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Biochemistry 1 > Test 1 > Flashcards

Test 1 Flashcards

1
Q

Van der Waals forces strength

A

0,4 - 4,0 kj/mol

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2
Q

Hydrogen bond strength

A

12 - 30 kj/mol

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3
Q

Ionic interactions strength

A

20 kj/mol

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4
Q

Hydrophobic effect

A
  • Describes the interaction between water and hydrophobes
  • when nonpolar molecules (like fat) clump together rather than distributing themselves in the water
  • stronger interactions than the weak intermolecular forces
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5
Q

Hydrophobic (non polar) amino acids

A

Side chains are insoluble in water

Glycine, alanine, proline, Isoleucine, leucine, valine, methionine, tryptophan and phenylalanine

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6
Q

Polar amino acids

A

Side chains form hydrogen bonds

Cysteine, serine, threonine, tyrosine, asparagine and glutamine

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7
Q

Positively charged amino acids

A

Side chains carry a net charge at or near neutral pH

Lysine, arginine and histidine

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8
Q

Negatively charged amino acids

A

aspartic acid (Aspartate) and glutamic acid (glutamate)

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9
Q

Branched amino acids

A

Leucine, valine and isoleucine

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10
Q

Finding the pI of amino acids

pK1 = 2.4
pK2 = 9.6

A
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11
Q

Chirality

A

when something is not identical to its mirror image

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12
Q
A

Left - L-amino acid, right - D-amino acid

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13
Q
A

Selenocysteine, the 21st amino acid

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14
Q
A

Remember N-terminus and C-terminus at the ends

NH3+

C connected to O- and then to O with a double bond

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15
Q

Proteins often get disulfide bonds, how?

A
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16
Q

Primary protein structure

A

A simple chain with peptide bonds

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17
Q

Secondary protein structure

A
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18
Q

Tertiary protein structure

A
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19
Q

Quaternary protein structure

A
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20
Q

What is protein denaturation?

A

When a protein loses its structure and therefore its ability to work properly

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21
Q

Why do proteins get denatured?

A
  • Extreme changes in pH
  • Detergents
  • High temperature
  • Heavy metals
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22
Q

Globular protein

A

spherical or oval in shape, soluble in water or other solvents and digestible.

haemoglobin, alpha immunoglobulin, beta immunoglobulin

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23
Q

Fibrous proteins

A

Fiber like in shape, insoluble in water and resistant to digestion.

keratins, collagens, myosins, and elastins

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24
Q

Conjugated proteins

A

protein that functions in interaction with other (nonpolypeptide) chemical groups (called prosthetic group) attached by covalent bonding or weak interactions.

Nucleoproteins, glycoproteins, lipoproteins, phosphoproteins and chromoproteins.

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25
Q

Glutathione oxidized vs reduced form

A
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26
Q

Collagen structure

A

It consists of the amino acids Proline, Glycine and Hydroxyproline coiled together

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27
Q

Collagen synthesis

A
  1. Translation on the ribosome
  2. hydroxylation of pro and lys
  3. release from ribosome
  4. glycosylation
  5. triple helix formation
  6. secretion from cell
  7. removal of N- and C- terminal domains
  8. crosslink formation
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28
Q

Heme as a prosthetic group

A

Hemeproteins:
oxygen transport and storing (hemoglobin, myoglobin);

O2 activation for oxidation

electron transfer as a part of the electron transport chain

29
Q

Binding of oxygen to heme

A

Reversible binding of O2 to the skeletal structure of the heme prosthetic group.

30
Q

Myoglobin structure

A
31
Q

Myoglobin binding of oxygen

A

The ability of myoglobin and hemoglobin to bind oxygen depends on the presence of a heme molecule.

When oxygen concentration in muscles falls to low levels, myoglobin releases its oxygen, thus functioning as an oxygen “battery” that delivers oxygen fuel when needed and holding onto it under all other conditions.

32
Q

hemoglobin structure

A
33
Q

Evolution of hemoglobin and myoglobin

A

Hemoglobin is derived from the myoglobin protein

500 million years ago the myoglobin gene duplicated and part of the gene became hemoglobin

100 million years later, the hemoglobin gene duplicated again forming α and β subunits.

34
Q

Types of hemoglobins

A

HbA1

HbA2

HbF

HbA1C

35
Q

Myoglobin vs hemoglobin - Oxygen saturation curves

A

O2 is bound more tightly with myoglobin than with hemoglobin.

pO2 needed for half saturation (50% binding) of myoglobin is about 1 mm Hg (1 Torr) compared to about 26 mm Hg for hemoglobin.

36
Q

Cooperativity of oxygen binding to hemoglobin

A

One molecule of hemoglobin (with four hemes) can bind with four molecules of O2 .

