Mod 1 Flashcards
When does the central dogma fail
- RNA viruses - They only follow RNS to Protein
- Non coding RNAs - Not translated into proteins. DNA > RNA > Nothing
What are the types of RNA
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
What are the purines and pyrimidines
Purines
* 2 rings A, G
Pyrimidines
* single ring C,u,t
What are differences between DNA and RNA
- 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
What are some chemical properties of nucleic acids
- 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
What are the components of amino acids
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
What are polypeptides
- 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
What are proteins
- 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
What are the strong chemical bonds
- 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
What is Electronegativity
- 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
How does EN predict bond character
- 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
Briefly describe bond geometry
- 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
What is peptide resonance
- 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
What is the significance of polar covalent bonds
- use 3d structure to deterine polarity
- Seperayed by positiv and negative dipole moment
- Dipole is directional and represented by a small arrow (see diagrams)
What are the polar covalent bonds in molecules
- 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
What are the ionic interactions between biomolecules
- 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
What are the types of weak Chemical bonds
- 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
What are van der waals forces
- 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
What is the hydrophobic effect
- 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
What is hydrophobocity and entropy
- 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