A Biology Primer Part II: DNA, RNA, replication, and reproduction Vasileios Hatzivassiloglou University of Texas at Dallas.

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