1
Q
what is molecular biology?
A
the study of essential cellular molecules, including DNA, RNA, and proteins, and the biological pathways between them
2
Q
what is the central dogma of molecular biology?
A
the theory states that biological information flows in the following direction:
DNA->RNA->Protein
3
Q
what are the two exceptions to the central dogma of molecular biology?
A
- RNA Viruses: viruses that have RNA as their “genetic” material (RNA->DNA)
- Non-Coding RNA: RNA molecules that are not translated into protein (DNA->RNA, but no protein)
4
Q
What is transcription?
A
- a section of DNA is used as a template to make RNA copy
- the enzyme RNA polymerase reads the template sequence of DNA and incorporates completemntary nucleotides to make a strand RNA
5
Q
the information coded within DNA directs the synthesis of what 3 types of RNA?
A
- mRNA: messenger RNA
- rRNA: ribosomal RNA
- tRNA: Transfer RNA
6
Q
What is mRNA?
A
- messenger RNA
- a transient molecule that carries the instructions for building a specific protein (that is encoded within DNA) to the preexisitng ribosomes
7
Q
w
when is mRNA synthesized?
A
mRNA is synthesized during transcription, where the enzyme RNA polymerase reads a strand of the DNA molecule and pairs RNA bases to the bases in DNA.
This results in a single stranded RNA molecule, that has a sequence directed by DNA
8
Q
What happens to mRNA following (after) transcription?
A
mRNA carries the DNA message physically out of the nucleus (in eukaryotic cells) to the ribosomes waiting in the cytosol. Here, the mRNa will be translated into a protein
9
Q
How many mRNAs can one gene encode? How many proteins can be made from one mRNA?
A
- one gene can encode several mRNAs
- one mRNA can be the template for many proteins
10
Q
What is rRNA?
A
- ribosomal rna
- the rna component of a ribosome, which is the structure within the cytoplasm that is necessary for protein synthesis
- rRNA is the most abundant type of RNA in a cell comprising nearly 85% of all RNA
11
Q
What forms the ribosome complex?
A
several strands of rRNA combine with many different ribosomlal rpoteins to form the ribosome complex, creating a factory for protein synthesis
in bacterai and eukaryotes, the ribosome consists of a large subunit and a small subunit
12
Q
Across different species, the size and base composition of rRNA molecules are very highly _______________
A
conserved
13
Q
what is the adaptor molecules in protein synthesis?
A
tRNA are the adaptor molecules, they function as an adaptor between the nucleic acid and protein
14
Q
what is tRNA?
A
tRNA serves to transfer individual amino acids from the cytoplasm to their approproate location in the growing polypeptide chain during protein synthesis
15
Q
what are RNAs (all of them) transcribed from?
A
DNA genes
15
Q
what is the anticodon of a tRNA?
A
- each tRNA contains a sequence of 3 bases, called the anticodon
- this anticodon is complementary to a small section of the mRNA molecule, called the codon (the codon codes for a specific amino acid, which is bound to the tRNA molecule)
- when two amino acid linked tRNAs align sd=ide by side on the mRNA, the amino acids attached to the tRNA can be joined together, producing a growing polypeptide chain. this process is known as translation
16
Q
what is the group of functional RNAs?
A
- rRNA and tRNA molecules constitute a group of functional RNAs
- they fold into 3 dimensoional shapes involved in the synthesis of every type of protein
17
Q
what is unique about mRNA in terms of their shape?
A
while rRNAs and tRNAs fold into 3 specific dimensional shapes, each mRNA type are transient molecules specific for each different protein
18
Q
what is a nucleotide?
A
an organic molecule that is the basic structural unit for DNA and RNA
19
Q
what are the 3 key components of a nucleotide?
A
- a nitrogenous base
- a pentose (or five carbon) sugar: ribose or deoxyribose
- at least one phosphate group
20
Q
what are the purines?
A
purines have two rings within their structure. there are two purines found in nucleic acids:
* adenine
* guanine
21
Q
what are the pyrimidines?
A
only have one ring in their structure. there are 3 found:
* cytosine
* uracil
* thymine
22
Q
what are the three fundamental differences between dna and rna?
