Module 01 - Section 1 Flashcards
What is molecular Biology?
Study of essential cellular molecules, including DNA, RNA and proteins, and the biological pathways between them
What other areas of biology and chemistry does molecular biology overlap with the most? (2)
Genetics and biochemistry
How many amino acids are there?
20
What is the Central Dogma of molecular biology?
Biological information flows in this direction:
DNA->RNA->Protein
What are the 2 exceptions to the central Dogma
RNA viruses, Non-coding RNAs
Why are RNA viruses exception to the central dogma?
They have RNA as their genetic material (RNA->RNA)
Why are non-coding RNAs exception to the central dogma?
RNA molecules are not translated into protein (DNA->RNA, but no protein)
What is transcription?
The process where DNA is used as a template to make and RNA copy
What is the enzyme responsible to read the DNA template and incorporate complementary nucleotide to make a strand RNA?
RNA polymerase
What are the 3 types of RNA?
mRNA, tRNA, rRNA
Which type of RNA is a transient molecule?
mRNA or Messenger RNA
What is the function of mRNA?
Carries the instruction for building specific proteins from the nucleus(DNA) to the ribosomes in the cytosol for translation
True or False: one gene can encode several mRNAs, and one mRNA can be the template for many proteins
True
Which RNA type is responsible to carry the instructions to translate specific proteins from the nucleus to the cytosol?
mRNA
What is rRNA?
the RNA component of a ribosome
Which type of RNA is the most abundant? (about 85% of all RNA)
rRNA
What is the function of rRNA?
rRNA combine with many different ribosomal proteins to form the ribosome complex, creating a factory for protein synthesis
Which type of RNA is called the adaptor molecule?
tRNA
What is the function of tRNA
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
Outline the mechanism of tRNA
(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
What are the building blocks/components of Nucleic Acids? (3)
(1) Nitrogenous Base
(2) Pentose(5-carbon) sugar; ribose or deoxyribose
(3) At least 1 phosphate group
Name the two Purines
Adenine and Guanine
PURple flAG
Name the 3 pyrimidines
Cytosine, Thymine, Uracil
PYRamids are sharp and may CUT
What are the 3 fundamental differences between DNA and RNA?
(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)
What type of bonds link 2 nucleotides?
phosphodiester bonds
What is a phosphodiester bond?
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
What is the directionality of nucleic acids
5’ to 3’, based on their free ends which are called termini
What does having directionality means for nucleic acid
Nucleotide can only be added on the 3’ end
What are the building blocks/components of amino acids? (3)
(1)Amino group
(2)Carboxyl Group
(3) R Group
All of which are attached to the central (alpha) carbon
What kind of bonds link amino acids together?
Peptide bonds
What is a peptide bond?
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
What are Amino acid resisudes
Amino acids, once incorporated into a polypeptide chain
What is the directionality of polypeptide chains?
N-terminus(amino) to C-Terminus (carboxyl)
What determines how a polypeptide will fold?
the interaction between the R groups and the external environment
What determines a protein’s function?
its 3-dimensional structure
What are some roles of proteins?
Catalyzing biochemical reactions, structural roles, receiving/transmitting chemical signals, transport of ions across membranes
What determines the interactions, affinity and functions of nucleic acids and proteins?
their chemical properties
What stems from chemical properties?
How biomolecules interacts and function and waht affinity or specificity they have
What are the two types of strong chemical bonds?
Covalent and Ionic
Describe Strong Chemical Bonds (3)
(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)
Describe covalent bonds (2)
(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
Describe ionic bonds
(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
What is Electronegativity?
Propensity of an atom within a moelcule to attract electrons to itself
Electronegative atoms = tendency to gain electrons
Electropositive atoms = tendency to lose electrons
How to predict bond character?
Difference in electronegativities between 2 atoms
0-0.4 = Nonpolar covalent bonding
0.4-1.67=polar covalent bonding
1.67+=ionic bonding
What is Valence?
The maximum number of covalent bonds a particular atom can form to completely fill its outer shell
How many, respectively, can H, O, N and C form?
1, 2, 3, 4
What are the 2 bond geometry important to this module?
Tetrahedral, planar
Describe Tetrahedral geometry
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)
Describe a planar geometry
3 equally space sp2 hybrid orbitals at 120 degrees angles (eg C2H4)
What is resonance?
Phenomenon where molecules that contian single and double bonds adjacents to each other can exist as an average of multiple structures
What is a resonance hybrid?
Molecule that exists in an average of two possible forms
As a result of resonance, where must the chemical groups that make up the peptide bond be located?
In the same plane, due to the partial double-bond characte of the carbonyl and amino bonds which restricts rotation about these positions
What is the conjugated ring system?
Ring-structured molecule that has alternating double and single bonds (ex adenosine)
Where does resonance exist in nucleic acids?
In the bases, because they are conjugated ring systems, and in the phosphate group of the phosphodiester bonds
How are dipole moments created?
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
how are dipole moments indicated?
They are directional and as such are indicated by a small arrow starting from the positive charge and pointing to the negative charge
What is a salt bridge?
Ionic interaction between pairs of oppositely charged molecules, such as amino acid side chains like arginine and glutamic acid.
What are the 2 interactions involved in salt bridges?
(1)Hydrogen bonding and (2)electrostatic interactions
What are the 3 types of weak chemical bonds?
(1) van der Waals forces
(2) hydrophobic interactions
(3) hydrogen bonds
What are van der Waals forces? and explain the mechanism
(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
What is the van der Waals radius of an atom?
Distance at which these attractive and repulsive forces are balanced and is characteristic for each atom
What needs to be exact for effective van der Waals interaction?
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
What are 2 common examples of van der Waals interaction in living system?
(1) antibody-antigen interaction
(2) ligands fitting into a ligand-bonding pocket
How can van der Waals interactions become exceptionally strong?
the additive effect of many van der Waals forces can be exceptionally strong
How do hydrophobic interactions arise?
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
Name a few cellular functions where the hydrophobic effect is critical
insertion of protein molecules into membranes
secretion of hormones and other signaling moelcules
What is entropy?
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
Describe the effect of hydrophobicity on the entropy of an aqueous environment
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
Describe the importance of hydrophobicity in DNA molecules
Favourable hydrophobic interactions between the aromatic rings of adjacent DNA bases allow for pi stacking. This contributes to nucleic acid stability
What is Pi stacking?
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
What is the driving force in protein folding and stabilization?
Hydrophobic forces
Why are hydrophobic interactions the driving in protein folding and stabilization?
The interior of folded proteins usually contains many hydrophobic amino acids and limited water. Unfolding a protein is an energetically expensive process.
Explain the mechanism of hydrogen bonds
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
Describe hydrogen bonds (2 characteristics)
(1) they are highly directional
(2) they have some covalent character, which is more pronounce when donors are more electronegative
Describe what is meant by “Hydrogen bonds are highly directional” and its consequences
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
Describe the importance of hydrogen bonds in DNA
The two complementary strands of DNA are held together by hydrogen bonds between nucleotide base pairs
What causes the minor major grooves in the double helix structure?
Hydrogen bonds between nucleotide base pairs
Where are proteins that recognize specific DNA sequences most likely to interact with the DNA molecule?and why?
Major grooves, because of its larger size which make it more accessible
Where are positively charged amino acids most likely to interact with a DNA molecule
with the negatively charged DNA sugar backbone
What role does hydrogen bonds play in proteins
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
