1
Q
When does the central dogma fail
A
- RNA viruses - They only follow RNS to Protein
- Non coding RNAs - Not translated into proteins. DNA > RNA > Nothing
2
Q
What are the types of RNA
A
Messenger RNA
* carries instructions for building proteins
* Where RNA polymerase reads DNA molecule and pairs RNA bases to bases with DNA
* mRNA carries DNA messahe to ribosome outside of nucleus
* One gene can code for many mRNA and they can encode several proteins
Ribosomal RNA
* Structural component of ribosome in cytoplasma
* Most abundant DNA by 85%
* Several strands combine witrh different ribosomal proteins to form the complex
Transfer RNA
* transfer amino acids from cytoplasms to their approporaite location to growing peptide chain
* each tRNA carries sequence of 3 bases ca;;ed amtocpdpm
* codon codes for specific amino acid bound to tRNA moelcule called codon
* codon codes for specific amino acid to tRNA molecule
* when acid linked tRNAs allign side by side with mRNA amino acids are tattached to the tRNA
3
Q
What are the purines and pyrimidines
A
Purines
* 2 rings A, G
Pyrimidines
* single ring C,u,t
4
Q
What are differences between DNA and RNA
A
- DNA is double stranded
- DNA nucleotides contain deoxyribose sugar RNA has ribose
- difference there is a 2’ OH group
- DNA has thymine not uracil
- Uracil lacks methyl group at carbon 5 atom
5
Q
What are some chemical properties of nucleic acids
A
- Strands of DNA and RNA composed of polymers of nucleotide monomoers
- They are linked together to sugar groups
- phosphodiester bonds formed between 5’ Phosphate and 3’ OH of adjacent nucleotide
- Defined by cheical convention of numbering carbon atoms in pentose suga rring
- Nucleotides have directionality
6
Q
What are the components of amino acids
A
Amino groups
* Nitrogen group
* can have 1-3 Hs depending on the pH of the solution
* Partipiatestes in a peptide bond
Carboxyl group
* can lose H from C acid
* giving negative charge at physio pH
* when OG is lost it can partipitate in a peptide bond
* Also called he alpha carboyl group since directly conded to the alpha carbon
R group
* Unique side chains
* Vary in structure size, electrical charge and hydrophobicity
7
Q
What are polypeptides
A
- Chain of amino acids
- once added to chain called amino acid residues
- peptide bonds formed between amino group of 1 and the carboxyl group the adjacent
- polypeptide chains hhave directionality at their termini. Amino to carboxyl or N-terminus to C-terminius
8
Q
What are proteins
A
- Functional protein composed of single or multiple polypeptide subunits
- Interactions between R groups and external environment determine how polypeptide will fold
- Creates a 3d Structure
- Proteins are abundant in all cells
- Perform many functions
- Catalyzing Biochemical reactions - enzymes
- Serve structural roles - membranes
- Recieving and transmitting chemical signals - neurotransmitters
- Transpport specific ions nadm olecules across cellular membranes
9
Q
What are the strong chemical bonds
A
- Involve short distance interactions between 2 atoms
- Generally require a catalyst to break them
Covalent bonds
* 2 atoms share electrons to fill theur octets
* Involved non-metal sharing electrons with another non metal
Ionic bonds
* One or more electrons completely transffered from one atom to another
* One atom will be positively charged and the other will be negatively
* The electrostatic attraction between those 2 forces is what keeps them together
10
Q
What is Electronegativity
A
- Determines whether 2 atoms are likely to form a bond
- Unequal electron sharing reflects different affinities of bonded atoms for electrons
- Those that lose electrons are electroopositive atoms
11
Q
How does EN predict bond character
A
- difference in EN can detemine what kind of bond is present
- < 0.4 Nonpolar covalent
- 1.7 > x > 0.4 Poalr covalent bondings
- > 1.7 is ionic bond
12
Q
Briefly describe bond geometry
A
- Single binds permit free rotation around bond
- Double bonds create rigid planar structures
tetrahedral
* Bond angle 10.5 and sp3 hybridization
Planar
* equally spaced sp2 orbitals
* Arranged 120 degrees
13
Q
What is peptide resonance
A
- Resonacne in chemical bonds make up peptide bond
- Must be located in same plane
- Due to partial double bond character of the carbonyl amino bonds
- Restricts Rotation about these poistions
