
Aromatic: Phe, Trp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

AAs with polar side chain?

A

Aliphatic: Ser, Thr, Cys, Asn Gln
Aromatic: Tyr

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

AAs with net pos. charge at pH 7

A

Aliphatic: Arg, Lys
Aromatic: His

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

AAs with net neg. charge at pH 7

A

Aliphatic: Asp, Glu

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

The sulfur in Met is called a..

A

Thioether

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

The sulfur in Cys is called a…

A

Thioalcohol

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

The alcohol in Ser is a…

A

Primary alcohol

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

The alcohol in Thr is a…

A

Secondary alcohol

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

What is the hydropathy index?

A

A number representing a proteins’s hydrophilic or hydrophobic properties. (Larger nr. -> more hydrophobic)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the most hydrophobic AAs according to hydropathy index?

A

Ile, Val

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

What are the most hydrophilic AAs according to hydropathy index?

A

Arg, Lys

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

Which AA’s are H donors?

A

Trp, Ser, Thr, Tyr, Asn, Gln, His

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

Which AA’s are H acceptors?

A

Asp, Glu, Asn, Gln

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

Isoelectric point

A

pH at which a particular molecule or surface carries no net electrical charge

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

Primary structure

A

The AA sequence along the backbone of the protein attached by peptide bonds

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

Secondary structure

A
  • Polypeptide chains form alpha-helices and beta-sheets

- Hydrogen binds between backbone amide and carboxyl groups

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

Stability of the alpha-helix and beta-sheet is based on…?

A
  • Minimized steric repulsion between the side chains

- Maximized H-bonds between the peptide groups

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

How many AAs are in each turn of an alpha-helix?

A

3.6 residues per turn

25
Q

Stability of an alpha-helix is decreased by:

A
  • Electrostatic repulsion (or attraction) of adjacent pos./neg. side chains
  • Bulkiness of adjacent side chains
  • Ionic interactions between AAs spaced 3-4 residues apart
  • Pos. AA at C-terminal, neg. AA at N-terminal
  • Presence of proline
26
Q

What does beta-sheets consist of?

A

Beta-strands -> stretch of polypeptide chain 3-10 AAs long

Connected laterally by at least 2-3 backbone H-bonds

27
Q

What is a beta-turn?

A
  • Connection between the ends of anti-parallel beta sheets
  • Gly and Pro occur frequently
  • Often found near the surface of the protein
28
Q

What mostly determines tertiary structure?

A

Primary structure

29
Q

Types of interactions for tertiary and quaternary structure

A
  • Nonpolar (Wan der Waals)
  • Polar
  • H bonds
  • Ionic interactions
30
Q

What is a Ramachandran plot?

A
  • Prediction of secondary structure via possible conformations of pi and psi angles
31
Q

Mention three fibrous proteins

A
  • Collagen
  • Alpha-keartin
  • Silk fibroin
32
Q

Structure of alpha-keratin

A
  • Nonpolar AAs
  • Upper portion: 2 right handed alpha-helices
  • Lower portion: Left handed supercoil of 2 helices
33
Q

Structure of silk fibroin

A

Primary: repeated sequence of Ser-Gly-Ala-Gly
Secondary: Anti-parallel beta-sheets
Tertiary: Stacked beta-sheets connected by H-bonds and nonpolar interactions

34
Q

Structure of collagen

A

Primary: Repeat sequence of Gly-X-Y (where X,Y mostly Pro, HyPro
Secondary: Left handed helix with 3 residues per turn

35
Q

How is tropocollagen built up?

A

3 left handed collagen helices -> 1 right handed triple helix

36
Q

What is Bohr effect?

A

Increasing concentration of protons and/or carbon dioxide will reduce the oxygen affinity of hemoglobin

37
Q

Sickle cell anemia (Hemoglobin S)

A

Point mutation in the beta-globin chain in Hb (glu6 replaced by valine) causing sickle shaped RBC’s

38
Q

What Hb has the highest affinity to oxygen?

A

Myoglobin has the highest affinity to oxygen, out of the hemoglobins HbF has the highest affinity

39
Q

Mention some ser proteases

A

Chymotrypsin, trypsin, thrombin and elastase

40
Q

Inhibitor of ser proteases

A

DIFP (di-isopropyl fluoro phosphate)

41
Q

What does chymotrypsin cleave?

A

Peptide amide bonds when carboxyl side of the amide bond is a tyrosine, tryptophan or phenylalanine (has a big non polar pocket)

42
Q

What does trypsin cleave?

A

Lysine and arginine, except when either is followed by a proline (has a negatively charged pocket)

43
Q

What does elastase cleave?

A

Glycine, alanine and valine (has a small pocket)

44
Q

Competitive inhibition

A

Substrate and inhibitor bind to same site.

Km increases, Vmax stays the same

45
Q

Non-competitive inhibition

A

Substrate and inhibitor bind to different places.

Vmax decreases, Km same

46
Q

Un-competitive inhibition

A

Inhibitor only binds to ES complex, increasing enzymes affinity to substrate -> decrease in Km and Vmax

47
Q

How is a hemiacetal formed?

A

Derived from aldehydes when the alcohol is added to the carbonyl

48
Q

What are anomers?

A

2 stereoisomers that only differs at the anomeric carbon (C1)

49
Q

What is a glycosidic bond?

A

A type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be a carbohydrate

50
Q

What are reducing disaccharides?

A

Any sugar capable of acting as a reducing agent because it has a free aldehyde or ketone group
Eg. cellobiose and maltose

51
Q

What are non-reducing disaccharides?

A

The component monosaccharides bond through an acetal linkage between their anomeric centers. This results in neither monosaccharide being left with a hemiacetal unit that is free to act as a reducing agent
Eg. sucrose

52
Q

What are polysaccharides?

A

10 or more monosaccharide units joined by glycosidic bonds

homopolysaccharide: only 1 type monosaccharide present

53
Q

Mention some important polysaccharides (4) and what sugar they are built up of

A
  • Glycogen (alpha-D-glucose)
  • Starch (alpha-D-glucose)
  • Cellulose (beta-D-glucose)
  • Dextrane (alpha-D-glucose)
54
Q

Mention 5 heteropolysaccharides (more than on monosaccharide present) and where they can be found

A

1) Hyaluronic acid - synovial fluid, cartilage and skin
2) Chondroitin - cornea, bone and skin
3) Dermatan sulphate - skin, heart wall vasculature
4) Keratan sulphate - Cartilage, cornea
5) Heparin - cartilage, mast cell, liver

55
Q

What is true for Ser proteases?

a) These enzymes cut the peptide bond at serine residues
b) There is a specific serine in the active center
c) The acyl enzyme is a tetrahedral intermedier
d) Formation of tetrahedral intermediers decrease the activation energy
e) Chymotrypsin cuts peptide bond after Lys and Arg

A

b, d

56
Q

What is plotted on the axis of a Lineweaver-Burk plot?

A 
X-axis: 1/substrate conc.
Y-axis: 1/v
--------------------------
Slope: Km/Vmax
Intersect Y-axis: 1/Vmax
Intersect X-axis: -1/Km
57
Q

Function of His in Hb?

  • Prox. His
  • Distal His
A

Proximal His: Holds the heme

Distal Histidine: Bent mode binding of oxygen (weakens CO binding)

58
Q

Which coat protein mediates endocytosis?

A

Clathrin

59
Q

Nucleotide bases with amino group

A

Adenine, cytosine and guanine (?)

Biochemistry (9 decks)

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