Transcript Biological Background

Biological Background
Ecological
Physiological
SPECIES
ORGANISM
Biological
CELL
Chemical
MOLECULE
Physical
ATOM
Molecular Biology
Concepts
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Role of molecules in cells
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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
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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
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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
deoxyribose nucleic acid
Basic unit = nucleotide
Sugar,Phosphate,Base (A, G, T, C)
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
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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:
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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:
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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
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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 twothirds rRNA and one-third protein.
Termination
Amino Acids
• Proteins consist of amino acids linked by
peptide bonds
• Each amino acid consists of:
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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
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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?
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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
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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:
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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:
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Presence of a distinct nucleus with a nuclear
membrane
have organized chloroplasts and mitochondria
genetic material organized into structures
called chromosomes.