Study Guides (238,637)
Canada (115,266)
Biochemistry (220)

Final Exam Notes (McLachlin Lectures)

8 Pages
Unlock Document

Biochemistry 2280A
Derek Mc Lachlin

McLachlin Topic 18 Lecture Notes: Introduction to DNA and RNA Learning Objectives  Explain the chemical structure of nucleic acid polymers, without memorizing structures of the nitrogenous bases  Describe B-DNA and the higher order structures formed by RNA, and the important forces that stabilize these structures  Identify chemical and structural similarities and differences between DNA and RNA Major Functions of DNA and RNA  DNA – carries genetic material  RNA o Template for producing proteins (mRNA) o Makes up much of the ribosome (rRNA) o Carries amino acids to ribosome (tRNA) Building Blocks of RNA  Ribonucleotides, composed of three parts: a sugar, a nitrogenous base, and a phosphate Nitrogenous Bases  Two types of nitrogenous bases – purines and pyrimidines o All purines and pyrimidines are planar and hydrophobic  Purines found in DNA and RNA are adenine and guanine o They join to C1’ of ribose or deoxyribose via the N9 position  Pyrimidines are cytosine, which is found in both DNA and RNA, thymine, which is found in DNA but not RNA, and uracil, which is found in RNA but not DNA o Uracil is identical to thymine except that uracil lacks the methyl group o Pyrimidines join to C1’ of ribose or deoxyribose via the N1 position Polynucleotides  Phosphates are attached to C5’ position of ribose or deoxyribose by a phosphoester linkage  After a phosphate is attached to this position of a nucleoside, a nucleotide is formed  Nucleotides can be strung together to make polynucleotides  Sugars are joined to each other via phosphodiester linkages between C3' and C5'  The 5’ end of the polynucleotide is where the 5’ carbon is not attached to another monosaccharide  The 3’ end is where the 3’ carbon is not attached to another monosaccharide  Presence or absence of phosphate does not matter in identifying 3’ or 5’ end Direction of Convention  By convention, sequences are written 5' to 3'  For example, in the sequence GATC, the G has a hydroxyl or phosphate on its 5' carbon, and C has a free 3' hydroxyl (or phosphate)  Whether the molecule is DNA or RNA is usually clear from the context  Because there are 4 different monomer building blocks that can be used to assemble RNA polymers, the number of possible sequence combinations that can be made for an RNA molecule made of 100 nucleotides is 4 100 The DNA Double Helix (1953)  Two DNA strands associate to form a double helix  Model-building, constrained by 3 pieces of evidence Chargaff’s Rule  Erwin Chargaff analyzed DNA composition, late 1940s  Base composition of DNA varies among species  Within a species, base composition is same regardless of tissue, age, or environment  % of A = % of T and %of G = % of C Diffraction Pattern  Pattern suggests double-helix with a periodicity of 3.4 nm containing 10 repeating units Correct Tautomeric Forms of Bases  Different tautomers have different hydrogen bonding capabilities Double Helix: “B-DNA”  Sugar phosphate backbone, each one with a base attached to it  Two strands come together to form hydrogen bonds in between, and along the strands  Antiparallel – one strand runs 5’ to 3’ and the other is 3’ to 5’ o Opposite orientation pr chemical “polarity”  Phosphate groups are on the outside, with bases in the middle o This arrangement minimizes charge repulsion between phosphates and allows for salt stabilization of the phosphates’ negative charges  Right-handed Forces Stabilizing the Double Helix 1. Hydrophobic interactions  Bases are planar so they can stack on top of each other  Bases run perpendicular to the axes Bases are hydrophobic,  Stabilized by van der Waals interactions parallel to proteins – bases  Water is excluded are the most hydrophobic  Not sequence-specific component of DNA, thus 2. Base pairing they are found on the inside  Hydrogen bonds between nitrogenous bases  Water cannot interfere (it is excluded from the helix)  Sequence-specific Watson-Crick Base Pairing  A-T = 2 hydrogen bonds  G-C = 3 hydrogen bonds  Backbones are always the same distance apart Q: What sequence is complementary to AAATTT? o This is because each base pair consists of one purine A: AAATTT (5’ to 3’) and one pyrimidine base, giving a uniform base pair 5’ 3’ size AAATTT o Also, because