Option B: Biochemistry HL

Question 1

How many dissociation constants does a cationic form of 2-amino acids with non-ionizable side-chain have?

Answer 1

two: -COOH and -NH3^+
- COOH has relatively higher acidity and dissociates more easily than the protonated amino group, so pKa1 characterizes the equilibrium between the cation and the zwitterion

Question 2

Acid-base buffer

Answer 2

Contains a weak conjugate acid-base pair which can neutralise small amounts of strong acids and bases without significantly changing the pH.

Question 3

Buffer pH range of an amino acids as acid-base buffer and why?

Answer 3

from pH = pKa1 - 1 to pKa1 + 1
and
from pH = pKa2 - 1 to pKa2 + 1

outside of these ranges, the amino acids exist predominately as a single ionic species and loses its ability to maintain a constant pH of the solution

Question 4

What is the role of protein buffers?

Answer 4

They maintain a constant pH of biological fluids, which is essential for the integrity of body tissues and enzyme functions

Question 5

Allosteric site

Answer 5

Many enzymes can temporarily bind to specific molecules via weak non-covalent interaction.
When allosteric site is occupied, the shape of the enzyme changes, which alters the configuration of the main active site, which affects the stability of the enzyme-substrate complex

Question 6

Non-competitive inhibition

Answer 6

When substrate and the inhibitor have different chemical structures and bind to different sites of the enzyme.

Question 7

Competitive inhibition

Answer 7

When substrate and the inhibitor have similar chemical structure and the inhibitor may occupy the main active site fo the enzyme

Question 8

Michaelis-Menten equation

Answer 8

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

v: actual reaction rate
Vmax: maximum reaction rate
Km: Michaelis constant, which is equal to the substrate concentration when v=0.5Vmax

Question 9

Turnover number

Answer 9

the maximum number

of substrate molecules that one molecule of enzyme can convert to product per second

Question 10

What does small km (Michaelis constant) mean?

Answer 10

A small Km
indicates high affinity, which means that
enzyme–substrate complex ES is particularly stable and the rate will approach Vmax
even at relatively low substrate concentrations

Question 11

Protein assay

Answer 11

Analytical procedure that detects proteins and the determines their concentrations in solutions

Question 12

UV-vis spectroscopy

Answer 12

Technique that measures the absorption of UV and/or visible light by proteins or their complexes with organic dyes and transition metal ions

Question 13

Why almost all proteins absorb UV light?

Answer 13

• due to the presence of aromatic rings in phenylalanien, tyrosine and tryptophan residues
• complexes of proteins with transition metal ions absorb visible light due to d-orbital electron transitions

Question 14

Absorbance of a sample

Answer 14

The logarithmic ration between the intensity of light emitted by the monochromator (Io) and the intensity of light passed through the sample (I)

A = log (Io/I)

Question 15

Beer-Lambert law

Answer 15

A = εcL

where L is the cuvette length and ε is a constant (known as the molar absorptivity or extinction coefficient) that depends on the solvent nature and the temperature of the solution

Question 16

Nucleic acids

Answer 16

Condensation polymers of nucleotides

Question 17

Nucleotides

Answer 17

Products of condenstaion of a nitrogenous base, a pentose sugar (ribose or deoxyribose) and phosphoric acid.

Question 18

Nitrogenous bases

Answer 18

Heterocyclic aromatic amines that contain several nitrogen atoms and act as proton acceptors in aqueous solutions

• derived from two parent amines: pyrimidine and purine
• crystalline substance with high melting points due to the presence of multiple polar groups
• insoluble in water because their molecules are held togehter by strong hydrogen bonds

Question 19

Pyrimidine

Answer 19

cytosine, thymine, uracil

Question 20

Purine

Answer 20

adenine, guanine

Question 21

Diester bridge

Answer 21

When nucleotides combine with one another, the phosphate groups form a digester bridge between 3’ and 5’ carbon atoms of adjacent pentode residues

Question 22

At what end of the strand does the synthesis of nucleic acid begin?

Answer 22

5’

Question 23

What is the sequencing of human genome useful for?

