Bio quiz 3

4.6

The earth formed from a huge cloud of dust and rocks about _ billion years ago

bombardment

early earth was repeatedly hit by enormous pieces of rock and ice, a process known as _

4

about _ billion years ago, bombardment decreased enough that conditions on earth became more stable

3.8

chemical signatures dating to _ billion years ago suggests life may have existed

3.5

the earliest direct fossil evidence for life on earth comes from _ billion year old prokaryotes

individual free-floating cells, mats

The earliest organisms, prokaryotes, lived either as _ or in dense communities called _, where many cells lived together.

1.8

the first eukaryotes appeared _ billion years ago

600

multicellular eukaryotes didn’t appear until _ million years ago

small molecules, macromolecules, protocells, self-replication

The 4 stages to cell production:

abiotic synthesis of small organic molecules

1st step to cell production. Idea was that simple molecules present on early earth could have combined through nonliving chemical processes to produce small organic molecules

Ex: amino acids, nitrogenous bases (components of nucleic acids like RNA and DNA)

organic molecule

a carbon-containing molecule associated with living systems (i.e amino acids)

contains C-H bonds

small molecules join into macromolecules

2nd step to cell production. occurred when proteins, nucleic acids, carbohydrates, and lipids formed.

animo acids → proteins (perform chemical reactions)

nucleotides → nucleic acids (store genetic information)

protocells

3rd step to cell production. These are primitive cell-like structures containing molecules enclosed within a membrane-like boundary. important as it separated internal chemistry and outside environment.

Allowed molecules to stay concentrated together (rather than dispersing), making reactions more likely

self-replication

4th step to cell production. Important as molecules needed to be capable of making copies of themselves. caused inheritance, which allowed for natural selection.

inheritance

the transmission of biological information from one generation to the next.

(genetic) natural selection

if one molecule reproduces faster or more accurately than another, it can become more common.

• water vapor

• NO free oxygen (O2)

• hydrogen gas (H2)

• methane (CH4)

• ammonia (NH3)

• hydrogen sulfide (H2S)

• carbon dioxide (CO2)

early earth’s atmosphere had:

condensed, forming liquid water, which formed oceans

As earth cooled, water vapor…

Some hydrogen eventually escaped into space.

Oparin and Haldane’s hypothesis

2 scientists independently proposed an idea that Earth’s early atmosphere could have allowed organic molecules to form from simpler molecules, proposing that the environment was reducing. Believed energy needed for these chemical reactions could have from from things such as lightning or UV radiation.

reducing

A _ environment is one in which chemical reactions tend to add electrons.

oxidizing

An _ environment is one in which chemical reactions tend to remove electrons.

Haldane’s idea of “primitive soup”

Idea that essentially stated early oceans might have accumulated organic molecules.

earth’s atmosphere produced organic molecules → rain/ocean collects them -? ocean becomes chemically rich → increasingly complex chemistry leads towards life

Miller-Urey Test

2 scientists tested Oparin and Haldane’s hypothesis. They put simple gases into a closed system, provided energy (electrical sparks to stimulate lightning), and observed whether organic molecules formed.

Produced a variety of amino acids and other organic compounds.

Showed that organic molecules can form abiotically under certain conditions

reducing, neutral

The flaw in the original Miller-Urey model was that Earth’s atmosphere, as previously predicted, wasn’t strongly _, and was actually _. It consisted largely of nitrogen and carbon dioxide.

This didn’t destroy the origin of life hypothesis, as later Miller-Urey experiments using these gases also produced organic molecules. Also, particular locations on early Earth may have had very different chemistry.