37
Q

T and R states of hemoglobin

A

Tense and relaxed states

38
Q

Transport of CO2 by hemoglobin

A

CO2 is an allosteric inhibitor of hemoglobin.

CO2 is bound to the N-terminal amino acids of hemoglobin

The combination of CO2 with NH2 groups is called a carbamate.

39
Q

Bohr effect

A

The regulations of O2 binding by H+ and CO2

The binding of oxygen to hemoglobin decreases with increasing H+ concentration (lower pH) or when the hemoglobin is exposed to increased partial pressure of CO2 (pCO2 ).

primarily responsible for the release of O2 from the oxyhemoglobin to the tissues.

40
Q

Effect of 2,3-bisphosphoglycerate on O2 binding by hemoglobin

A

2,3-BPG is produced as an intermediate of glycolysis.

It specifically binds to deoxyhemoglobin (and not to oxyhemoglobin) and decreases the O2 affinity to Hb (facilitates the release of O2 from the Hb)

41
Q

Hemoglobin S - Sickle cell disease (also sickle cell anemia)

A

inherited disorders - affects shape of red blood cells

In sickle cell anemia, some red blood cells are shaped like sickles or crescent moons. These sickle cells also become rigid and sticky, which can slow or block blood flow

In HbS, the nonpolar amino acid valine has replaced the polar surface residue glutamate in position 6 of the β subunit, generating a hydrophobic “sticky patch” on the surface of the β subunit of deoxyHbS.

42
Q

Thalassemia

A

genetic defects - result from partial or total absence of one or more α or β chains of hemoglobin.

most common genetic blood disorder characterized by decreased hemoglobin production (anemia). Over 750 different mutations have been identified.

43
Q

Biological membranes

A

define the boundaries of all cells

asymmetric, sheetlike structures.

44
Q

Selective permeability of membranes

A

Prevents unwanted molecules from diffusing inside the cells

Allows the cell to take up specific molecules and remove unwanted one

external cell membrane

internal membranes

45
Q

Structure and properties of fatty acids (lipids)

A

usually contain an even number of carbon atoms (typically 12–20)

Monounsaturated fatty acids contain one carbon-to-carbon double bond.

Polyunsaturated fatty acids contain two or more carbon-to-carbon double bonds

46
Q

Classification of fatty acids (by lenght)

A
47
Q

Delta nomeculature

A
48
Q

Omega nomeculature

A
49
Q

Saturated fatty acids

A

have only single bonds

50
Q

Unsaturated fatty acids

A

Have one or more double bonds

51
Q
A

Phosphoglyceride

a phospholipid

52
Q
A

Sphingomyelin

phospholipid and a sphingolipid

53
Q
A

Cerebroside

Sphingolipid and a glycolipid

54
Q
A

Sphingolipids, sphingomyelins

55
Q
A

Glycolipids, cerebrosides

56
Q
A

Cholesterol, characterized by four fused carbon rings.

One of cholesterol’s functions is to reduce the fluidity of the membrane. To do so, it forms strong interactions with phospholipids using its rigid steroid ring structure

57
Q

peripheral versus integral membrane proteins

A

Different treatments have to be applied to remove proteins from the lipid membrane

pH change -> peripheral

detergent, enzymes -> integral

58
Q

types of integral membrane proteins

A

Most transmembrane proteins are embedded in the membrane using α-helices composed of nonpolar amino acids

Glycophorin

59
Q

lipid linked membrane proteins

A

proteins located on the surface of the cell membrane that are covalently attached to lipids embedded within the cell membrane.

60
Q

channel proteins

A

can be formed from b-strands

61
Q

Glycoproteins

A

proteins containing glycans attached to amino acid side chains

62
Q

Mosaic model of biological membranes

A

describes the structure of the plasma membrane as a mosaic of components —including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character

63
Q

Cell signaling - membrane signal transduction mechanism

A

the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events

64
Q

Transport via diffusion

A

Net transport via diffusion only occurs when there is a concentration gradient.

65
Q

Passive transport

A

does not require energy to move substances across cell membranes.

66
Q

Active transport

A

Many important transport systems function to move molecules against a concentration gradient. This is known as active transport. Because such movement is unfavorable and brings the system further from equilibrium, active transport must be coupled to a process that provides energy.

67
Q

Active transport

A

the movement of molecules or ions across a cell membrane from a region of lower concentration to a region of higher concentration—against the concentration gradient

68
Q

Membrane carriers, channels and pumps

A

Channels - ion channels allow ions to flow rapidly across membranes down the gradients

Carriers - utilize the gradient of one ion to drive the transport of another against its gradient

Pumps - energy transducers in that they convert one form of free energy into another.

Biochemistry 1 (19 decks)

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