Macromolecules - Nucleic Acids PDF

Announcement Make sure you got 100% for “Grade”  “Roll call attendance” !! Notify me by 10 pm, Thursday Jan 12th if you were present in first class but didn’t receive 100%. Some Fundamentals The importance of ‘carbon’ The carbon atom (C) is the most important atom in the biological molecule C...

Announcement Make sure you got 100% for “Grade”  “Roll call attendance” !! Notify me by 10 pm, Thursday Jan 12th if you were present in first class but didn’t receive 100%. Some Fundamentals The importance of ‘carbon’ The carbon atom (C) is the most important atom in the biological molecule Carbon containing compounds owe their diversity and stability to specific bonding patterns of carbon -Valence of 4 - Interacts and bonds with other atoms by sharingthe 4 available electrons to establish a full set of 8 electrons in bonding – octet rule The importance of ‘bonding’ Bonding can be single, double or triple bonds. The more the bonding the stronger the interaction, and breaking them requires more energy Energy required to break bonds is called bond energy - measured by ‘calories’ The types of ‘bonding’ Ionic bonding (based on exchange of +ve or –ve charge; strongest) Covalent bonding (sharing orbital electrons, strong) Di-sulfide bonding – a type of covalent bond (strong) Hydrogen bonding (milder) Van derWaals forces (weak interactions) Khansacademy Hydrophobic interactions (interactions for fear of water) Socratic wiki sciencenotes Macromolecules 1. Robert Hooke first discovered and named “cell” in 1665, but what was he observing? a) Tiny hollow compartments b) Animal cell c) Plant cell wall devoid of its contents d) Plant cell e) Rodriquez Hernandez Macromolecules Proteins: orchestrates cellular mechanics Nucleic acids: information storage, transmission and conservation Several cellular processes are controlled within the confines of membranes https://opm.phar.umich.edu/biological_membranes The importance of ‘self-assembly’ Several synthesized macromolecules (proteins, nucleic acids, lipids) have the property of self assembly Meaning that once they are synthesized, they assemble into distinct conformations or structures, and they can be reconstituted in vitro (outside the cell) Molecular chaperones assist the assembly (proper folding) of proteins Hierarchical Assembly provides advantages to the cell Quality control can be exerted at each level of assembly The Macromolecules of the Cell 4 types of macromolecules, proteins, nucleic acids Polysaccharides, and lipids ‘Monomer s’ ‘Monomers’ are building blocks of macromolecules Macromolecules Monomers Most biological macromolecules in cells are synthesized from about 30 common small molecules (aka. ‘monomers’) Assembly of the small molecules ‘monomers’ into different lengths and configurations creates self-identity and diversity of macromolecules. Macromolecules synthesis Macromolecules synthesis 1. Are always synthesized by the stepwise polymerization of similar or identical molecules called “monomers” 2. The addition of each monomer occurs with the removal of water molecule, and is therefore termed a “ condensation reaction” 3. The monomeric units that are to be joined must be present as an activated monomers, before condensation occurs. Activation usually involves coupling of the monomers to a carrier molecule 4. The energy required to couple monomers to the carrier is provided by a molecule called adenosine tri- phosphate (ATP) or related high-energy compound 5. Because of the way they are synthesized, macromolecules have an inherent directionality. This means that the 2 ends of the molecule are chemically different from each other 2. _______ is the most important atom in the biological realm a) Nitrogen b) Oxygen c) Hydrogen d) Carbon 1. Macromolecules: Nucleic Acids Nucleic Acids  Nucleic acids are linear polymers of nucleotides  The two major types of nucleic acids are: 1. DNA (deoxyribonucleic acid), and 2. RNA (ribonucleic acid) *DNA and RNA differ in their chemistry and role inside cells  Only in DNA Only in RNA Nucleic Acid Components Nomenclature  Nucleosides are the precursors, sugars-attached- to a base (so 2 parts: (1) Sugar and (2) base) Adenosine, Guanosine, Cytidine, Uridine (RNA) Deoxyadenosine, deoxyguanosine, deoxy cytidine and deoxy thymidine (DNA)  Nucleotides have one or more phosphate group attached to sugar + Base (so 3 parts: (1) phosphate, (2) Sugar and (3) base) For Example: Adenosine monophosphate (AMP) has one, Adenosine diphosphate (ADP) has two, and adenosine triphosphate (ATP) has three phosphate groups  Polymers of nucleotides are the nucleic acids RNA, and DNA Nucleotides are the monomers, and building blocks of nucleic acids Phosphorylated forms of Adenosine ATP, GTP, CTP and TTP (or UTP) are the activated monomer used in nucleic acid The Polymers Are DNA and RNA Adenosine triphosphate (ATP) The Polymers Are DNA and RNA  Nucleic acids are linear polymers of nucleotides  Nucleotides are linked by a 3ʹ,5ʹ phosphodiester bridge (a phosphate group linked to two adjacent nucleotides via two phosphodiester bonds)  The polynucleotide formed by this