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Life in a cell
Goals
Learn about cell metabolism
• Learn about energy and carbon sources
• DNA, genomes, and genes
• The role of mutations
•
Cell Metabolism
Every cell functions to conduct chemical reactions and processes that
process, provide, and distribute energy and basic nutrients to its
structures.
The sum of all these processes for an organism is called metabolism.
Metabolic processes have three key necessities, we shall review each in
turn.
Three necessities for metabolism: #1—raw materials
The raw materials
– Carbon compounds;
– Primary macronutrients (N, P, K);
– Secondary macronutrients (Ca, Mg, S);
– Micronutrients (B, Cl, Mn, Fe, Zn, Cu, Mo, Se).
Eukaryotes
– Plants absorb raw materials from soil;
– Animals and fungi digest dead or decaying organisms;
– Parasitic animals digest nutrients robbed from organisms;
– Some plants are parasites on other plants or fungi.
Prokaryotes
– Bacteria and archaea obtain nutrients from the surroundings, or
from other organisms, depending upon the prokaryote.
Three necessities for metabolism: #2—energy
ATP
–
–
–
–
aka adenosine triphosphate;
each phosphate bond is a powercell;
created in the mitochondria;
break a bond, get energy.
ATP  ADP + energy
ADP  AMP + energy
Three necessities for metabolism: #3—waste removal
If waste products are allowed to accumulate, they result in a toxicity
situation that can damage or even kill the cell.
Examples of waste products
– CO2
– O2
– CH4 (methane)
– Alcohol
– Urine
– Feces
Carbon and energy
Carbon
All life on Earth is carbon-based. Therefore, all life on Earth must
get carbon, one way or another.
Energy
All life on Earth uses energy. Therefore, all life on Earth must get
energy, one way or another.
It is sensible to classify organisms into categories that are based on
how they obtain their carbon and energy.
Let us begin…
Carbon sources for organisms
Auto = self; i.e., automobile = self-moving;
Hetero = different; i.e., heterosexual = other sexual;
Troph = feeding.
How do organisms obtain their carbon or other nutrients?
Autotrophic life forms
– Organisms that absorb raw mineral nutrients from their surroundings;
– Most higher plants and algae, blue-green bacteria.
Heterotrophic life forms
– Organisms that absorb processed nutrients by consuming other organisms
(alive, dead, or decaying);
– Animals, fungi, some parasitic or carnivorous plants, many bacteria and
archaea.
Energy sources for organisms
How do organisms obtain their energy?
Phototrophic life forms
–
–
–
–
Organisms that absorb energy by absorbing light;
On Earth, nearly all phototrophic life forms absorb sunlight;
The organisms convert sunlight into ATP via photosynthesis;
Examples are higher plants and algae, blue-green bacteria.
Chemotrophic life forms
– Organisms that absorb energy by consuming chemicals that have energy
stored in their chemical bonds;
– Some consume organic chemicals from living, dead, or decaying
organisms;
– Examples include you, fungi, many bacteria and archaea.
Weird strategies for obtaining energy and carbon
We are so used to the paradigm that “plants absorb minerals and catch light, animals
eat the plants” that some organismal strategies seem relatively bizarre!
Consider this strategy, used by some bacteria, to obtain both energy and carbon from
simple chemicals such as sulfide molecules….
4H2 + SO42-  H2S +2OH-+ 2H2O + energy
[Energy is harvested]
2H2S + CO2 + energy  (CH2O) + H2O + 2S
[Carbohydrates are manufactured]
No sunlight is required! Just nasty sulfur compounds!
Carbon-Energy classification
Energy source
Carbon source
Organic
CO2
compounds
(autotrophs)
(heterotrophs)
Sunlight (phototrophs)
Photoautotrophs
Most plants and photosynthetic
bacteria.
Chemicals (chemotrophs)
Chemoautotrophs
Energy source is based on
reactions involving iron, sulfur,
ammonia.
Bacteria and archaea, especially
extremophiles.
Photoheterotrophs
Some bacteria, archaea.
Carnivorous plants.
Chemoheterotrophs
Energy source is based on
consuming organic compounds.
Animals, fungi, many microbes,
parasitic plants.
Underwater hydrothermal vents
Black smokers, white smokers
Deep sea sources of superheated water 60-460ºC (140-860ºF)!
Associated with volcanically active sites;
Typically 2100 m;
As deep as 5000 m;
Highly acidic (pH=2.8) waters;
Rich in sulfides (black smokers), Ba-Ca-Si (white smokers);
Chimneys can be up to 60 m.
One species of green-sulfur bacterium (Chlorobiaceae) called GSB1
uses the faint red glow of black smokers to power photosynthesis!
Chemotrophic bacteria extract energy from sulfide reactions, and give
the energy to worms they live in. The worms return the favor with
carbon compounds.
Water: the final critical aspect of life
All forms of life require liquid water. It helps transport chemicals into the
cells, it allows metabolites to diffuse within the cells, it allows for the
removal of waste products from the cells.
The search for extraterrestrial life hinges on the search for liquid water.
Could other liquids fulfill the role that water does?
Hydrocarbons (similar to gasoline); ammonia, methane, have liquid forms.