• Volcanoes have localized reducing conditions

• hydrothermal vents provided conditions favorable for early chemical reactions

Takeaway: organic molecules could have potentially formed in specific local environments

hypothermal vents

places on the seafloor where hot water and minerals emerge from Earth’s interior (deep-sea vents).

hot sand, clay, rock

Under certain conditions, small molecules naturally join together into larger molecules (like the 4 bases of RNA, A, C, G, and U). Amino acids and RNA molecules can spontaneously form polymers when exposed to surfaces such as:

catalysts

amino acid polymers are not necessarily modern proteins. Many could have instead acted as weak _

vesicle

a fluid-filled compartment surrounded by a membrane-like structure. Some form spontaneously when certain organic molecules are placed in water due to their amphipathic qualities

amphipathic

molecules having both hydrophobic and hydrophilic properties are called:

montmorillonite clay

a soft clay mineral produced through weathering of volcanic ash, providing surfaces where organic molecules become concentrated. Increase the rate at which vesicles self-assemble. Vesicles can also absorb _ particles carrying RNA or other organic molecules

molecules become concentrated → collisions become more likely → chemical reactions more likely to occur

_, despite being abiotic vesicles, can demonstrate life-like properties, including:

• Grow: increasing in size without diluting contents

• Divide: split into smaller vesicles

• maintain an internal environment: membrane can separate internal chemistry from external chemistry

• carry out chemical reactions: some vesicles with selectively permeable membranes can perform metabolic reactions using external reagents

selective permeable

a _ membrane allows some substances to cross more easily than others.

metabolism

the collection of chemical reactions that allow an organism to acquire and use energy and materials

DNA replication requires

enzymes, nucleotides, energy, and other cellular machinery

RNA, DNA, proteins, DNA, RNA

_ may have come before _. This is because the former can store information AND catalyze reactions.

• _ can catalyze reactions

• _ can store information

_ can do both

ribozymes

an RNA molecule that catalyzes a chemical reaction.

Some can make complementary copies of short RNA sequences when provided with nucleotide building blocks.

RNA can do foundational steps of self-replication

RNA, nucleotide sequence

unlike DNA’s double-stranded, relatively uniform double helix, _ can fold into many different 3D shapes. The _ determines the shape.

Some might replicate faster, more accurately, or more efficiently than others. This leads to molecular natural selection.

molecular natural selection

Suppose:

RNA A → replicates slowly

RNA B → replicates moderately

RNA C → replicates quickly

If all have access to the same resources, RNA C will produce more descendants. Therefore, RNA C becomes more common. This process is called _.

Now suppose RNA C makes an occasional copying error, and RNA D forms, which replicates even faster. This would make RNA D have more descendants and become the most common.

Over generations, molecules with advantageous properties can become increasingly common.

RNA world hypothesis

a theory that in early life, RNA served as both a storage of genetic information and a catalyst. Small RNA molecules could potentially:

1. store information

2. catalyze reactions

3. replicate

4. undergo variation

5. be acted upon by natural selection

genetic inheritance

Suppose there’s an RNA-containing vesicle, and a vesicle without RNA. The vesicle containing RNA has the advantage if the RNA helps it acquire resources, grow, divide, or reproduce its RNA.

When the vesicle divides, some RNA molecules can pass into its “daughter” vesicles. This exemplifies _.

This shows natural selection can also act on protocells, not just individual molecules.

chemically stable, accurate, primary

DNA has an advantage to RNA as it is more _ (or less reactive). It is also better suited to _ long-term storage of genetic information.

As genomes get larger, accuracy becomes increasingly important. This leads to even larger genomes becoming possible, leading to more complex biological characteristics becoming encoded.

Explains why DNA eventually became the _ genetic material

stromatolite, 3.5, 3.1, 2.8

a layered rock structure produced through the activities of certain microorganisms, especially photosynthetic prokaryotes (cyanobacteria). The oldest date to _ billion years ago, and found in shallow marine environments.

_ billion years ago, they formed 2 distinct morphologies (structures)

_ billion years ago, they also appeared in salty lakes (along w marine environments).

This shows there was ecological and evolutionary change.

3.5

fossilized prokaryotic cells date back to _ billion years old, found in rocks in australia.

cyanobacteria

photosynthetic prokaryotes that perform oxygen-generating photosynthesis. They began releasing oxygen into Earth’s atmosphere.