A
- dna is doublestranded while rna is single stranded
- dna contains the five carbon sugar deoxyribose, wherase rna nucleotides contain ribose sugar. the difference between these two sugars is a hydrozyl group on the 2’ carbon
- in addition, dna contains the base thymine, rather than uracil found in rna. uracil lacks a methyl group at carbon 5 atom
23
Q
what are the strands of dna and rna composed of?
A
composed of polymers of nucleotide monomers. means that the individiual nucleotide within dna and rna are linked together to form polynucleotides.
24
how do polynucleotides form?
this occurs through the pentose sugar groups on the nucleotides, where phosphodiester bonds are formed between the 5' phsohpate (PO4) on one nucleotide and the 3' hydroxyl (OH) of the adjacent nucleotide (as defined by the chemical convention for numbering carbon atoms in the pentose sugar ring)
25
what is the directionality of nucleic acids?
5'-->3' based on their free ends
26
what is the similar structure of all 20 common amino acids?
* a central carbon atom called an alpha carbon atom which is bonded to four different chemical groups: an amino group, a carboxyl group, an R group, and a lone hydrogen atom
27
what is the amino group of an amino acid?
ex. H3N
this group can have 1-3 hydrpgens depending on the solutions pH and whether the nitrogen is participating in a peptide bond. it is called an a-amino group since it is bonded directly to the a-carbon
28
what is the carboxyl group of an amino acid?
COO-
this group can lose the hydrogen from the carboxyllic acid, giving it a negative charge at physiological pH. A hydroxyl is lose when it participates in a peptide bond. it is called an a-carboxyl group since it is bonded directly to the a-carbon
29
what is the R group of an amino acid?
each amino acid has a unique side chain, or R group, bonded to the a carbon. these r groups vary in structure, size, electrical charge, and hydrophobicity
30
what is a polypeptide?
simply a chain of amino acids
31
once incorporated into a polypeptide chain, what is an individual amino acid referred to as?
amino acid residues
32
when are peptide bonds formed?
formed between the amino group of one amino acid and the carboxyl group of the adjacent amino acid
therefore, polypeptide chains also have directionality at their termini (amino acid to carboxyl- N terminus to C terminus)
33
What can a functional protein be comprised of
a functional protein can be composed of a single polypeptide or multiple polypeptide subunits
34
What role do the R groups play in terms of a polypeptide?
the interactions between the R groups and with the external environment will determine how a polypeptide will fold
35
what is important about the 3 dimensional structure of a protein?
the 3 dimensional structure of a protein determines the proteins function
36
what are some functions of proteins?
* catalyzing biochemical reactions
* serving structural roles
* receiving and transmitting chemical signals within and among cells
* transporting specific ions and molecules across cellular membranes
37
what is the signifigance of chemical properties of biomolecules?
* the interactions, affinity, and functions of nucleic acids and proteins stem from their chemical properties
* chemical features are at work determining how DNA, RNA, and proteins fold, react, and interact
38
what is a molecule's affinity fro another molecule based on?
based on molecular function and specificity, and is a consequence of the number and types of interactions they form
39
what are chemical bonds?
attractive forces that hold atoms together, to create atomic aggregates
40
what are strong chemical bonds?
* involve short distance interactions between atoms
* generally require a catalyst to break them
* play a major role in the formation and stability of nucleic acid and amino acid polymera, since these molecules are joined together by covalent chemical bonds
41
what are the two types of strong chemical bonds?
* covalent bonds
* ionic bonds
42
what are covalent bonds?
two atoms share eelctrons to fill the outer shell between their positively charged nuclei
covalent bonds usually involve a non metal sharing electrons with another non metal
43
what are ionic bonds?
* one or more electrons completely transferred from one atom to another
* one atom now has a positive charge, while the other is negatively charged
* it's the electrostatic attraction of these oppositely charged ions that hold them together
* ionic bonds usually involve a non metal and a metal
44
what is electronegativity?
is the tendancy of an atom within a molecule to attract electrons to itself
45
what does unequal sharing of electrons mean?
unequal sharing of electrons reflects different affinities of the bonded atoms for electrons
46
what are atoms with a tendancy to gain electrons referred to as?
electronegative atoms
47
what are atoms with the tendancy to lose electrons referred to as?
electropositive atoms
48
what is the pauling scale of electronegativity?