water is excluded from the interior of the TTTAAA double-helix, it cannot compete with the bases for hydrogen bonding positions 3’ 5’  Because A pairs only with T, and G pairs only with C (and vice versa), the sequence on one strand dictates the sequence on the other o Thus, sequences are said to be complementary Features of DNA Double Helix (B-DNA)  Narrow, about 2 nm thick  Distance between base pairs = “rise” = 0.34 nm  One complete turns every 10.4 base pairs  Can be very long  Major and minor grooves (used by proteins to read sequence)  Reason for major and minor grooves o Bases are not symmetrically orientated relative to the backbone Differences between DNA and RNA  DNA has 2’ deoxyribose and RNA has ribose o RNA is degraded into mononucleotides in alkaline solution, but DNA is stable o Presence of a hydroxyl group at the 2’ position of ribose makes the phosphodiester bond of RNA - sensitive to base (OH)  DNA has thymine, RNA has uracil o RNA lacks a methyl group, base pairs with adenine just like thymine o Difference with lack of methyl group does not affect base pairing properties  In general, DNA strands are longer than RNA strands  DNA is usually double-stranded, while RNA is usually single-stranded o RNA strands base-pair with themselves, resulting in irregular structures  Nitrogenous bases are more likely to be modified in RNA than DNA, and the variety of modifications is larger RNA Structure  DNA structure is sequence independent; RNA structure is sequence-dependent (like proteins) o In DNA, any sequence forms essentially the same structure Summary – Intro to DNA and RNA  Nucleic acids are composed of nucleotide monomers (sugar + nitrogenous base + phosphate)  B-DNA is a right-handed, antiparallel double helix stabilized by hydrogen bonding and hydrophobic interactions  RNA is usually single-stranded and forms sequence-dependent structures McLachlin Topic 19 Lecture Notes: Chromatin Learning Objectives  Explain the different levels of structural organization displayed by DNA in eukaryotic cells  Describe the structure of the nucleosome  Explain the effect of DNA packaging on gene expression and identify, in general terms, the key mechanisms cells use to alter DNA packaging to regulate gene expression Human DNA must be Condensed  The human genome is about 3 x 10 base pairs long  At 0.34 nm per base pair in the double helix, that’s 102 cm  Two copies of each chromosome per cell  Human DNA must be condensed about 10,000-fold to fit inside the nucleus DNA Packaging  Highly organized  Despite being condensed, DNA must remain available for replication, repair and gene transcription  Eukaryotic DNA is condensed with the help of specialized proteins  The protein/DNA complex is called chromatin Histones  Eukaryotic proteins involved in condensing DNA (prokaryotes use different proteins)  Contain fewer than 200 amino acids  Rich in lysine and arginine residues (positively charged which is ideal to interact with negatively charged DNA)  Five types: H1, H2A, H2B, H3 and H4  Histones are rich in arginine and lysine o Have 2-3 times more arginine and lysine than in other proteins Histone Octamers  Octamers contain two copies each of histones H2A, H2B, H3 and H4  The DNA double helix wraps around the histone octamer 1.65 times (146 base pairs) Nucleosomes  Histone octamers are called nucleosome core particles  Core particles are linked by stretches of DNA 3 – 80 base pairs long o Linker region  A nucleosome consists of a core particle and one adjacent linker region  Nuclosomes compact the DNA strand by a factor of about three 30-nm Chromatin Fibres  Second level of DNA packaging  Nucleosomes can pack into a coil called 30-nm chromatin fibre  Requires histone H1, which stabilizes the fibre  Structure is still controversial  In the 30-nm chromatin fibre, the length of DNA has been compacted by factor of about 100 Higher Levels of DNA Packaging  30-nm fibres form loops of 30-200 kbp  Loops are anchored to the nuclear matrix, made up of RNA and non- histone proteins  Loops are packed together to form the chromosome, which is about 1400 nm thick in its fully condensed form, just before cell division Chromosome Remodeling  Packaged DNA is unavailable for transcription  Chromosome remodel
More Less

Related notes for Biochemistry 2280A

Log In


Don't have an account?

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.