Introduction to Molecular Biology, Genetics and

Genomics

References: www.biostat.wisc.edu/

Lecture 1

Overview

Molecular biology crash course: The different parts of a cell DNA, RNA, chromosomes, nucleus, cytoplasm Bio-chemical entities of a cell: mRNA, proteins genes, heredity, transcription, translation, gene

regulation, gene expression, alternative splicing

Life Two categories:

Prokaryotes (e.g. bacteria) Unicellular No nucleus

Eukaryotes (e.g. fungi, plant, animal) Unicellular or multicellular Has nucleus

Prokaryote vs. Eukaryote

Eukaryote has many membrane-bounded compartment inside the cell Different biological processes occur at different

cellular location

Organization of biological information

Organism

Tissue

Chromosome

Cell

http://publications.nigms.nih.gov/thenewgenetics/chapter1.html

Chemical contents of cell

Water Macromolecules (polymers) - “strings” made by

linking monomers from a specified set (alphabet)

ProteinDNARNA…

Small moleculesSugarIons (Na+, Ka+, Ca2+, Cl- ,…)Hormone…

The central dogma of Molecular biology

DNA

RNA

Proteins

Transcription

Translation

image from the DOE Human Genome Programhttp://www.ornl.gov/hgmis

DNA Short for Deoxyribonucleic acid

composed of small chemical units called nucleotides (or bases) adenine (A), cytosine (C), guanine (G) and

thymine (T) ATGC is the alphabet

DNA is double stranded: made up two twisting strands

Each strand of DNA is a string composed of the four letters: A, C, G, T

Nucleotides A nucleotide has 3 components

Sugar ring (ribose in RNA, deoxyribose in DNA) Phosphoric acid Nitrogen base

Adenine (A) Guanine (G) Cytosine (C) Thymine (T) or Uracil (U)

Polymerization: Nucleotides => nucleic acids

Phosphate

Sugar

Nitrogen Base

Phosphate

Sugar

Nitrogen Base

Phosphate

Sugar

Nitrogen Base

G

A

G

T

C

A

G

C

5’-AGCGACTG-3’

AGCGACTG

Phosphate

Sugar

Base

1

23

4

5

Often recorded from 5’ to 3’, which is the direction of many biological processes.e.g. DNA replication, transcription, etc.

5’

3’

DNA

Free phosphat

e

5 prime 3 prime

DNA is a double helical molecule

DNA molecules consist of two strands arranged in a double helix

DNA is made up of nucleotides

Double-helical structure is needed for the DNA molecule to store and pass with great precision

James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin

Watson-Crick Base Pairs

A always bonds to T C alwaysbonds to G

This is called base pairing.A and G are double ringed structures called purines.C and T single ringed structures called pyrimidines

5’ and 3’ of a DNA molecule• The backbone of this molecule has

alternating carbon and phosphate molecules

each strand of DNA has a “direction” at one end, the terminal carbon

atom in the backbone is the 5’ carbon atom of the terminal sugar

at the other end, the terminal carbon atom is the 3’ carbon atom of the terminal sugar

therefore we can talk about the 5’ and the 3’ ends of a DNA strand

DNA double helix

G-C pair is stronger than A-T pair

DNA stores the blue print of an organism

The heredity molecule

Has the information needed to make an organism

Base pairing enables self-replication: one strand has all the information

Chromosomes All the DNA of an organism is

divided up into individual chromosomes

prokaryotes (single-celled organisms lacking nuclei) typically have a single circular chromosome

eukaryotes (organisms with nuclei) have a species-specific number of chromosomes

Image from www.genome.gov

Different organisms have different numbers of chromosomes

Organism # of chromosomes

Yeast 32

Human 46

Fly 8

Mouse 40

Arabidopsis 10

Worm 12

Human Chromosomes

Genes

genes are the basic units of heredity

a gene is a sequence of bases which specifies a protein or RNA genes

the human genome comprises ~ 25,000 protein-coding genes (still being revised)

One gene can have many functions

One function can require many genes

…GTATGTCTAAGCCTGAATTCAGTCTGCTTTAAACGGCTTC…

Structure of genes

DNA

GeneNon-coding Promoter

Gene A Gene B Gene C

Genomes

Refers to the complete complement of DNA for a given species

the human genome consists of 2X23 chromosomes

every cell (except egg and sperm cells and mature red blood cells) contains the complete genome of an organism

Some Greatest Hits

Some Genome Sizes

Number of sequenced genomes

The central dogma of Molecular biology

DNA

RNA

Proteins

Transcription

Translation

RNA

RNA is like DNA except: single stranded U is used in place of T

a strand of RNA can be thought of as a string composed of the four letters: A, C, G, U

Transcription

In eukaryotes: happens inside the nucleus

RNA polymerase is an enzyme that builds an RNA strand from a gene

RNA Pol II is recruited at specific parts of the genome in a condition-specific way.

