1. A Zero-Knowledge Based Introduction to Biology
Cory McLean
24 Sep 2010
Thanks to George Asimenos

2. Cells: Building Blocks of Life
cell, nucleus, cytoplasm, mitochondrion
Humans have 100 trillion cells (10^14)
Prokaryotes: Bacteria and archaea. Lack cell nucleus (and usually unicellular). Instead they have a nucleoid, which is where all genetic material is (usually circular double-stranded DNA).
Eukaryotes have nucleus.
Cytoplasm: Entire contents of cell within plasma membrane: cytosol, organelles, and inclusions (random garbage like silicon dioxide just floating around)
Cytoskeleton: Provides structure for the cell
ER: Do protein translation (ribosomes stuck on rough ER), protein folding and transport
Extracellular matrix: Provides structural support for cells.
Golgi apparatus: Modifies proteins delivered from rough ER, transports lipids, creates lysosomes
Lysosome: Digests foreign bodies, old organelles
Mitochondria: Produce energy (ATP) in citric acid cycle. Has its own genome.
Nucleus: Holds all chromosomes
Peroxisome: Break down fatty acid molecules
Plasma membrane: Like skin, protects inner contents of cell from outside environment
© Coriell Institute for Medical Research

3. DNA: “Blueprints” for a cell
Genetic information encoded in long strings of double-stranded DNA
DeoxyriboNucleic Acid comes in only four flavors: Adenine, Cytosine, Guanine, Thymine

4. to previous nucleotide
deoxyribose, nucleotide, base, A, C, G, T, purine, pyrimidine, 3’, 5’
purines
to previous nucleotide
Adenine (A)
Guanine (G) O 5’ H
to base O O P O C
Thymine (T)
Cytosine (C) H O- C C H H H H
pyrimidines C C H 3’
Let’s write “AGACC”!
to next nucleotide

5. “AGACC” (backbone)

6. “AGACC” (DNA)
deoxyribonucleic acid (DNA) 3’ 5’ 5’ 3’

7. DNA is double stranded AGACC TCTGG DNA is always written 5’ to 3’
strand, reverse complement
AGACC
TCTGG 5’ 3’ 3’ 5’
DNA is always written 5’ to 3’
AGACC or GGTCT

8. DNA Packaging
histone, nucleosome, chromatin, chromosome, centromere, telomere
telomere
centromere
nucleosome
Supercoiling H1
DNA
H2A, H2B, H3, H4
~146bp
chromatin

9. The Genome
The genome is the full set of hereditary information for an organism
Humans bundle two copies of the genome into 46 chromosomes in every cell
= 2 * ( X/Y)

10. Building an Organism Every cell has the same sequence of DNA
Subsets of the DNA sequence determine the identity and function of different cells

11. From DNA To Organism ?
Proteins do most of the work in biology, and are encoded by subsequences of DNA, known as genes.

12. RNA T  U O 5’ H O O P O C H O- C C H H H H C C 3’ OH
ribose, ribonucleotide, U
purines
to previous ribonucleotide
Adenine (A)
Guanine (G) O 5’ H
to base O O P O C
Uracil (U)
Cytosine (C) H O- C C H H H H
pyrimidines C C
T  U 3’ OH
to next ribonucleotide

13. Genes & Proteins gene, transcription, translation, protein
Double-stranded DNA 5’ 3’
TAGGATCGACTATATGGGATTACAAAGCATTTAGGGA...TCACCCTCTCTAGACTAGCATCTATATAAAACAGAA 3’ 5’
ATCCTAGCTGATATACCCTAATGTTTCGTAAATCCCT...AGTGGGAGAGATCTGATCGTAGATATATTTTGTCTT
(transcription)
Single-stranded RNA
AUGGGAUUACAAAGCAUUUAGGGA...UCACCCUCUCUAGACUAGCAUCUAUAUAA
(translation)
protein

14. Gene Transcription promoter 5’ 3’ 3’ 5’
G A T T A C A . . . 5’ 3’ 3’ 5’
C T A A T G T . . .
Transcription occurs at a rate of ~20-50 nt per second

15. Gene Transcription
transcription factor, binding site, RNA polymerase
G A T T A C A . . . 5’ 3’ 3’ 5’
C T A A T G T . . .
Transcription factors: a type of protein that binds to DNA and helps initiate gene transcription.
Transcription factor binding sites: Short sequences of DNA (6-20 bp) recognized and bound by TFs.
RNA polymerase binds a complex of TFs in the promoter.

