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Medical Biochemistry (Until Mid-term Spring 2023) > Med Biochem L1 - The Foundations of Biochemistry > Flashcards

Med Biochem L1 - The Foundations of Biochemistry Flashcards

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USMLE® Step 1 flashcards
1
Q

Biochemistry describes …

A

in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms

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2
Q

The smallest cells, certain bacteria known as …

A

mycoplasmas

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3
Q

Mycoplasmas are … nm in diameter and have a volume of about 10^-14 mL

A

300

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4
Q

A single bacterial ribosome is about … nm

A

20

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5
Q

Similarity between bacterial cell and animal cell

A

They have cytoplasm, plasma membrane, ribosomes

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6
Q

Differences between bacterial cell and animal cell

A

1) Bacterial cell is 1 micrometer;
Animal cell is 50 micrometer.

2) Bacterial cell has nucleoid;
Animal cell has nucleus, nuclear membrane, membrane-bounded organelles.

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7
Q

Presence of nuclear membrane: … and …

A

Eukaryotes and Prokaryotes

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8
Q

According to the evolutionary phylogenetic relationship: …, …, and …

A

Bacteria, Archaea, and Eukarya

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9
Q

Phototrophs

A

trap and use sunlight

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10
Q

Chemotrophs

A

derive their energy from oxidation of chemical substances

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11
Q

Lithotrophs

A

minerals

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12
Q

Organotrophs

A

organic matter

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13
Q

Autotrophs

A

can synthesize all of their biomolecules from CO2

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14
Q

Heterotrophs

A

need preformed organic nutrients for synthesis of their biomolecules

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15
Q

Cyanobacteria is

A

photoautotroph

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16
Q

Humans are

A

chemoheterotrophs

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17
Q

Both bacteria and archaea are

A

prokaryotes

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18
Q

… organisms derive energy from the transfer of electrons from fuel molecules to oxygen within the cell

A

Aerobic

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19
Q

… obtain energy by transferring electrons to nitrate (forming N2), sulfate (forming H2S), or CO2 (forming CH4)

A

Anaerobic

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20
Q

Many organisms that have evolved in anaerobic environments are … anaerobes: they die when exposed to oxygen.
Others are … anaerobes, able to live with or without oxygen.

A

obligate;
facultative

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21
Q

Oxidation = …

A

Lose electron

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22
Q

Both aerobic and anaerobic organisms …

A

burn fuel molecules to produce energy.

“Burn” means oxidation; Fuel molecules are oxidized, which means “lose electrons”.
So, some substances should take the electrons, which means “reduced”.

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23
Q

In aerobic organisms, for example, …

A

Glucose + O2 = CO2 + H2O

(Electrons are transferred from glucose to O2)

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24
Q

Anaerobic organisms also need an oxidant. In this case, the oxidant is not …, but …

A

not O2;
but nitrate, sulfate, CO2 etc

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25
Q

Prokaryotic cells have:

A

1) Cell membrane;
2) Cytoplasm;
3) Nucleoid;
4) Pili;
5) Flagella.

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26
Q

Eukaryotic cells have a variety of organelles:

A

1) Nucleus;
2) Mitochondria;
3) Endoplasmic reticulum and Golgi complexes;
4) Peroxisomes;
5) Lysosomes;
6) Vacuoles (in plants);
7) Chloroplasts (in plants).

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27
Q

Peroxisomes:

A

long chain fatty acids are oxidized

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28
Q

Lysosomes:

A

filled with digestive enzymes to degrade unneeded cellular debris

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29
Q

Vacuoles (in plants):

A

store organic acids

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30
Q

Chloroplasts (in plants):

A

synthesis of ATP

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31
Q

Cell membrane …

A

… has a lipid bilayer structure;
… mainly composed of phospholipids;
… also has proteins

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32
Q

Cell membrane occupies about 50% of cell membrane volume and perform various biological activities: …, …, … .

A

1) Integral proteins;
2) Peripheral proteins;
3) Lipid-anchored proteins.

