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BHCM218 > Module 01 - Section 1 > Flashcards

Module 01 - Section 1 Flashcards

1
Q

What is molecular Biology?

A

Study of essential cellular molecules, including DNA, RNA and proteins, and the biological pathways between them

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2
Q

What other areas of biology and chemistry does molecular biology overlap with the most? (2)

A

Genetics and biochemistry

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3
Q

How many amino acids are there?

A

20

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4
Q

What is the Central Dogma of molecular biology?

A

Biological information flows in this direction:

DNA->RNA->Protein

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5
Q

What are the 2 exceptions to the central Dogma

A

RNA viruses, Non-coding RNAs

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6
Q

Why are RNA viruses exception to the central dogma?

A

They have RNA as their genetic material (RNA->RNA)

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7
Q

Why are non-coding RNAs exception to the central dogma?

A

RNA molecules are not translated into protein (DNA->RNA, but no protein)

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8
Q

What is transcription?

A

The process where DNA is used as a template to make and RNA copy

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9
Q

What is the enzyme responsible to read the DNA template and incorporate complementary nucleotide to make a strand RNA?

A

RNA polymerase

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10
Q

What are the 3 types of RNA?

A

mRNA, tRNA, rRNA

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11
Q

Which type of RNA is a transient molecule?

A

mRNA or Messenger RNA

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12
Q

What is the function of mRNA?

A

Carries the instruction for building specific proteins from the nucleus(DNA) to the ribosomes in the cytosol for translation

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13
Q

True or False: one gene can encode several mRNAs, and one mRNA can be the template for many proteins

A

True

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14
Q

Which RNA type is responsible to carry the instructions to translate specific proteins from the nucleus to the cytosol?

A

mRNA

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15
Q

What is rRNA?

A

the RNA component of a ribosome

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16
Q

Which type of RNA is the most abundant? (about 85% of all RNA)

A

rRNA

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17
Q

What is the function of rRNA?

A

rRNA combine with many different ribosomal proteins to form the ribosome complex, creating a factory for protein synthesis

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18
Q

Which type of RNA is called the adaptor molecule?

A

tRNA

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19
Q

What is the function of tRNA

A

Functions as an adaptor between nucleic acid and protein - it transfers individual amino acids from the cytoplasm to their appropriate location in the growing polypeptide

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20
Q

Outline the mechanism of tRNA

A

(1) Each tRNA contains a sequence of 3 bases called the anticodon which is complementary to a small section of the mRNA molecule called the codon
(2) The codon “codes” for a specific amino acid which is also bound to the tRNA molecule
(3) When 2 amino acid-linke tRNAs align side by side, the amino acids attached to the tRNAs can be joined together

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21
Q

What are the building blocks/components of Nucleic Acids? (3)

A

(1) Nitrogenous Base
(2) Pentose(5-carbon) sugar; ribose or deoxyribose
(3) At least 1 phosphate group

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22
Q

Name the two Purines

A

Adenine and Guanine

PURple flAG

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23
Q

Name the 3 pyrimidines

A

Cytosine, Thymine, Uracil

PYRamids are sharp and may CUT

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24
Q

What are the 3 fundamental differences between DNA and RNA?

A

(1) DNA is double stranded, RNA is generally single-stranded
(2) DNA has deoxyribose as a sugar (missing hydroxyl -OH group on the 2’carbon) RNA has ribose as sugar
(3) DNA contains the base Thymine whereas RNA has Uracil (they differ by a methyl group on 5’ carbon of the uracil base)

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25
Q

What type of bonds link 2 nucleotides?

A

phosphodiester bonds

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26
Q

What is a phosphodiester bond?

A

A chemical bond joining successive sugar molecules in a polynucleotide, between the 5’ phosphate (PO4) or one nucleotide and the 3’ hydroxyl (OH) of the adjacent nucleotide

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27
Q

What is the directionality of nucleic acids

A

5’ to 3’, based on their free ends which are called termini

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28
Q

What does having directionality means for nucleic acid

A

Nucleotide can only be added on the 3’ end

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29
Q

What are the building blocks/components of amino acids? (3)

A

(1)Amino group
(2)Carboxyl Group
(3) R Group
All of which are attached to the central (alpha) carbon

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30
Q

What kind of bonds link amino acids together?