16. Gene Transcription The two strands are separated 5’ 3’ 3’ 5’
G A T T A C A . . . 5’ 3’ 3’ 5’
C T A A T G T . . .
The two strands are separated

17. Gene Transcription
G A T T A C A . . . 5’ 3’ 3’
G A U U A C A 5’
C T A A T G T . . .
An RNA copy of the 5’→3’ sequence is created from the 3’→5’ template

18. Gene Transcription 5’ 3’ 3’ 5’ pre-mRNA 5’ 3’ G A T T A C A . . .
C T A A T G T . . .
G A U U A C A . . .
pre-mRNA 5’ 3’

19. RNA Processing
5’ cap, polyadenylation, exon, intron, splicing, UTR, mRNA
5’ cap
poly(A) tail
exon
intron
mRNA
5’ UTR
3’ UTR

20. Gene Structure introns 5’ 3’ promoter exons 3’ UTR 5’ UTR coding
non-coding

21. How many? (Human Genome)
Genes:
~ 20,000
Exons per gene:
~ 8 on average (max: 148)
Nucleotides per exon:
170 on average (max: 12k)
Nucleotides per intron:
5,500 on average (max: 500k)
Nucleotides per gene:
45k on average (max: 2,2M)

22. From RNA to Protein
Proteins are long strings of amino acids joined by peptide bonds
Translation from RNA sequence to amino acid sequence performed by ribosomes
20 amino acids  3 RNA letters required to specify a single amino acid

23. Amino acid There are 20 standard amino acids H O H N C C OH H R
Alanine
Arginine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine H O H N C C OH H R
There are 20 standard amino acids 23

24. Proteins H O N C C H R N-terminus, C-terminus to previous aa
to next aa H R H OH
N-terminus
(start)
C-terminus
(end)
from 5’ ’ mRNA

25. Translation
ribosome, codon
mRNA
P site
A site
The ribosome (a complex of protein and RNA) synthesizes a protein by reading the mRNA in triplets (codons). Each codon is translated to an amino acid. 25

26. Translation 26 G GGG Gly GAG Glu GCG Ala GUG Val A GGA Gly
GAA Glutamic acid (Glu)
GCA Ala
GUA Val C
GGC Gly
GAC Asp
GCC Ala
GUC Val U
GGU Glycine (Gly)
GAU Aspartic acid (Asp)
GCU Alanine (Ala)
GUU Valine (Val)
AGG Arg
AAG Lys
ACG Thr
AUG Methionine (Met) or START
AGA Arginine (Arg)
AAA Lysine (Lys)
ACA Thr
AUA Ile
AGC Ser
AAC Asn
ACC Thr
AUC Ile
AGU Serine (Ser)
AAU Asparagine (Asn)
ACU Threonine (Thr)
AUU Isoleucine (Ile)
CGG Arg
CAG Gln
CCG Pro
CUG Leu
CGA Arg
CAA Glutamine (Gln)
CCA Pro
CUA Leu
CGC Arg
CAC His
CCC Pro
CUC Leu
CGU Arginine (Arg)
CAU Histidine (His)
CCU Proline (Pro)
CUU Leucine (Leu)
UGG Tryptophan (Trp)
UAG STOP
UCG Ser
UUG Leu
UGA STOP
UAA STOP
UCA Ser
UUA Leucine (Leu)
UGC Cys
UAC Tyr
UCC Ser
UUC Phe
UGU Cysteine (Cys)
UAU Tyrosine (Tyr)
UCU Serine (Ser)
UUU Phenylalanine (Phe) 26