* consists of dimensionless values ranging from 0.7-3.98 for each atom
* a higher number indicates a higher electronegativity
* on the periodic table, the number underneath each element repersents the electronegativity value
49
what can the difference in electronegativities between two atoms be used for?
can be used to predict te type of bonding between them
50
what does it mean when the difference in electronegativities if very small or zero?
the bond is purely covalent
51
what does it mean when the difference between two atoms is greater than zero but less than 1.67?
the bond is polar covalent
52
what does it mean if the electronegativity difference between atoms is greater than 1.67?
ionic bond
53
what is a non polar covalent bond?
electrons are shared equally
54
what is polar covalent bonding?
electrons are shared unequally
55
what is ionic bonding?
electrons are transferred
56
what is a atoms valence?
* the maximum number of covalent bonds that a particular atom can form is called its valence
* the valence of the atom dictates its chemical properties, and ultimately the behavior of these molecules, even for large polymers such as nucleic acids and proteins
57
why do single bonds and double bonds differ in there geometrics?
* single bonds permit free rotation of the bound atoms around the bond, while double bonds give rise to more planar geometrics and are more rigid
58
# w
what is tetrahedral bond geometry?
a central atom is located at the center with four substituents that are located at the corners of the tetrahedron
59
what is planar bond geometry?
a planar molecular geometry is made up of three equally spaced sp2 hybrid orbitals arranged at 120 degree angles
60
what does it mean if some bonds can have partial double character?
there is restriction of rotation around the bond, resulting in planar geometry. this typically occurs in molecules that undergo resonance
61
what is resonance?
when molecules that contain single and double bonds adjacent to each other can exist as an average of multiple structures. a resonance hybrid is a molecule that exists in an average of two possible forms
62
what is resonance in peptides?
* an example of resonance in biology is the molecular structure around the peptide bond
* as a result of resonance, the chemical groups that make up the peptide bond must be located in the same plane
* this is due to the partial double bond character of the carbonyl and imino bonds, which restrict rotation about these positions
* this has big impact on the structure and function of proteins
63
# w
what is resonance in nucleic acids?
* resonance can exists within the bases and phosphate group of the phosphodiester bond
* this gives the phosphodiester bon a tetrahedral geometry, where the negative charge on the phosphate group can shift between two oxygen atoms that are not bound to sugars in the backbone
* the bases themselves are conjugated ring systems- that is they have alternating double and single bonds, which gives rise to shared electrons around the rings
* also the accuracy of base pairing between the two dna strands, A with T and C with G results from the dominance of particular resonance structures of the bases
64
does resonance add or decrease stability to molecules?
adds
65
How does resonance play a role in the benzene ring? How do electrons be delocalized around the benzene ring and how does that lead to the formation of a resonance hybrid?
* benzene has 3 double bonds in the ring
* the double bonds can switch positions
* benzene is always in between the two possible structures and double bonds
* the lower energy state structure is when the electrons and bonds are delocalized
66
what is an electric dipole moment?
* combination of separated positive and negative charges in a molecule
* a dipole moment is directional and is repersented by a small arrow pointing from the positive charge toward the negative charge
67
what type of molecule is water considered to be?
a polar molecule
68
if a molecule has no separation of charged and has balanced charges, what is it
non polar
69
what does the large size of proteins and nucleic acids allow molecules to be?
allows polar and non polar regions to exist within the same molecule
70
What are hydrogen bonds and what role do they play in terms of the polarity of water?
* hydrogen bonds are weak bonds
* the polarity of water, which fosters interactions with polar sections of proteins, plays a large role in protein sructure and function via hydrogen bonds
71
describe the polarity of the cell membrane.
the interior of the cell membrane is hydrophobic and therefore the regions of transmembrane proteins that pass through it are also hydrophobic, while the protein regions on the outer surface of the cell membrane are hydrophillic and make contact with water.
72
Where can ionic interactions occur?
ionic interactions cn occur between pairs of oppositely charged amino acid side chains in biomolecules, such as (but not limited to) arginine and glutamic acid.
73
What is a salt bridge?
a salt bridge involves a combination of two weak interactions: hydrogen bonding and electrostatic interactions.
the amino acids with side chains that most often form side bridges are: arginine, lysine, aspartic acid, and glutamic acid
74
what are the side chains that most often form side bridges?
arginine, lysine, aspartic acid, and glutamic acid
75
what are the components of a salt bridge?
