Ch 3,5-16 Flashcards
Week 6: DNA and energy
List 4 main features of DNA structure
- Directionality (5’ to 3’) (phosphate group to hydroxyl group)
- Hydrogen bonds between bases (A–T, C—G)
- Antiparallel strands
- Double-stranded DNA (two complementary chains of nucleotides)
- Uniform diameter
Identify DNA building blocks
- sugar(deoxyribose)
- phosphate (makes up sugar phosphate backbone)
- nucleotide bases (adenine, guanine, thymine, cytosine)
Define Gene and describe how DNA is divided and organized in the cell
Gene: functional unity of DNA
- translated and transcribed into RNA or proteins
DNA molecules are divided into chromosomes
(23 different chromosomes and 2 copies of each)
(1 DNA molecule = 1 chromosome)
Heredity
transmitting information (traits) from one generation to the next (molecular basis of inheritance is DNA)
Describe how DNA is condensed into chromatin
- “beads-on-a-string”
closely packed nucleosomes are comprised of a string (DNA) and series of “beads” which are nucleosome core particles
Nucleosome core particles
- complex of eight histone particles along with segment of double-stranded DNA (147 nucleotides long) that winds around the histone octamer
Function of Histone
- histone tails get charged with positively charged amino acids (positive charges help histones bind to negatively charged sugar-phosphate backbone)
- like charges repel other histone tails (loosen up DNA structure), opp charges attract other histone tails (tighten histone tails)
- chromatin fiber
- nucelosomes further packed to generate compact structure (via conformational changes due to histone) - Chromatin fibers folded into loops
- nonhistone chromosomal proteins bind to specific DNA sequences to create a clamp at the base of each loop - mitotic chromosome (final level of packing)
Describe 3 features of chromosomes
Features of chromosomes enable segregation and maintenance
- Centromeres:
specialized DNA sequence that allows duplicated chromosomes to separate during M phase (nuclear and cytoplasmic division) (spindles attach to it ) - Telomeres:
Repetitive nucleotide sequence that caps ends of chromosomes: used to counteract the tendency of chromosomes to shorten its ends after each replication - Origin of Replication
Where DNA replications begins (there are many sites on each chromosome)
Discuss the highly dynamic nature of chromatin, and the molecular basis for this dynamic behaviour
Chromatin packing varies within one chromosome
Heterochromatin: densly packed DNA (exists as mitotic chromsomes)
- used to make certain DNA features inaccessible (closed) to enzymes such as telomeres and centromeres
euchromatin: less dense DNA (exists as beads on string or chomatin fiber)
- used to make DNA segments accessible to enzymes (allows for repllication, repair, and mRNA synthesis)
Dynamic behaviour due to reversible chemical modification of histones
- histone tails are subject to covalent modifications (addition / removal of acetyl, phosphate, or methyl groups)
- changes can either reduce affinity of tails for adjacent nucelosomes and thereby loosen chromatin structure
- tails serve as docking sites to regulatory proteins (each modification attracts specific nonhistone chromsomal proteins to particular stretch of chromatin which can promote condensation or expansion)
Distinguish chromosomes from chromatin
Chromatin:
complex of DNA and proteins that makes up the chromosomes in eukaryotic cell
Chromosome:
long string-like structure composed of DNA and proteins that carries genetic information:
Chromatin is a condensed version of chromosomes when cell is not dividing
What is the correct mode of DNA replication
semi-conservative model
1. parent strand becomes a template for complementary daughter strand
Identify where on chromosome replication begins
Begins on origins of replication
Identify proteins involved in DNA replication and discuss how they allow DNA synthesis
- Helicase
- uses ATP to unwind DNA double helix ahead of replication fork - DNA polymerase
- catalyzes addition of nucleotides to 3’ end of growing strand - Primase
- synthesizes RNA primers along lagging-strand template - Nuclease
- degrades RNA primers and repair polymerase replaces it with DNA bases - Ligase
- uses ATP to join Okazaki fragments made on lagging-strand template - Single strand binding proteins
- found on lagging strands: prevents base pairs from re-forming before lagging strand can be replicated - Topoisomerase
- produces transient nicks in DNA backbone to relieve tension built up due to DNA unwinding ahead of DNA helicase)
What direction does DNA polymerase synthesize?