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33
Q

Integral proteins:

A

Proteins that pass through or inserted into the cell membrane and have a hydrophilic cytosolic domain.
(Ion channels, proton pumps, receptors)

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34
Q

Peripheral proteins:

A

Have transient interactions with cell membranes.
(Some enzymes and hormones)

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35
Q

Lipid-anchored proteins:

A

Proteins that form a covalent bond with one or several lipid molecules in the cell membrane (G proteins)

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36
Q

(Mitochondria)
Inner membrane contains …

A

electron transport circuits and proteins for oxidative phosphorylation

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37
Q

Mitochondria has its own …

A

DNA

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38
Q

Rough Endoplasmic Reticulum - …

A

Main protein synthesis site

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39
Q

Smooth Endoplasmic Reticulum (planar cytoplasmic reticulum) - …

A

site of lipid synthesis and drug metabolism

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40
Q

Ribosomes - …

A

structures that synthesize proteins

41
Q

The main components of the endomembrane system are … (5)

A

endoplasmic reticulum;
Golgi apparatus;
vesicles;
cell membrane;
nuclear envelope.

42
Q

(Cytosol)
Substances other than the nucleus and organelle as part of the …

A

cytoplasm

43
Q

Glycogen:

A

A polymer of glucose that is abundant in muscle and liver cells and, when necessary, breaks down glycogen into glucose for use in various organs (glycogen granules)

44
Q

Lipids:

A

Stored mainly in adipocytes in the form of triglycerides and present in the form of lipid droplets in various cells

45
Q

Crystals:

A

Located everywhere in the cell and thought to be a crystalline form of a specific protein

46
Q

Pigment:

A

Melanin in skin and hair, etc

47
Q

The cytoskeleton is divided into … (3)

A

microfilaments (actin filaments);
intermediate filaments;
microtubules.

48
Q

Actin filaments

A
  • finest fiber
  • present in muscle cells
  • cytokinesis, amoeboid movement, cell motility, cell shape endocytosis, exocytosis, cell contractility, mechanical stability
49
Q

Microtubules

A
  • thickest fiber
  • it has a structure with a hole in the middle
  • contributes to maintaining cell structure
  • composes cilia and flagella
  • providing a platform for intracellular movement
  • mitotic spindle during cell division
50
Q

Intermediate filaments

A
  • not involved in cell movement
  • contributes to maintaining structure by providing mechanical strength of cells or tissues
51
Q
  • Growth delay - the average height of a 10-year-old is similar to that of a 3-year-old child;
  • Death of cardiovascular disease, usually around the age of 13;
  • Structural protein lamin A cannot be converted from precursor to active form.
A

Hutchinson-Gilford progeria syndrom

52
Q
  • Acute visual loss due to optic nerve damage;
  • Caused by a point mutation in mitochondrial DNA
A

Leber’s hereditary optic neuropathy

53
Q
  • Severe muscular weakness in early neonatal period;
  • Caused by mutations in genes for peroxisome proteins
A

Zellweger spectrum syndrome

54
Q

Lysosomal storage disease: ex, …

A

1) Gaucher’s disease;
2) Niemann-Pick disease;
3) Tay-Sachs disease;
4) Hunter syndrome

55
Q

There is a striking similarity between yeast and human/other animals when …

A

it comes to glucose break down

56
Q

The current understanding that all organisms share a common evolutionary origin is based in part on this observed universality of chemical intermediates and transformations - …

A

Biochemical Unity

57
Q

Elements:

A

basic components that no longer break down into other substances

58
Q

Compound:

A

A substance composed of two or more elements (the element loses its original properties and acquires new properties)

59
Q

Mixture:

A

A state made up of two or more subtances without chemical bonding between them

60
Q

Atom:

A

The most basic chemically indivisible particle

61
Q

Molecules:

A

A substance composed of one or two or more atoms, which is a basic particle that exhibits the intrinsic properties of a substance

62
Q

Trace elements:

A

present in small amounts in cells, but essential for life as they could be co-factors of enzymes or participate in enzymatic reactions

63
Q

Three-dimensional structure of carbon bonds:

A

Four single bonds around carbon form a terahedral structure, C-C single bonds are freely rotatable, C=C double bonds are short and non-rotatable, and planar structures

