1. Human Genetics
The Human Genome 1

2. Genome
The genome of an organism is the complete set of genes specifying how its phenotype will develop (under a certain set of environmental conditions).
Diploid organisms (like us) contain two genomes, one inherited from our mother, the other from our father.
The total DNA of an organism.
Nuclear genome refers to the total DNA in the nucleus, which is distinguished from organellar genomes of the mitochondria and chloroplast.

3. Genome size variation

4. Comparison of genome organization

5. Eukaryotic Genomes are Variable in Size
Marbled lungfish
139,000,000,000
Salamander
50,000,000,000
Homo sapiens
3,000,000,000
Pufferfish
400,000,000
Fruit Fly
165,000,000
Arabidopsis
100,000,000
Baker’s yeast
12,067,280

6. Why the big differences?
Do Marbled Lungfish differ from Pufferfish?
Are Lilies all that much different than Arabidopsis?
These differences exist because:
Genomes have duplicated (chromosome doubling)
Individual genes have duplicated.
DNA exists that has no coding function.

7. Gene structure I. Gene definition II. Genome organization (eukaryotic)
1. Genes and their noncoding regulatory sequences
2. “Nonfunctional” DNA
3. Duplicated genes
4. Repetitive DNA
III. Mobile DNA
IV. Gene Regulation

8. Some Terms
A duplicate of a gene may acquire mutations and emerge as a new gene.
Noncoding DNA: a sequence of DNA contained in eukaryotic genomes that does not encode any genetic information and often consists of repetitive sequences.
Expression: DNA transcribed into RNA and RNA turned into protein are expressed. The regulation of this process is called gene expression.

9. Nomenclature on DNA quantity
bp = one base pair within a double-stranded DNA
kb = 1,000 base pairs of double-stranded DNA
mb = 1 million base pairs of double-stranded DNA
n = number of chromosomes in a haploid genome
2n = number of chromosomes in a diploid genome

10. Definition(s) of a Gene
1. A hereditary unit that is composed of a sequence of DNA and occupies a specific position or locus.
2. Broadly, any genetic determinant of a specific functional gene product.
3. Molecular definition:
Entire nucleic acid sequence necessary for the synthesis of a functional polypeptide (protein chain) or functional RNA

11. Genes and Their Products
The majority of genes are expressed as the proteins they encode.
The process occurs in two steps:
Transcription = DNA -> RNA
Translation = RNA -> protein
This is the “Central Dogma" of Biology:
DNA makes RNA makes protein.

12. The Central Dogma of Molecular Biology
WHY?
The DNA can retain integrity
The RNA step allows amplification
Multiple steps allow multiple points of control
Protein
DNA
Translation
RNA
Transcription

13. Most Genes Encode Proteins
Original Concept of the Gene:
One gene = one enzyme
This concept does not hold for those proteins that consist of two or more different subunits.
Revised Concept:
One gene = one messenger RNA = one peptide.

14. RNA Genes
Some RNAs (tRNA, rRNA, snRNA, mtRNA) don’t code for proteins that are translated.
However, these are still referred to as genes-they are specific functional gene products.
Other DNA sequences regulate the transcription of other genes and can act like genes in some ways.

15. Genes are interspersed along DNA molecules, being separated by DNA sequence of unknown function (intergenic regions)

16. Coding region
Nucleotides (open reading frame) encoding the amino acid sequence of a protein
The molecular definition of gene includes more than just the coding region.

17. Noncoding regions Regulatory regions Introns
RNA polymerase binding site
Transcription factor binding sites
Introns
Polyadenylation [poly(A)] sites

18. “Nonfunctional” DNA Higher eukaryotes have a lot of noncoding DNA
80 kb
Higher eukaryotes have a lot of noncoding DNA
Some has no known structural or regulatory function (no genes)

19. Duplicated genes Encode closely related (homologous) proteins
Clustered together in genome
Formed by duplication of an ancestral gene followed by mutation
Five functional genes and two pseudogenes

20. Mobile DNA Moves within genomes
Most of moderately repeated DNA sequences found throughout higher eukaryotic genomes
L1 LINE is ~5% of human DNA (~50,000 copies)
Alu is ~5% of human DNA (>500,000 copies)
Some encode enzymes that enable movement

21. Transposition Movement of mobile DNA
Involves copying of mobile DNA element and insertion into new site in genome

22. Why? Molecular parasite: “selfish DNA”
Probably have significant effect on evolution by facilitating gene duplication, which provides the fuel for evolution, and exon shuffling

23. RNA or DNA intermediate
Transposon moves using DNA intermediate
Retrotransposon moves using RNA intermediate

24. LTR (long terminal repeat)
Flank viral retrotransposons and retroviruses
Contain regulatory sequences
Transcription start site and poly(A) site

25. LINES and SINES Nonviral retrotransposons
RNA intermediate
Lack LTR
LINES (long interspersed elements)
~6000 to 7000 base pairs
L1 LINE (~5% of human DNA)
Encode enzymes that catalyze movement
SINES (short interspersed elements)
~300 base pairs
Alu (~5% of human DNA)

26. Human Disease and Mobile DNA
Movement (transposition) of LINES and SINES can cause mutations and genetic disease by insertion into essential genes
Hemophilia (blood clotting factor VIII gene)
Muscular dystrophy (DMD)
Colon cancer (APC)

27. RNA Transcription
The process of releasing information contained in a DNA sequence, because DNA itself is used only for storage and transmission.
The sequence of bases in the DNA template is copied into an RNA sequence, which is either used directly or translated into a polypeptide.

