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—energyATP

– 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

CarbonAll life on Earth is carbon-based. Therefore, all life on Earth must get carbon, one way or another.

EnergyAll 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

Photoautotrophs

Most plants and photosynthetic bacteria.

ChemoautotrophsEnergy source is based on reactions involving iron, sulfur, ammonia.

Bacteria and archaea, especially extremophiles.

Photoheterotrophs

Some bacteria, archaea.

Carnivorous plants.

ChemoheterotrophsEnergy source is based on consuming organic compounds.

Animals, fungi, many microbes, parasitic plants.

Energy source

Sunlight (phototrophs) Chemicals (chemotrophs)

Car

bon

sour

ce

Org

anic

CO

2

co

mpo

unds

(h

eter

otro

phs)

(aut

otro

phs)

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 basesOn Earth, four molecules are used as bases:

Adenine (A)

Cytosine (C) Guanine (G)

Thymine (T)

Adenine and thymine make a base pair.

Cytosine and guanine make a base pair.

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

GenomeThe complete set of all the base pairs in an organism.We have about 3×109 base pairs in our genome.

GenesA 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.

ChromosomesTightly 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.

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?

3-Base Genetic Code

T C A G

T

TTTTTC

TTA

TTG

Phenylalanine “ “

Leucine

“ “

TCTTCC

TCA

TCG

Serine

“ “

“ “

“ “

TATTAC

TAA

TAG

Tyrosine

“ “

Stop

“ “

TGTTGCTGA

TGG

Cysteine“ “

Stop

Tryptophan

T

C

A

G

C

CTTCTC

CTA

CTG

Leucine

“ “

“ “

“ “

CCTCCC

CCA

CCG

Proline

“ “

“ “

“ “

CATCAC

CAA

CAG

Histidine

“ “

Glutamine

“ “

CGTCGC

CGA

CGG

Arginine

“ “

“ “

“ “

T

C

A

G

A

ATTATC

ATA

ATG

Isoleucine

“ “

“ “

Met/Start

ACTACC

ACA

ACG

Threonine

“ “

“ “

“ “

AATAAC

AAA

AAG

Asparagine

“ “

Lysine

“ “

AGTAGC

AGA

AGG

Serine

“ “

Arginine

“ “

T

C

A

G

G

GTTGTC

GTA

GTG

Valine

“ “

“ “

“ “

GCTGCC

GCA

GCG

Alanine

“ “

“ “

“ “

GATGAC

GAA

GAG

Aspartic acid

“ “

Glutamic acid

“ “

GGTGGC

GGA

GGG

Glycine

“ “

“ “

“ “

T

C

A

G

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 DNAMutations 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?