27. 5’ . . . A U U A U G G C C U G G A C U U G A . . . 3’
Translation
5’ A U U A U G G C C U G G A C U U G A ’
Translation occurs at a rate of ~15-20 AA per second
UTR
Met
Start Codon
Ala
Trp
Thr
Stop Codon 27

28. 5’ . . . A U U A U G G C C U G G A C U U G A . . . 3’
Translation
Met
Trp
Ala
5’ A U U A U G G C C U G G A C U U G A ’
Polysomes 28

29. Errors?
mutation
What if the transcription / translation machinery makes mistakes?
What is the effect of mutations in coding regions?
mutations are changes in DNA/RNA (failure to repair)

30. Reading Frames G C U U G U U U A C G A A U U A G30

31. Synonymous Mutation G G C U U G U U U A C G A A U U A G
synonymous (silent) mutation, fourfold site G
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
Ala Cys Leu Arg Ile
G C U U G U U U G C G A A U U A G
Ala Cys Leu Arg Ile 31

32. Missense Mutation G G C U U G U U U A C G A A U U A G
Ala Cys Leu Arg Ile
G C U U G G U U A C G A A U U A G
Ala Trp Leu Arg Ile 32

33. Nonsense Mutation A G C U U G U U U A C G A A U U A G
Ala Cys Leu Arg Ile
G C U U G A U U A C G A A U U A G
Ala STOP 33

34. Frameshift G C U U G U U U A C G A A U U A G
Ala Cys Leu Arg Ile
G C U U G U U A C G A A U U A G
Ala Cys Tyr Glu Leu 34

35. Gene Expression Regulation
Regulation, signal transduction
When should each gene be expressed?
Regulate gene expression
Examples:
Make more of gene A when substance X is present
Stop making gene B once you have enough
Make genes C1, C2, C3 simultaneously
Why? Every cell has same DNA but each cell expresses different proteins.
Signal transduction: One signal converted to another
Cascade has “master regulators” turning on many proteins, which in turn each turn on many proteins, ...

36. Gene Regulation Gene expression is controlled at many levels:
DNA chromatin structure
Transcription
Post-transcriptional modification
RNA transport
Translation
mRNA degradation
Post-translational modification
Post-transcriptional modification: Process where primary transcript RNA converted into mature RNA (e.g. splicing, 5’ capping, 3’ polyadenylation).
RNA transport: Transcription occurs in the nucleus (where the chromosomes are). Translation occurs in the cytoplasm.
Translation: Ribosome picks which mRNAs to make next
mRNA degradation: After certain amount of time (dependent on particular mRNA, in mammals several minutes to days), mRNA degrades and can no longer be translated into protein
Post-translational modifications: Attaches functional groups (lipids, carbohydrates, phosphates) to existing proteins, enzymes cleave proteins, etc.

37. Transcription Regulation
Much gene regulation occurs at the level of transcription.
Primary players:
Binding sites (BS) in cis-regulatory modules (CRMs)
Transcription factor (TF) proteins
RNA polymerase II
Primary mechanism:
TFs link to BSs
Complex of TFs forms
Complex assists or inhibits formation of the RNA polymerase II machinery

38. Transcription Factor Binding Sites
Short, degenerate DNA sequences recognized by particular TFs
For complex organisms, cooperative binding of multiple TFs required to initiate transcription
Binding Sequence Logo

39. Transcription Regulation Mechanisms
enhancer, silencer, insulator
Transcription Factor Specificity:
Enhancer:
Silencer:
Insulator:

40. Unicellular vs. Multicellular

41. Non-coding RNAs
RNAs transcribed from DNA but not translated into protein
Structural ncRNAs: Conserved secondary structure (A-U, C-G, G-U)
Involved in gene regulation
miRNAs involved in down-regulating gene expression by forming double-stranded RNA that is targeted for degradation.

42. Summary All hereditary information encoded in double-stranded DNA
Each cell in an organism has same DNA
DNA  RNA  protein
Proteins have many diverse roles in cell
Gene regulation diversifies protein products within different cells

43. The end?