A Biology Primer Part II: DNA, RNA, replication, and reproduction Vasileios Hatzivassiloglou...
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Transcript of A Biology Primer Part II: DNA, RNA, replication, and reproduction Vasileios Hatzivassiloglou...
A Biology PrimerPart II: DNA, RNA, replication, and
reproduction
Vasileios Hatzivassiloglou
University of Texas at Dallas
Last time we covered
• Biological classification
• Organisms, tissues, cells and organelles
• Main cell functions and the role that proteins play
• Primary structure of proteins as a sequence of amino acids
Protein manifestation
• Amino-acid sequence provides primary structure (one dimensional)
• Specifies protein’s native state in the physical world
• Actual form of protein folding affected by other things as well – a major bioinformatics problem
Protein secondary structure
• Alpha-helix is the main secondary structure (local folding)
• Scale: 0.5 nm wide, 1.5 nm long per amino acid
• Connection every four amino acids
Tertiary structure and beyond
Example protein structure
Significance for biology
• Three-dimensional folding affects what the protein can do
• Predicting three-dimensional structure from amino acid sequence enables understanding of protein function
• Statistical and rule-based (including grammar-based models)
Deoxyribonucleic acid (DNA)
• Another macromolecule (polymer) found in the nucleus of cells
• Contains all genetic information• Consists of connected nucleotides• Each nucleotide is connected via
infrastructure consisting of a phosphate and a sugar molecule (deoxyribose)
• The structural blocks are the nucleotides or bases
DNA Bases
• Only four bases– Adenine (A)– Cytocine (C)– Guanine (G)– Thymine (T)
• One-dimensional structure• Chemical properties impose ordering (like
proteins) from 5’ end to 3’ end
DNA base pairing
• Hydrogen bonds between A-T and C-G (order matters)
DNA in three dimensions
• Famous double helix
• Can be “unzipped”
• Anti-parallel configuration between the two strands (5’-to-3’ with 3’-to-5’)
The Double Helix
DNA size
• Measured in bases (kb or Mb)
• In bacteria, one circular helix
• In more complex organisms, organized into chromosomes (each one helix)
• E. coli: one helix, 4.6 Mb
• Yeast: 15 Mb
• Humans: 23 double chromosomes, smallest has 50 Mb, total 3 Gb
DNA information content
• Different types of regions:– Regions that code for a protein (genes)– Regions that regulate when the gene is
expressed as a protein, typically nearby– Regions that we don’t know what their
function is (“junk” DNA)
Number of genes
• Varies by complexity of organism• E. Coli: about 4,000• Yeast: about 6,000• C. Elegans (1mm worm): about 13,000• Humans: about 32,000 (thought to be 100,000)
• Genes packed and uniformly distributed in prokaryotes, not so in eukaryotes
• Only 3-10% of human DNA is “useful”
The genome
• Total gene content for an organism
• Genes will vary from individual to individual, but will be substantially identical (99.9% in humans)
Ribonucleic acid (RNA)
• Very similar chemically to DNA
• Differences:– the base uracil (U) replaces thymine (T).
Similar chemically, both bond with adenine (A).
– the sugar ribose replaces deoxyribose– generally single-stranded– partially self-hybridizes (thus forming three
dimensional structure)
RNA function
• Can pack the same information as DNA
• Serves as an intermediate stage during gene expression
• Carries information around the cell
• Is part of certain cell structures (ribosomes)
Major biological processes
• Replication (from DNA to DNA)– occurs during cell division both internally and
when the organism is reproducing
• Gene expression (from DNA to protein via RNA)– may occur once or often
Reproduction
• Three main mechanisms– In single-cell organisms, one cell division
(binary fission) is enough– Asexual reproduction can do the same on a
larger scale (many cells), e.g., plants that grow from cuttings
– Sexual reproduction is used by the majority of complex organisms
Cell division
• Simpler in prokaryotic organisms (single-cell)
• A parent cell produces two identical or nearly identical daughter cells (exponential growth)
• Mutations can occur here (especially in bacteria)
Phases of a cell’s life
• Growth (G1)
• Replication (S)
• Growth (G2)
• Division (M)
• Repeat until eventual apoptosis (cell death)
Replication
• The DNA double helix is “unzipped” into two single complementary strands by an enzymatic protein (DNA polymerase)
• Each DNA strand attracts the corresponding base from a “soup” of free nucleotides
• The two strands join together (with the same hydrogen bonds between A-T and C-G)
DNA replication
Complications in replication
• Replication can only occur in the 5’-to-3’ direction (can only add to the 3’ end)
• One strand is replicated normally
• The other strand is replicated in short pieces
• Another protein (DNA ligase) puts the fragments together
• Errors can occur!
Binary fission
Cytokinesis
• Actual division of the cell
• Cytosol and organelles are distributed about equally
• Slightly different process in animals (via cleavage) and plants (via cell plate)
Cleavage in animal cells
• Cleavage furrow formed by actin and myosin
Diploid vs. haploid
• Diploid cells contain paired chromosomes from father and mother (homologues)
• Haploid cells have only one chromosome of each kind
• Organisms can be diploid (humans), haploid (fungi), or alternate between the two stages (marine algae)
How organisms reproduce
• In asexual reproduction, a single cell division is enough
• In sexual reproduction, two haploid cells join together to form the new organism– Haploid organisms can just join– Diploid organisms must produce special
haploid cells (germ cells)
Division in diploid eukaryotes
• DNA replication (S, synthesis phase)
• Cell division (M, mitosis) for somatic cells
• Special double division (M, meiosis) division for germ cells or gametes
Mitosis
• Breakdown of nuclear membrane
• Chromosomes duplicate creating sister chromatids attached at the centromere
• Chromosomes separate and each is guided towards one area of the cell
• Cytokinesis occurs
Mitosis