28. Noncoding DNA can be Part of Transcribed Genes
Regulatory regions (Promoters)
Introns
Poly A+ Addition sites
5’ untranslated regions
3’ untranslated regions.

29. Basic Gene Structure -35 -10 Prokaryotes like E. coli GC CAAT TATA
Humans and other Eukaryotes

30. Bacterial Gene

31. Human Genes Most have introns
Produce monocistronic mRNA: only one encoded protein
Large ( 1000->1,000,000 base pairs)

32. Gene Transcription and Regulation

33. A Puzzle about Cells
Each Cell has a complete copy of all the DNA. And yet, cells are different.
This is the theoretical basis of organism cloning.
So cells are only using some of the DNA to make RNA to make proteins at any time.
How does the cell know which DNA to chose to transcribe?
External environment sends signals that are recognized, and transcription is turned on or off in response to the signals.

34. Transcription
Transcription is the synthesis of RNA from a DNA template.
Main Types of RNA each have different roles in the cell:
mRNA= Messenger RNA
tRNA = Transfer RNA
rRNA = Ribosomal RNA
mtRNA = Mitochondrial RNA
snRNA = Small nuclear RNA

35. rRNA and tRNA are Cogs in the Machinery
rRNA is a structural part of the ribosome
tRNA helps the protein machinery to read the mRNA
Neither of these types of RNAs actually carries any information

36. Messenger RNA
Messenger RNA carries the information in the DNA to the protein translation machinery (ribosomes)
Serves as the template for protein synthesis
Which mRNAs are transcribed in a cell decide the fate of that cell since they dictate which information in the DNA is read by the protein translation machinery

37. RNA molecules Synthesized by RNA polymerases using DNA as a template.
Polymer of ribonucleotides, where each consists of a phosphate group (PO4), ribose sugar, and a base (adenine, guanine, cytosine, or uracil).
Following synthesis of an RNA strand, it remains single-stranded.

38. Gene Regulation can occur at any of these steps
Initiation- highly regulated step
Elongation- the rate at which the mRNA is made can control how quickly its made
Termination- premature termination can mean that the whole mRNA never gets made and neither does what it codes for:
Like receiving only part of the instructions on how to put together your “easy to assemble” bookcase/desk/whatever

39. Steps of RNA Transcription
Initiation
Elongation
Termination
All RNA transcription is performed by enzymes called RNA polymerases.
RNA transcription starts at a Promoter sequence (analogous to ORI for DNA replication).

40. Transcription of mRNA in Humans
Steps involved are the same as in prokaryotes:
Initiation
Elongation
Termination
Mediated by RNA polymerase II:
Very complex enzyme with many subunits

41. Human Transcription Protein DNA Nucleus
Has to be more control of how more complex genetic material is read to create more variety (multicellular)
RNA has to be transcribed in the nucleus and then transported to the protein translation machinery in the cytoplasm before it can be read.
Protein
DNA
Nucleus

42. Human genes Most have introns
Produce monocistronic mRNA: only one encoded protein
Large genes

43. Initiation
Initiation occurs at promoters as in prokaryotes- eukaryotic promoters are not well-characterized but have some well conserved elements- including the TATA box and CAAT box (both have A=T pairs)
In addition to the promoters there are region in the DNA called enhancers to which transcription factors bind and regulate which DNA is read and encoded in mRNA

44. Transcription Factor FunctionTF
mRNA
Pol
Promoter
Enhancer
Gene
Promoter
Enhancer
Gene TF
TF= Transcription Factor

45. Transcription Factors
Although transcription is performed by RNA Polymerase, it needs other proteins to produce the transcript.
These proteins are either associated directly with RNA Polymerase or help it bind to the DNA sequences upstream of the initiation of translation..
These associated proteins are called transcription factors.

46. RNA transcription begins by the assembly of the RNA polymerase on a promoter region.

47. Orientation of promoter elements specifies the direction of transcription
-35
-10
prokaryote GC
CAAT
TATA
eukaryote

48. Transfer of Information
Gene
mRNA
exon | intron | exon | intron | exon
Exon - portion of the gene that contains DNA sequences that will be translated into protein.
Intron - portion of the gene that will be cut out before translation

49. Transfer of Information

50. Reading the Genes in the Genome
Signal recognizing
Transcribing
Processing
AAA
mRNA
Translating
Protein