- Bases themself have conjugated ring system
- Have alternating double and single bonds
- Gives rise to shared electrons around the ring
- Accuracy of base pairing between 2 DNA strands with A T and C with G from dominance of a pair
14
Q
What is the significance of polar covalent bonds
A
- use 3d structure to deterine polarity
- Seperayed by positiv and negative dipole moment
- Dipole is directional and represented by a small arrow (see diagrams)
15
Q
What are the polar covalent bonds in molecules
A
- Large size of proteins and nucleic acid allows polar and nonpolar regions to exist within the same molecule
- Other surfaces of proteins that function in aqueous environments of cytoplasms tend to be polar
- Favours interactions with poalr water molecules
- Proteins that function in nonpolar environment of cell membranes tend to have nonpoalr surfaces
- Plays large role in protein structure via hydrogen bonds
16
Q
What are the ionic interactions between biomolecules
A
- Between pairs of oppositely charged amino acid side chains
- Not limitedt o arginine and glutamic acid
- FOrms a salt bridge
- Involves combination of 2 weak interactions - H bonding and electrostatic interactions
- see diagram
17
Q
What are the types of weak Chemical bonds
A
- Hydrophobic interactions
- Hydrogen bonds
- Van der waals forces
- Weak bonds involve greater distances between atoms
- They are easily broken and transient
- Properties can be useful in biological systems wjere transient chemicla interactions are essential part of cellular function
- Weak bonds mediatet interactions of proteins with small molecules
- DNA and other proteins
18
Q
What are van der waals forces
A
- nonspecific contacts between 2 atoms
- when 2 atoms approach each other
- Induced by fluctuating charges between them
- Depends heavily on distance between the interacting atoms as distance decreases below a force iis caused by overlap of the atoms outer electron shells
- Van der waals radius 0 distance when attractive and resplsive forces are balanced
Interactions in biomolecules
* fit must be exact
* Distance between 2 interacting atoms must not be much different from the sum of their van der waals radii.
* Strongest van der waals happen when macromolecules contain surface that precisely fits shaoe of the molecule that binds
* Antibody-antigen interactions or ligand fitting into a ligand-bonding pocket
* Althought van der waals interactions are weak additive effect of many van der waals forces can be strong
19
Q
What is the hydrophobic effect
A
- Means water fearing
- Refers to nonpolar molecules in water
- Arise from exclusion of nonpolar groups by wtaer molecules causing nonpolar molecules to adhere to one another
- Includes insertion of protein molecules into membrane and secretion of hormones and signalling molecues
20
Q
What is hydrophobocity and entropy
A
- Nonpolar molecules cannot form H bonds with water molecules
- This distorts the shape of water and causes water lattices to form
- Water is in constant motion and does not like being organized
- This is energetically unfavourable since it reduces randomness of the system and entropy
- Nonpolar molecules do not push water away. Water just does not want to interact with these molecules
21
Q
How is hydrophobicity found in DNA
A
- Pi stacking involves noncovalent interatcions between aromatic rings
- Favourable hydrophobic interactions between adjacent DNA bases contribute to nucleic acid stability
- pi interactions, pi electrin to pi electrin called aromatic or piui bonding occurs when 2 aromatic rings approach
- With sucessive pi-bonded systems stacked like layers. Bi bonding stacking firces contribute to stability
22
Q
What is hydrophobicitu in proteins
A
- Driving force in protein stabilization and folding
- Interior of folded proteins usually contains hydrophobic amino acids and limited water
- Unfolding a protein is energetically expensive process. Energy required to do so mainlu goes toward disrupting the stabilizaing hydrophobic effect
23
Q
What are hydrogen bonds
A
- Partner bonder to strong electronegative atom like O,N,F
- Called H bond donor
- Hydrogen has parttially postive charge with large charge densitu that can attract lone pair of electrons from a non-hydrogne atom with partial negativity
24
Q
What are strong H bonds
A
- Not simple attraction between positive nad negative