A

Peptide bonds

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31
Q

What is a peptide bond?

A

A covalent bond linking 2 consecutive amino acid monomers along a peptide chain, between the amino group of one amino acid and the carboxyl group of the adjacent one

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32
Q

What are Amino acid resisudes

A

Amino acids, once incorporated into a polypeptide chain

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33
Q

What is the directionality of polypeptide chains?

A

N-terminus(amino) to C-Terminus (carboxyl)

34
Q

What determines how a polypeptide will fold?

A

the interaction between the R groups and the external environment

35
Q

What determines a protein’s function?

A

its 3-dimensional structure

36
Q

What are some roles of proteins?

A

Catalyzing biochemical reactions, structural roles, receiving/transmitting chemical signals, transport of ions across membranes

37
Q

What determines the interactions, affinity and functions of nucleic acids and proteins?

A

their chemical properties

38
Q

What stems from chemical properties?

A

How biomolecules interacts and function and waht affinity or specificity they have

39
Q

What are the two types of strong chemical bonds?

A

Covalent and Ionic

40
Q

Describe Strong Chemical Bonds (3)

A

(1) Involved short distance interaction between atoms
(2) Generally require a catalyst to break them
(3) Play major roles in the formation and stability of nucleic acids and amino acid polymers (joined by covalent bonds)

41
Q

Describe covalent bonds (2)

A

(1) 2 atoms share electrons to fill the outer shells between their positively charged nuclei
(2) Usually involves non-metal sharing electrons with a non-metal

42
Q

Describe ionic bonds

A

(1) One or more electrons are completely transferred from one atome to another
(2) Results in 1 atom with a positive charge and 1 with a negative charge
(3) The electrostatic attraction of these oppositely charged ions that holds them together
(4) Usually involve a metal and a nonmetal

43
Q

What is Electronegativity?

A

Propensity of an atom within a moelcule to attract electrons to itself
Electronegative atoms = tendency to gain electrons
Electropositive atoms = tendency to lose electrons

44
Q

How to predict bond character?

A

Difference in electronegativities between 2 atoms
0-0.4 = Nonpolar covalent bonding
0.4-1.67=polar covalent bonding
1.67+=ionic bonding

45
Q

What is Valence?

A

The maximum number of covalent bonds a particular atom can form to completely fill its outer shell

46
Q

How many, respectively, can H, O, N and C form?

A

1, 2, 3, 4

47
Q

What are the 2 bond geometry important to this module?

A

Tetrahedral, planar

48
Q

Describe Tetrahedral geometry

A

A central atom is located at the center with four substituents that are located at the corner of a tetrahedron. The bond angle is 109.5 and sp3 hybridized (eg: C2H6)

49
Q

Describe a planar geometry

A

3 equally space sp2 hybrid orbitals at 120 degrees angles (eg C2H4)

50
Q

What is resonance?

A

Phenomenon where molecules that contian single and double bonds adjacents to each other can exist as an average of multiple structures

51
Q

What is a resonance hybrid?

A

Molecule that exists in an average of two possible forms

52
Q

As a result of resonance, where must the chemical groups that make up the peptide bond be located?

A

In the same plane, due to the partial double-bond characte of the carbonyl and amino bonds which restricts rotation about these positions

53
Q

What is the conjugated ring system?

A

Ring-structured molecule that has alternating double and single bonds (ex adenosine)

54
Q

Where does resonance exist in nucleic acids?

A

In the bases, because they are conjugated ring systems, and in the phosphate group of the phosphodiester bonds

55
Q

How are dipole moments created?

A

when one atom is more electronegative than the other, or when an atom has one or more lone pairs of electrons, creating a separate positive and negative charge on the same molecules

56
Q

how are dipole moments indicated?

A

They are directional and as such are indicated by a small arrow starting from the positive charge and pointing to the negative charge

57
Q

What is a salt bridge?

A

Ionic interaction between pairs of oppositely charged molecules, such as amino acid side chains like arginine and glutamic acid.

58
Q

What are the 2 interactions involved in salt bridges?

A

(1)Hydrogen bonding and (2)electrostatic interactions

59
Q

What are the 3 types of weak chemical bonds?