* the blue bars represent the nitrogen atoms in the arginine side chain
* the red bars represent the oxygen atoms in the glutamic acid side chain
* the negative charges on the oxygen attract the positive charges on the nitrogen, forming a salt bridge
76
what are the 3 kinds of weak chemical interactions?
* van der waals forces
* hydrophobic interactions
* hydrogen bonds
77
What is the difference of weak bonds compared to strong bonds?
* weak bonds involve greater distance between atoms
* are easily broken
* are individually transient
* these properties can be useful in biological systems, where transient chemical interactions are an essentialm part of cellular functions
78
what are van der waals forces?
* they are non specific contacts between atoms
* when atoms approach each other, as they get closer, induced fluctuating charges between them cause a weak, nonspecific attractive interation
* this interaction depends heavily on the distance between the interacting atoms
* as the distance decreases below a certain point, a more powerful van der waals repulsive force is caused by overlap of the atoms outer electron shells
79
what is the van der waals radius of an atom?
it is the distance at which these attractive and repulsive forces are balanced and is characteristic for each atom
80
why does the intermolecular fit be exact for atoms to interact effectively using van der waals forces?
the intermolecular fit must be exact, because the distance between any two interacting atoms must not be much different from the sum of their van der waals radii
81
how do hydrophobic interactions arise?
it arises from the exclusion of non polar groups by water molecules, causing nonpolar molecules to adhere to one another
82
how does water molecules have a decreased randomness/entropy?
* a nonpolar molecule cannot form hydrogen bonds with water molecules, so it distorts the usual water structure, forcing the water into a rigid lattice of hydrogen bonded water molecules, which surround the nonpolar molecule.
* water molecules are normally in constant motion, and the formation fo such lattices restrict the motion of a number of water molecules; the effect is to increase the structural organization of water
83
what is pi stacking?
* involves attractive non covalent interactions between aromatic rings
* this type of bonding can occur between the rings in adjacent dna bases and involves favourable hydrophobic interactions that contribute to nucleic acid stability
* pi interactions are pi electron to pie electron, called aromatic or pi bonding, occurs when two aromatic rings (conjugated p systsems) approach each other with the planes of their aromatic rings overlapping, with successive p bonded systems stacked like layers in a cake
* pi bond stacking froces contribute to nucleic acid stability
84
what is a driving force in protein folding and stabilization?
hydrophobic interactions
85
what are hydrogen bonds?
* one partner in the bond is a hydrogen atom (H)
* must be covalently bonded to a strongly electronegative atom, such as oxygen, nitrogen, or flourine
* The hydrogen is referred to as the H-bond donor, and this hydrogen has a positive charge with a large charge density that can attract the lone-pair of electrons from a non hydrogen atom with a partial negative charge, referred to as the H-bond acceptor
* the atom which donates its hydrogen atom is called the h-bond donor, while the atom that accepts the hydrogen atom is called the h-acceptor. the resulting bond is called a hydrogen bond.
86
hydrogen bonds are highly (fill in blank) .
directional
* hydrogen ond has a directional preference and some characteristics of a covalent bond
* this covalent characer is more pronounced when acceptors form hydrogen bonds with donors on more electronegative atoms
87
what is a strong hydrogen bond?
the attraction is greatest when the three atoms involved in the bond lie in a straight line
88
what is a weak hydrogen bond?
when the hydrogen bonded moieties are structurally constrained (ex. when they are parts of a.single protein molecule), the ideal line geometry may not be possible and the resulting hydrogen bond is weaker
89
how does hydrogen bonding play a role in the structure of the double helix?
* as a consequence of hydrogen bonding, the structure of the double helix is composed of major and minor grooves
* each groove is lined by potential hydrogen bond donor and acceptor atoms that eable specific interactions with proteins
* the larger the size of the major groove in dna makes it more accessible for interactions with proteins that reckignize specific dna sequences
90
how does hydrogen bonding play a role in the structure of proteins?
h-bond donor and acceptors found on amino acid residues within a polypeptide can interact with each other and cause the polypeptide to fold in a very specific manner
91
BCHM218 Module 1
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