- have directional preferneces and some characteristics of a covalent bond
- More pronounced when acceptors form H bonds with donors on more EN atoms
25
What are strong and weak H bonds
* Attraction is greatest when 2 atoms involved in the bond are in a straight line
weak
* when the H bonded moieties are structurally constrained
* When an ideal straight line is not possible
26
What are the H bonds in DNA
* 2 complementary strands are held together by H bonds
* G/C has 3 H bonds
* A/T has 2 H bonds
* The helix ecomes composed of major and minor grooves
27
What is a Helix major and minor grooves
* grooves lined by potential H bond donor and acceptor atom that enables specific interactions in proteins
* larger size of the major groove, DNA is more accessible for interactions with proteins that recognize specific DNA sequences
28
What are the H bonds in proteins
* Key role in 3d stricture
* H bond donors and acceptors found on amino acid residues wiythin a polypeptide can interact with each other
* Causes the polypeptide to fold in a specific manner
29
What is the basic structure of proteins
* categorized by chemical properties
* Side hcains distinguish R group of the amino acid
* Alpha carbon in the middle
* Amino group can be primary, secondary or teritiary, and a carboxyl group
30
What are the 5 types of amino acids
NONPOLAR
* Aliphatic
* Aromatic
POLAR
* Uncharged
* Negatively charged
* Positively Charged
31
What is a basic overview of Nonpolar amino acids
* 7/20 amino acids
* Side chains are composed of Hydrocarbon chains
* This makes them nonpolar and hydrophobic
* They usually end up on the interior of proteins to minimize contact with water
32
What are the nonpolar amino aicds
GLYCINE
* Smallest side chain
* only a single H atom in the R group contributes veryy little to Hydrophobic effect
ALANINE,VALINE,LEUCINE,ISOLEUCINE
* All have Side chains made of simple chains
* varying in arrangements
METHIONINE
* R group is a functional group connectibbity of C-S-C
PROLINE
* Only amino acid with side chain that connects to the amino group
* Causes a 5 membered ring to be rigid and limits conformations
33
What is an overview of the aromatic amino acids
* Phenylalanine, tryosine, tryptophan
* Very bulky
* relatively hydrohpbic
* contribute greatly to hydrophobicity
* Phenylalanine is most hydrophobic
* Tyrosine OH group and impart polarity to these rediues all participate in Hydrophobic interaction
34
What are the chemical propertoes of aromatic amino acids
* Tryptophan and tyrosine and to a much lesser exttent phenylalanine
* Can absorb light
* By the amino acids accounts for characteristics of light by most proteins at wavelength 280
35
What are the polar Uncharged Amino acids
* Polar uncharged side chains interact extensively with water or atoms through H bonding
* Serine, Theorine, asparagine, glutamine, and cysteine
CYSTEINE
* Contains a sulfhydryl group
* 2 cysteines togetner make a disulfide bond
* contains 2 regions of 1 or more polypeptide chains within a protein and acts as a molecule cross-brace to enhance protein stability
* Cysteine plays a structural role
* Residues are important catalytic functions of many enzymes as deprotenated SH is a good nucleophile
ASPARAGINE
* Contains an amide group
* can be a donor or acceptor of electrons
* Can also contain a carbonyl grpip that partipiates in H bonding and dipole-dipole interactions
SERINE and THEORINE
* have OH group
* Can form H bonds
* Can also be pshophorylated along with OH of tyrosine by kinases
* Results in protein mods
36
How do disulfide bonds stabilize some proteins
* They are the strongest bonds and connect large parts of polypeptides together
37
negatively What aret he polar positively charged amino acids
* Aspartate and glutamat
* Side chains have a carbonyl group and carry negative charge at pH 7.0 they are weak acids
* reffered as aspartic and glutamic acid
38
What are the polar positively charged amino acids
* carry positive charge at pH 7.0
* Lysine, arginine, histidine
* Lysine has a side cjain amino group
* Arginine has a guandinum group
* Histidine contains imidazole group
39
What are the locations of the charged amino acids
* They are hydrophillic
* typically make ionic bonds \ and H bond with water
* Located on the exterior of proteins
40
How do charged amino acids work for enzyme function