Answer 23

• treating various diseases
• designing new forms of medication
• understanding human ancestry, migration, evolution and adaptation to environmental changes

Question 24

What are the concerns of the man genome project?

Answer 24

1) possible discrimination of genetically disadvantaged people
2) gene modification
3) access to genetic information

Question 25

Initiator proteins

Answer 25

Group of enzymes that separate the two DNA strands and create short polynucleotide fragments (primers) paired with the separated strands by complementary nitrogenous bases

Question 26

DNA polymerase

Answer 26

Group of enzymes that add more nucleotides to the primers using the existing DNA strands as templates

Question 27

RNA polymerase

Answer 27

During transcription, it reads the DNA sequence and produces an RNA molecule complementary to an existing DNA strand

Question 28

point mutation

Answer 28

Single mismatched nucleotide in the DNA sequence

Question 29

What causes point mutations?

Answer 29

- can occur naturally - UV light - ionising radiation - free radicals - mutagens

Question 30

Diester bridge

Answer 30

When nucleotides combine with one another, the phosphate groups form a digester bridge between 3’ and 5’ carbon atoms of adjacent pentode residues

Question 31

At what end of the strand does the synthesis of nucleic acid begin?

Answer 31

5’

Question 32

What is the sequencing of human genome useful for?

Answer 32

- treating various diseases - designing new forms of medication - understanding human ancestry, migration, evolution and adaptation to environmental changes

Question 33

What are the concerns of the man genome project?

Answer 33

1) possible discrimination of genetically disadvantaged people 2) gene modification 3) access to genetic information

Question 34

Initiator proteins

Answer 34

Group of enzymes that separate the two DNA strands and create short polynucleotide fragments (primers) paired with the separated strands by complementary nitrogenous bases

Question 35

DNA polymerase

Answer 35

Group of enzymes that add more nucleotides to the primers using the existing DNA strands as templates

Question 36

RNA polymerase

Answer 36

During transcription, it reads the DNA sequence and produces an RNA molecule complementary to an existing DNA strand

Question 37

point mutation

Answer 37

Single mismatched nucleotide in the DNA sequence

Question 38

What causes point mutations?

Answer 38

- can occur naturally - UV light - ionising radiation - free radicals - mutagens

Question 39

Biological pigments

Answer 39

Coloured compounds produced in living organisms Have extensive systems of alternate single and double carbon-carbon bonds.

Question 40

What does the colour of the biological pigment depend on?

Answer 40

Molecular structure and on the number of delocalised electrons

Question 41

Antioxidants

Answer 41

Protects cells from UV light, peroxides and free radicals, including a highly reactive single oxygen produced by photosynthesis

Question 42

Porphyrins

Answer 42

Biological pigments that are complexes of metal ions with large cyclic ligands. The organic backbone of porphyrins (porphin) contains four nitrogen atoms in a highly conjugated heterocycle

Question 43

Haemoglobin in venous blood

Answer 43

Has a slightly lower pH and higher CO2 concentration than arterial blood, protons and CO2 bind to side-chains of amino acids in haemoglobin and act as non-competitive inhibitors

Question 44

Cytochrome c oxidase

Answer 44

a large metalloprotein assembly containing four heme prosthetic groups and several ions of other metals includingcopper, magnesium, and zinc.

Question 45

Anthocyanins

Answer 45

Biological pigments that give bright colours of flowers, ripe fruits, berries and vegetables Are water soluble and concentrate in the vacuoles of plant cells

Question 46

Stereoisomers

Answer 46

Molecules that have the same sequence of atoms and chemicalbonds but different arrangements of atoms in space

Question 47

Configurational isomers

Answer 47

Stereoisomers that cannot be | transformed into one another without breaking a chemical bond

Question 48

What are the two types of configurational isomers?

Answer 48

1) cis-/trans- isomers | 2) optical isomers

Question 49

CORN rule

Answer 49

- identifies enantiomers of 2-amino acids: 1) CO-R-N: COOH, R. and NH2 2) position the molecule so that the H atom at the C2 carbon faces away from you 3) CORN is spelled clockwise for D-enantiomer and anti-clockwise for an L-enantiomer