DNA polymerase synthesizes DNA strand in 5’ to 3’ direction
Describe continuous and discontinuous DNA synthesis of the two parental strands
Continuous:
- Proteins involved: Helicase, primase, polymerase,
1. Helicase unnwinds DNA at replication forks
2. primase creates a primer for polymerase to start
3. polymerase adds 5’phosphate groups to 3’ acetyl groups until replication forks converge or there is no more DNA template strand left
Discontinuous:
- Proteins involved: Helicase, Primase, polymerase, ligase, single-strand binding proteins
1. Primase creates RNA primers on lagging strand
- Polymerase synthesizes new DNA until it reaches another RNA primer to create an Okazaki fragment
- Nuclease degrades RNA primers and DNA polymerase (called repair polymerase) replaces it with DNA bases)
- DNA ligase joints 5’ phosphate end to 3’ acetyl group
- As steps 1 - 4 are done repeatedly, single-stranded binding proteins prevent unwinded DNA from forming bonds
How do cells follow the first two laws of thermodynamics
- Conservation of Energy
Cellular metabolism = anabolic (synthesize) + catabolic (break down) reactions
- uses energy to make chemical bonds + large macromolecules - Universe tends towards disorder (cells create and maintain order from disorder) (releases heat into surroundings to maintain order)
Compare and contrast oxidation and reduction
LEO:
Loss of electrons is oxidation
GER:
Gain of electrons is redution
Name types of bonds that hold enzyme-substrate complex together
Van der Waals attractions,
Hydrogen bonds,
electrostatic attractions
Describe how enzymes accelerate chemical reactions and allow energetically unfavorable reactions to occur
enzyme (catalyze) lowers activation energy for a chemical reaction
- inrease rate of chemical reaction by allowing larger number of random collisions
- lowered activation energy = greater probability for reaction to occur
Describe how context affects energetically favorable reactions and can render them energetically unfavorable
Example:
Gradients
- if a product has a higher concentration than its reactants, the reaction will be less likely to proceed as the concentration gradient acts against the forward reaction.
- prevents overproduction of certain molecules within our bodies
State two ways an enzyme can make an energetically unfavorable reaction happen
- Coupled reactions
coupling an unfavourable reaction to energetical favourable one
(gibbs free enegy of total coupled reaction is negative (spontaneous)) - Siphon off
unfavourable reaction can be made favourable if other forces such as concentration gradient are strong
ex. Assume reaction X-Y and Y-Z. Y is likely to convert to X than X is to convert to Y BUT Y is more likely to convert to Z than it is to X. Thus, the concentration of Y decreases as it gets converted to Z. So, the equilibrium between X and Y shifts more towards Y and thus the reaction from X to Y is more energetically favourable.
Define activated carrier, list several activated carriers, discuss why activated carriers are important in the cell
Activated carrier: molecule that stores energy as transferable chemical group or as high energy electrons to be used in metabolic reactions.
Examples:
ATP, acetyl CoA, NADH, NADPH, FADH2, GTP .
Stores excess energy from energetically favourable reaction to fuel energetically unfavorable reactions.
Describe how ATP allows the unfavorable reactions of DNA synthesis, RNA synthesis, or protein synthesis to proceed
- Activated Step:
ATP transfers phosphate to produce a high-energy intermediate - Condensation step:
intermediate reacts with second molecule in reaction to form the desired product.
- results in release of inorganic phosphate
hydrolysis of product and inorganic phosphate is highly favourable and drives overall reaction in direction of polymucleotide synthesis