A

(1) van der Waals forces
(2) hydrophobic interactions
(3) hydrogen bonds

60
Q

What are van der Waals forces? and explain the mechanism

A

(1) They are non-specific contacts between atoms
(2) when 2 atoms approach each other, induced fluctuating charges between them cause a weak, non-specific attractive interaction as they get closer. below a certain distance a more powerful van der Waals repulsive force is caused by overlapping of the atoms’ outer electron shell

61
Q

What is the van der Waals radius of an atom?

A

Distance at which these attractive and repulsive forces are balanced and is characteristic for each atom

62
Q

What needs to be exact for effective van der Waals interaction?

A

the intermolecular fit must be exact, because the distance between 2 interacting atoms must not be much different from the sum of their their van der Waals radii

63
Q

What are 2 common examples of van der Waals interaction in living system?

A

(1) antibody-antigen interaction

(2) ligands fitting into a ligand-bonding pocket

64
Q

How can van der Waals interactions become exceptionally strong?

A

the additive effect of many van der Waals forces can be exceptionally strong

65
Q

How do hydrophobic interactions arise?

A

From the exclusion of nonpolar groups by water molecules causing nonpolar molecules to adhere to one another
- it maximizes hydrogen bonding between water molecules and minimizes area of contact with hydrophobic molecules

66
Q

Name a few cellular functions where the hydrophobic effect is critical

A

insertion of protein molecules into membranes

secretion of hormones and other signaling moelcules

67
Q

What is entropy?

A

The thermodynamic quantity representing the unavailability of a system’s thermal energy for conversion into mechanical work, often interpreted as the degree of disorder or randomness in the system

68
Q

Describe the effect of hydrophobicity on the entropy of an aqueous environment

A

Hydrophobic molecules distort the usual water structure, forcing them into a rigid lattice of hydrogen-bonded water molecule. This lattice restricts the motion of a number of water molecules. This is energetically unfavourable because it decreases the entropy of the population of water molecules

69
Q

Describe the importance of hydrophobicity in DNA molecules

A

Favourable hydrophobic interactions between the aromatic rings of adjacent DNA bases allow for pi stacking. This contributes to nucleic acid stability

70
Q

What is Pi stacking?

A

It involves attractive, noncovalent interactions between aromatic rings. It occurs when 2 aromatic rings approach each other with the planes of their aromatic rings overlapping, with successive p-bonded system stacked like layers in a cake. Pi bond stacking forces contribute to nucleic acid stability

71
Q

What is the driving force in protein folding and stabilization?

A

Hydrophobic forces

72
Q

Why are hydrophobic interactions the driving in protein folding and stabilization?

A

The interior of folded proteins usually contains many hydrophobic amino acids and limited water. Unfolding a protein is an energetically expensive process.

73
Q

Explain the mechanism of hydrogen bonds

A

H atom must be bonded to a strongly electronegative atom, such as O, N or F, called H-Bond donor. This results in a partial positive charge with a large charge density that can attract the lone-pair of electrons from a non-hydrogen atoms with a partial negative charge, called the H-bond acceptor

74
Q

Describe hydrogen bonds (2 characteristics)

A

(1) they are highly directional

(2) they have some covalent character, which is more pronounce when donors are more electronegative

75
Q

Describe what is meant by “Hydrogen bonds are highly directional” and its consequences

A

Hydrogen bonds have directional preferences. They are strongest when the 3 atoms involved in the bond lie in a straight line. They are weaker when the atoms are structurally constrained and the straight line geometry is not possible

76
Q

Describe the importance of hydrogen bonds in DNA

A

The two complementary strands of DNA are held together by hydrogen bonds between nucleotide base pairs

77
Q

What causes the minor major grooves in the double helix structure?

A

Hydrogen bonds between nucleotide base pairs

78
Q

Where are proteins that recognize specific DNA sequences most likely to interact with the DNA molecule?and why?

A

Major grooves, because of its larger size which make it more accessible

79
Q

Where are positively charged amino acids most likely to interact with a DNA molecule

A

with the negatively charged DNA sugar backbone

80
Q

What role does hydrogen bonds play in proteins

A

Folding of a single polypeptide chain and interaction of multiple subunits in a protein complex, due to the amino acid residues which interact with each other and cause a polypeptide to fold in a specific manner

BHCM218 (24 decks)

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