64
Q

Cells contain a group of small molecules that are converted by enzymes =>

A

metabolome (collection of low molecular weight metabolites produced by the cell during metabolism)

65
Q

Macromolecules are the main constituents of cells =>

A

proteome (complete set of proteins expressed in the organism/cell);
genome (complete set of genetic material)

66
Q

Stereochemistry = …

A

the arrangement of molecules’ atoms in 3D space

67
Q

Carbon-containing molecules exist as … = molecules with the same chemical bonds and the same chemical formula but different configurations (the fixed spatial arrangement of atoms)

A

stereoisomers

68
Q

Stereoisomers cannot …

A

convert into each other without breaking any bonds

69
Q

Isomers are …

A

molecules or polyatomic ions with identical molecular formulas

70
Q

Isomers:

A

1) Positional;
2) Geometric;
3) Optical isomers

71
Q

Positional isomers:

A

same carbon skeleton and the same functional groups

72
Q

Geometric isomers:

A
  • Different arrangement of substituents attached to non-rotatable double bonds;
  • Melting point, boiling point, solubility, crystal structure, biological role, etc. are different;
  • The cis and trans isomers fall into this category.
73
Q

Optical isomers

A
  • Chiral atom/chiral center: when all surrounding covalent members are different;
  • If there is one chiral carbon
74
Q

Two non-overlapping, mirror images of isomers:

A

Enantiomers
(Enantiomers have the same physical and chemical properties, opposite directions of rotation of polarized light, and different specificities in enzymatic reactions)

75
Q

A carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called …

A

chiral centers

76
Q

Chiral molecule:

A

Rotated molecule cannot be superimposed on its mirror image

77
Q

Achiral molecule:

A

Rotated molecule can be superposed on its mirror image

78
Q

… if they are mirror images

A

Enantiomers

79
Q

… if they are not mirror images

A

Diastereomers

80
Q

The configuration is (R) ( Latin …, ‘right’ )

A

rectus

[Clockwise (R)]

81
Q

The configuration is (S) ( Latin …, ‘left’ )

A

sinister

[Counterclockwise (S)]

82
Q

Molecular Conformation - …

A

the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom rotation about single bonds.

83
Q

Configuration and conformation are important in biological interactions of:

A
  • reactant with its enzyme;
  • hormone and its receptor on cell membrane surface;
  • antigen and antibody.
    Usually only one form exists in living organisms, not both at the same time
84
Q

Racemic mixture is …

A

a 50:50 mixture of two enantiomers.
Because they are mirror images, each enantiomer rotates plane-polarized light in an equal but opposite direction and is optically inactive. If the enantiomers are separated, the mixture is said to have been resolved.

85
Q

Types of non-covalent interactions in aqueous solutions:

A
  • hydrogen bond
  • ionic interactions
  • hydrophobic interactions
  • van der Waals interactions
86
Q

Hydrogen bonds in water molecules

A

A weak bond caused by the electrical force between oxygen in one water molecule and hydrogen in a neighboring water molecule.

87
Q

Characteristics of hydrogen bonding

A
  • much weaker than covalent bonds;
  • breaks and forms constantly
  • hydrogen bonds are formed between F, O, and H in polar solute and the hydrogens attached to F, O, and N on another molecule nearby
88
Q

Water is a … solvent, solute is hydrophilic

A

polar

89
Q

When the donor-hydrogen-acceptor is in … , its attraction is strongest

A

a straight line

90
Q

Water is … with non-planar compounds and does not dissolve => hydrophobic

A

immiscible

91
Q

When water is mixed with bipolar compouds, it forms …

A

micelles.

92
Q

Buffer solutions …

A

maintain a stable pH by neutralizing added acids or bases.

93
Q

Dynamic steady state:

A

A -> B -> C

94
Q

Equilibrium:

A

A <=> B

95
Q

Types of thermodynamic systems:

A

Isolated system;
Closed system;
Open system.

96
Q

Isolated system:

A

Both matter and energy cannot be exchanged with the outside

97
Q

Closed system:

A

Only energy can be exchanged with the outside

98
Q

Open system:

A

Both energy and material can be exchanged with the outside

Medical Biochemistry (Until Mid-term Spring 2023) (4 decks)

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