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