Transcription factor proteins are assigned the job of Pol II recruitment.

RNA that is transcribed from a gene is called messenger RNA (mRNA)

Transcription: Process of turning DNA into RNA

mRNA

The central dogma of Molecular biology

DNA

RNA

Proteins

Transcription

Translation

Translation

Process of turning mRNA into proteins.

Happens inside the cytoplasm in ribosomes

ribosomesare the machines that synthesize proteins from mRNA

Translation process reads one codon at a time

translation begins with the start codon

translation ends with the stop codon

Translation happens in ribosomes

Codons

Each triplet of bases is called codon How many codons are possible? Each codon is responsible for coding a

particular amino acid.

The Genetic Code

Proteins

Protein is the actual “worker” for almost all processes in the cell

Proteins are long strings ofcomposed of amino acids

There are 20 different amino acids known

The structure of a protein is intimately connected to its function

Protein: a polymer of amino acids

Amino Acids

Proteins are the workhorses of the cell

structural support storage of amino acids transport of other substances coordination of an organism’s activities response of cell to chemical stimuli movement protection against disease selective acceleration of chemical reactions

Proteins are complex molecules

Primary amino acid sequence

Secondary structure Tertiary structure Quaternary

structure

Some well-known proteins

Hemoglobin: carries oxygen

Insulin: metabolism of sugar

Actin: maintenance of cell structure

Hemoglobin protein HBA1

>gi|224589807:226679-227520 Homo sapiens chromosome 16, GRCh37.p9 Primary Assembly

1 CCCACAGACTCAGAGAGAACCCACCATGGTGCTGTCTCCTGACGACAAGACCAACGTCAA

61 GGCCGCCTGGGGTAAGGTCGGCGCGCACGCTGGCGAGTATGGTGCGGAGGCCCTGGAGAG

121 GATGTTCCTGTCCTTCCCCACCACCAAGACCTACTTCCCGCACTTCGACCTGAGCCACGG

181 CTCTGCCCAGGTTAAGGGCCACGGCAAGAAGGTGGCCGACGCGCTGACCAACGCCGTGGC

241 GCACGTGGACGACATGCCCAACGCGCTGTCCGCCCTGAGCGACCTGCACGCGCACAAGCT

301 TCGGGTGGACCCGGTCAACTTCAAGCTCCTAAGCCACTGCCTGCTGGTGACCCTGGCCGC

361 CCACCTCCCCGCCGAGTTCACCCCTGCGGTGCACGCCTCCCTGGACAAGTTCCTGGCTTC

421 TGTGAGCACCGTGCTGACCTCCAAATACCGTTAAGCTGGAGCCTCGGTGGCCATGCTTCT

481 TGCCCCTTTGG

DNA sequence (491 bp)

>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens GN=HBA1 PE=1 SV=2MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Amino acid sequence (142 aa)Protein 3d structure

Examples of proteins

RNA Processing in Eukaryotes

eukaryotes are organisms that have enclosed nuclei in their cells

in many eukaryotes,RNAs consist of alternating exon/intron segments

exons are the coding parts

introns are spliced out before translation

RNA Splicing

RNA Genes

not all genes encode proteins for some genes the end product is RNA

ribosomal RNA (rRNA), which includes major constituents of ribosomes

transfer RNAs (tRNAs), which carry amino acids to ribosomes

micro RNAs (miRNAs), which play an important regulatory role in various plants and animals

lincRNAs (long non-coding RNAs), play important regulatory roles.

Central Dogma revisited

DNA

RNA

Proteins

Transcription

Translation

ncRNA, miRNA, rRNAs

Non-coding RNA processing

Summary Key concepts in molecular biology

Central Dogma DNA, RNA, proteins Chromosomes, Nucleus, Ribosomes

Important processes Transcription Translation RNA splicing