* charged amino aacid side chains form hydrogen bonds and ionic inertactions with oppositely charged molecules including other amino acids
* Side chains are hydrophillic and located in the active suite of many enzymes such as DNA polymerase
41
How are amino acids zwitterions
* They are weak acid/bases
* At neutral pH they exist predominantly as zwitterions
* have ability to donate and accept proton H from their amino carboxyl groups
* Ammonium and carboxylate can be viewed as arising via kind of intramolecular Acid-base reaction
IONIZATION
* refers to charge state of molecule
* charge on amino, carboxyl, and some R groups determined by pH
* R rgoups of amino acid can ionie and in peptidecontribute to overall acid-base properties
* acid-base behaiour can be predicted by its free amino and alpha carbpxyl groups combines with nature and number of ionizable R groups
42
What are the pkA values of ionizable groups in amino acids
STRENGTH OF AMINO ACID IN SOLUTION
* lower pKa stronger acid, easier tendency to give up protons
* Higher pKa sttronger base and stronger tendency to accept electrons
* Aspargate and glutamate have low pKa values
* Makes these amino acids mor esuspectible to donate protons from their R groups
* Arginine and lysine have high pKa making these amino acids more susceptive to recieing protons via their R group
43
Why is pH important
* influences structure and function of many enzymes
* Some enzymes have a narrow range of pH activity such as pepsin which works best at ph2
* Works best becasue C.acid group in amino enzyme active site must be in protenated states
* at low pH group is protenated which allows it to catalyze chemical reactions of breaking chemical bonds
* ph values higher than 2. C. acid becomes deprotenated and is unable to partipate in chemical reactions
PEPSIN INACTIVATION
* pH mediated will unactive at high pH
* pH would be higher among existing stomahc environment where it is less acidic
44
How is cellular pH regulated
* Bodies use buffer system to regulate amount of Hydrogen ions present in bloodstream
* lungs use this system
* Lungs will expel it
* Combines blood to make carbonic acid - partially dissassociates into hydronium and bicarbonate
* when blood reaches lungs CO2 domes out of solution and expelled
45
How is Glycine ionized
* when amino acid lacking ionizble R rgoups
* dissolve water in neutral pH
* Exists as a zwitterion
* simple monoamino monocarboxylic alpha amino acid such as glycine diprotic acid when fully deprotenated
* Has 2 COOH groups and NH group that can yield protons
(SEE DIAGRAM)
46
What are the pH Equations
* pH = -log H
* pOH = -log OH
* pH + pOH = 14
47
What are conjugate acids and bases
* differ by each otehr by presence or absence of a single H ion
* every acid has a conjugate base
ACETATE AND ACETATE ION
* when acetic acid dissolved in water
* Water serves as base and accepts protons to become hydronium
* Acetate ion remains and consdered conjugate base
AMMONIA AND AMMONIUM
* WHen base dissolved in water proton moves from water to the base
* Water gives up proton to the amonnia results in products ammoumn and hydroxide
48
What are acids and pKA
ACID DISSASSOCIATION IN WATER
* Designation of acid or base as conjugate depends on context
* Ha dissaossicaed in squeous solution releasing proton H
ACID DISSOCIATION CONSTANT KA
* acids and bases are stronger than others
* Can be described by acid dissassociation constant Ka
PKA - LOGARITHIMIC CONSTANT
* Ka values can span many orders and magnitudes
* it describes a ratio of charged A to neutral Ha acid molecules at equilibrium in aqueous solution
* Larger value of pKa, the smaller
HENDERSON HASSELBALCH EQUATION
* eists between pH of solution and ratio of Base to Acid
* Ratio determines pH of a solution
* means that the pH of a solution withweak acid equals the pKa of weak acid plug log of ratio of concentration of its acid Ha and basic forms A
* when pH > PkA - ratio of A to HA to greater than 1
* when pH < pKa - ratio of A to HA less than 1
49
WHat happens when pH = pKa
group exists in a 50-50 mixture of acidic and conjugate nbase
if solution is less than pKa the further balance between acid and conjugate base is tipped
If pH is less than pKa, then acid form the compound predominates
if pH is greater than pKa conjugate base predominates
50
BCHM218
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