process has a directionality with a 5ʹ phosphate group at one end and a 3ʹ hydroxyl group at the other  Nucleotide sequences are conventionally written in the 5ʹ to 3ʹ direction Nucleic Acid Synthesis  A preexisting molecule is used to ensure that new nucleotides (NTPs for RNA, dNTPs for DNA) are added in the correct order  This molecule is called a template, and correct base pairing between the template and the incoming nucleotide is required to specify correct order  A complementary relationship exists between certain purines and pyrimidines  Hydrogen bonding Chargaff’s Rules Reveal That A = T and G = C  Erwin Chargaff showed that the DNA from different cells of a given species has the same percentage of each of the four bases. The base composition varies among species  Chargaff observed that for all DNA samples examined, the number of A = the number of T, and the number of G = the number of C  These are called Chargaff’s rules 3. I have a DNA of 500 base pairs. The total ‘G’ nucleotides account for 27%, how many ‘T’ nucleotides are there? a) 27% b) 46% c) 23% d) Ricardo Henriquez Nucleic Acid Synthesis Inside cells, Nucleic acids are synthesized by proteins, and it requires a pre-existing DNA or RNA molecule which is referred to as a Template The presence of a template ensures that the correct base pair is added to a complementary strand – therefore effectively copying cellular information  DNA is synthesized from existing DNA molecules by DNA-dependent DNA polymerases - the process is called DNA replication  RNA is synthesized from existing DNA molecules by DNA-dependent RNA polymerases – the process is called Transcription  These polymerases are found in all living organisms Nucleic Acid Synthesis: Exceptions Exceptions are seen in viruses  Some viruses (such as SARS-CoV2) replicate their RNA from existing RNA molecules and encode for RNA- dependent RNA polymerase or RNA Replicase (synthesize RNA from RNA)  Other viruses (such as retrovirus, HIV) encode for RNA- dependent DNA polymerase called reverse transcriptase to synthesize a DNA from RNA molecule Nucleic Acid Synthesis 5’ 3’ Nucleic acid synthesis end end progresses in the 5’  3’ direction Meaning, new nucleotides (monomers) are added, by joining an existing 3’ OH group with a new 5’ phosphate group. 3’ 5’ end end Nucleic Acid Synthesis (double-bond) Complementary Base Pairing 5’ 3’ end end is Facilitated by hydrogen bonding A – T (2 hydrogen bonds) G – C (3 hydrogen bonds) Synthesis progresses in an anti-parallel fashion 3’ (triple-bond) 5’ end end The DNA Molecule Is a Double-Stranded Helix It codes for the information contained within a cell It is hereditable into new progeny through DNA replication ( or duplication) DNA also contains information for the synthesis of RNA and proteins (central dogma of life) 4. Which component of DNA and RNA is responsible for the “acidic” part of nucleic acid? a) the phosphate group b) the 5-carbon sugar c) the nitrogenous base d) there is actually nothing acidic about DNA and RNA The RNA Molecule Is predominantly Single-Stranded  Hydroxyl group at C2’ in RNA can cleave the phosphodiester bridge formed between nucleotides, a property seen in Ribozymes (RNA enzymes)  Since this hydroxyl group is absent in DNA, the polymer is much more stable and lasts for a much longer time than it would with the hydroxyl. Thus, DNA can act as a stable long-term repository for genetic information. How stable? 1. RNA usually degrades within your cells in 30 minutes 2. DNA lasts your whole lifetime, and intact DNA thousands or millions of years old may be able to be recovered from frozen mammoth carcasses and mosquitoes trapped in amber. RNA-folding: H-bonding with complementary base pairs in the same strand RNA Base Pairing and RNA  RNA is normally single stranded  Secondary RNA structure also depends on base pairing  However, the pairing is usually between bases in different areas of the same molecule and is less extensive than that of DNA EXAMPLE of RNA folding  RNA folding can be extensive  RNA is capable of forming highly complex structures. RNA’s are but intermediates between DNA and Protein RNA-folding/structure translates to its function Types of RNA molecules based on structure/ function Functions are based on their structure and ability to bind: 1. Proteins, 2. RNA, 3. DNA 5. Which of the following are properties of RNA? a) Deoxyribose, uracil, and a globular structure b) Deoxyribose, ribose, and uracil c) Ribose, uracil, and a linear structure d) Ribose, thymine, and a linear structure 6. Which of the following is not a true characteristic of an RNA molecule? a) It contains deoxyribose sugar b) It contains the nucleotide uracil c) It can be single stranded d) It can be double stranded Nucleic acids also undergo hierarchical assembly DNA = double stranded helix, contains ’T’ RNA = usually single stranded, can form double strands in certain viruses, contains ‘U’ instead of ‘T’ Secondary and tertiary structures of RNA play critical roles in their function DNA functions can be controlled by its quaternary structure Becker’s World of the Cell Chapter 3 (pg 58-62)