Genetics and Heredity
On Earth, heredity from one cell generation to the
next is determined by the information stored in the
gigantic molecule called DNA (deoxyribonucleic
acid).
DNA is structured as a double helix (spiral). The
structures connecting the two strands (like rungs on a
ladder) are called “bases.”
The strands themselves are made out of phosphate
molecules.
DNA bases
On Earth, four molecules are used as bases:
Adenine and thymine
make a base pair.
Adenine (A)
Thymine (T)
Cytosine and guanine
make a base pair.
Cytosine (C)
Guanine (G)
DNA replication
When a cell divides into two cells, the genetic
information is duplicated.
1. The double helix is unzipped.
2. Free-floating bases assemble and attach the only
way they can.
3. Two new DNA molecules are formed.
This is VERY complicated. There must be an easier
way!
There HAS to be!
Genetics and Heredity
Genome
The complete set of all the base pairs in an organism.
We have about 3×109 base pairs in our genome.
Genes
A sequence of base pairs that, all together, provide the
directions for making proteins or conducting some aspect of life.
Mycoplasma genitalium: 470 genes (smallest prokaryotic genome);
Saccharomyces cerevisiae: 6144 genes (smallest eukaryotic genome);
Homo sapiens: 20,000-32,000 genes;
Triticum aestivum: 60,000 genes.
Chromosomes
Tightly bound bundles of DNA and supporting proteins. Humans have 23
pairs of chromosomes.
Reading DNA
The information in base pairs can be “read,” by
chunking the DNA information into sets of three
base pairs.
Cytosine-Cytosine-Adenine = Proline
– but –
Guanine-Thyamine-Thyamine = Valine.
This system of three-base-pair “words” gives
enough possibilities to code for all of the twenty
amino acids needed by life on Earth.
Read in this order by other proteins, DNA molecules
can cause the creation of specific amino acids, in the
exact order they are needed to make complicated
proteins needed by cells.
T
3-Base Genetic Code
C
A
G
T
TTT
TTC
TTA
TTG
Phenylalanine
“
“
Leucine
“
“
TCT
TCC
TCA
TCG
Serine
“ “
“ “
“ “
TAT
TAC
TAA
TAG
Tyrosine
“
“
Stop
“ “
TGT
TGC
TGA
TGG
Cysteine
“
“
Stop
Tryptophan
T
C
A
G
C
CTT
CTC
CTA
CTG
Leucine
“
“
“
“
“
“
CCT
CCC
CCA
CCG
Proline
“ “
“ “
“ “
CAT
CAC
CAA
CAG
Histidine
“
“
Glutamine
“
“
CGT
CGC
CGA
CGG
Arginine
“
“
“
“
“
“
T
C
A
G
A
ATT
ATC
ATA
ATG
Isoleucine
“
“
“
“
Met/Start
ACT
ACC
ACA
ACG
Threonine
“ “
“ “
“ “
AAT
AAC
AAA
AAG
Asparagine
“
“
Lysine
“
“
AGT
AGC
AGA
AGG
Serine
“
“
Arginine
“
“
T
C
A
G
G
GTT
GTC
GTA
GTG
Valine
“
“
“
“
“
“
GCT
GCC
GCA
GCG
Alanine
“ “
“ “
“ “
GAT
GAC
GAA
GAG
Aspartic acid
“
“
Glutamic acid
“
“
GGT
GGC
GGA
GGG
Glycine
“
“
“
“
“
“
T
C
A
G
Base pairs are read three at a time. Only two bases are needed to code for 16 of
the 20 amino acids (4×4=16). Does this hint to an earlier, simpler chemistry?
Noncoding DNA
Strangely, most of the DNA in humans (95%) and other organisms is
noncoding.
The pufferfish Takifugu rubripes has the same approximate genome
size as humans, but only 1/10 the junk DNA.
Some noncoding DNA is just long sequences of repeating codes.
Other noncoding DNA does not seem to be used by the organism.
This noncoding DNA is apparently without purpose, and is often
called junk DNA.
Is noncoding DNA purely structural? Is it an evolutionary holdover?
Does it indicate something we don’t understand?
Mutations and DNA
Mutations are changes in the genetic code that arise from errors
made in copying DNA, or from irreparable damages to the DNA.
DNA replication is amazing error-free
– 1 error per billion bases copied;
– This is comparable to copying 2400 “Life in the Universe”
books with only one word spelled wrong.
Example: sickle-cell anemia
– One thymine to adenine mutation in each gene in a pair;
– This mutation confers resistance to malaria.
Mutations are the basic fuel for evolution!
Adding a base pair can change the genome code more than just
making an error in a single base pair.
Heygalhowareyouandthedogareyousad
DNA can be transferred from one organism to another (lateral gene
transfer), complicating evolutionary trees.
RNA – the low-rent nucleic acid
RNA
– Only one strand (sometimes very convoluted).
– Uses uracil (U) instead of thymine.
– Critical in carrying out the commands of DNA.
– Messenger RNA=mRNA
– Transfer RNA=tRNA
– Ribosomal RNA=rRNA
Since RNA is a simpler molecule than double-stranded, helical
DNA, perhaps it would be easier to make RNA than DNA.
Could life be based on RNA?
What other molecules are possible?