Biological Background

ATOM

MOLECULE

CELL

ORGANISM

SPECIES

Physical

Chemical

Biological

Physiological

Ecological

Molecular Biology Concepts

• Role of molecules in cells – Perform various chemical reactions necessary for

life => diverse 3D structures necessary– Pass on the instructions for making an organism

=>simple 1D medium sufficient• Types of molecules in cells

– Proteins: 3D structures – DNA: 1D medium – RNA: intermediary between DNA and proteins – Lipids –compose mainly the membranes of the cell.– Sugars – small molecules. Main usage to transport

energy

Central Dogma of Molecular Biology

• Crick's central dogma. Information flow (with the exception of reverse transcription) is from DNA to RNA via the process of transcription, and thence to protein via translation.

• Transcription is the making of an RNA molecule off a DNA template. Translation is the construction of an amino acid sequence (polypeptide) from an RNA molecule. Although originally called dogma, this idea has been tested repeatedly with almost no exceptions to the rule being found (save retroviruses).

Central Dogma of Molecular Biology

DNA

Basic unit = nucleotideSugar,Phosphate,Base (A, G, T,

C)

deoxyribose nucleic acid

adenine, thymine cytosine, guanine.

DNA• DNA is double-stranded?

– Base pairs (A-T, G-C) are complementary– Known as Watson-Crick bps

• Length of DNA in bps (e.g. 100kbp)• A double-stranded DNA sequence can be

represented by strings of letters. 5' ... TACTGAA ... 3' 3' ... ATGACTT ... 5'

DNA

• Strands are antiparallel• Reverse Complementation

– To infer the sequence of one strand given the other

– Example: strand s: AGACGT (5'->3') Reverse s: TGCAGA

Replace each base by its complement: ACGTCT

Genome

• Chromosomes in any cell exist as identical pairs=Homologous pairs – humans = 23 pairs– corn = 10 pairs

• members of a pair are alike, but different from all other pairs

• one member of each pair comes from the female parent, and one member of the pair comes from the male parent. exist as sets or genomes.

• genome= complete set of chromosomes inherited from one parent.

Chromosomes, Alleles

• Terms describing the number of sets: – Haploid- single set of chromosomes found in a

gamete- pollen or egg – n - each chromosome represented once.

– Diploid- two complete sets of chromosomes one from each parent. This is the normal situation for the body cells of most living organisms. - 2n- each type of chromosome is represented twice.

• Alleles – genes that may appear in different forms, e.g., gene that codes for blood type in humans.

Transcription : making an RNA copy of a DNA

sequence

RNA polymerase opens the part of the DNA to be transcribed. Only one strand of DNA (the template strand) is transcribed. RNA nucleotides are available in the region of the chromatin (this process only occurs during Interphase) and are linked together similar to the DNA process.

RNA• Chemically, RNA is very similar to DNA. There

are some main differences: – RNA uses the sugar ribose instead of deoxyribose in

its backbone. – RNA uses the base Uracil (U) instead of Thymine (T).

U is also complementary to A.– RNA tends to be single-stranded.

• Functional differences between RNA and DNA– DNA single function, RNA many functions

• Example of types of RNA: tRNA, mRNA, rRNA

The Genetic Code: Translation of RNA code into protein

• The code consists of three bases. To code for the 20 essential amino acids a genetic code must consist of at least a 3-base set (triplet) of the 4 bases. If one considers the possibilities of arranging four things 3 at a time (4X4X4), we get 64 possible code words, or codons (a 3-base sequence on the mRNA that codes for either a specific amino acid or a control word).

Genomic Code

Protein Synthesis

• Promoters are sequences of DNA that are the start signals for the transcription of mRNA. Terminators are the stop signals. mRNA molecules are long (500- 10,000 nucleotides).

• Ribosomes are the organelle (in all cells) where proteins are synthesized. They consist of two-thirds rRNA and one-third protein.

Termination

Amino Acids

• Proteins consist of amino acids linked by peptide bonds

• Each amino acid consists of:– a central carbon atom– an amino group– a carboxyl group and– a side chain

• Differences in side chains distinguish the various amino acids

• 20 different amino acids found in nature

Amino acids

Proteins

• Different Roles of Proteins – Enzymes – Carry signals – Transport small molecules such as oxygen– Form cellular structures (tissues) – Regulate cell processes (such as defense

mechanisms)• What are proteins made of?

– Amino acids – chain of amino acids = protein

Backbone of polypeptide chain

• Convention – Begin at N-terminal– End at C-terminal

• Torsion or rotation angles around:– C-N bond ()– C-C bond ()

Protein Folding

THE CELL CYCLE

• Biochemically the G, part of the cycle is the most active for the cell.– S= synthesis– M= mitosis– G1,G2= Gaps, This is the busiest time for

the cell. Doing everything except divide.• M is the only time we can look at the cell and

actually see things happening.• C-value: Mass of nuclear DNA in an

unreplicated haploid genome in a given organism. Expressed in picograms. Measured spectrophotometrically.

Summary

Living things classified as

• Prokaryotes:– have genetic material, but not organized

into a defined nucleus, i.e. no membrane– Genetic material consists of a single

molecule of nucleic acid (usually circular DNA molecule)

– Do not have organized chloroplasts or mitochondria

– examples: bacteria, cyanobacteria (blue-green algae)

Living things classified as

• Eukaryotes:– Presence of a distinct nucleus with a nuclear

membrane– have organized chloroplasts and

mitochondria– genetic material organized into structures

called chromosomes.