Some are nitrogen-fixing (perform nitrogen fixation), and can grow using light, CO2, N2, water, or minerals. They don’t need to consume another organism for organic nutrients.

photosynthesis

uses light energy to drive chemical reactions. Water is split, producing oxygen (O2).

Formula: CO2 + H2O → C6H12O6 + O2

oxygen

_ can be extremely chemically reactive. In certain chemical forms, it can:

• attack chemical bonds

• damage cellular molecules

• inhibit enzymes

Increasing atmospheric _ was deadly to many early anaerobic organisms. Natural selection favored organisms capable of tolerating or using _.

cellular respiration

uses oxygen to help harvest energy stored in organic molecules. Involves transferring electrons through an electron transport chain.

Formula: O2 + C6H12O6 → CO2 + H2O

attached

While all prokaryotes are unicellular, some cells remain _ after division, forming chains or other groups.

surface area to volume ratio

A relatively large _ means a cell has lots of membrane surface compared with the amount of cytoplasm it needs to service. This is typically a feature of prokaryotic cells.

Useful because substances including oxygen, nutrients, and waste products need to cross the cell membrane. Small cells exchange materials with their environment efficiently.

As a cell gets larger, volume increases faster than surface area, and the _ decreases.

cell wall

a rigid structure outside the plasma membrane that maintains cell shape, protects the cell, and prevents the cell from bursting when water enters.

hypotonic

A _ environment has a lower concentration of solutes outside the cell than inside. Due to this, water tends to move into the cell due to osmosis.

plasmolysis

when water leaves the cell, the cell membrane can pull away from the cell wall. _ is the shrinking of the cell’s contents away from the cell wall due to water loss, interfering with reproduction.

Idea behind salt preserving food, as it causes many microorganisms to lose water.

_ → reduced cellular activity → reduced reproduction → long-lasting food

peptidoglycan

polymer: sugars + amino acids

found inside most bacterial cell walls, creating a strong molecular mesh around the bacterial cell.

Lacking in archaeal cell walls.

Gram staining

a staining technique that allows many bacteria to be categorized according to their cell wall structure. 2 categories:

1. gram-positive bacteria

2. gram-negative bacteria

gram-positive bacteria

bacterial cell walls with a thick peptidoglycan layer

gram-negative bacteria

bacterial cell walls with a thin peptidoglycan layer + outer membrane

Membrane makes _ more structurally complicated, as it contains lipopolysaccharides (LPS). Also creates a barrier that makes it harder for certain substances to enter the cell (including antibiotics) giving it increased resistance

Lipopolysaccharides (LPS)

molecules containing lipid + carbohydrate

Some can trigger strong immune responses

capsule

a dense, well-organized sticky outer layer of a prokaryotic cell wall. help cells:

• stick to surfaces

• stick to other cells

• avoid dehydration

This stickiness can allow cells to establish a colony, important for biofilms.

also help some disease-causing bacteria (pathogens) avoid being attacked by the host’s immune system

Rare in archaea

slime layer

a less organized sticky outer layer of a prokaryotic cell wall. help cells:

• stick to surfaces

• stick to other cells

• avoid dehydration

This stickiness can allow cells to establish a colony, important for biofilms.

rare in archaea

biofilm

a structured community of microorganisms (bacteria, fungi, algae) that stick to each other and to a surface, enclosed in a protective, slimy matrix

endospore

a highly resistant dormant structure containing a copy of the bacterial chromosome. Formed as an emergency strategy, like when environmental conditions lack water or essential nutrients. Process:

1. Bacterium copies its chromosome

2. One copy becomes enclosed in a specialized multilayered structure

3. The original cell breaks apart

4. The endospore is released

NOT reproduction, rather a survival mechanism

Can survive:

• boiling water (die at 121 degrees celsius)

• severe dehydration

• long periods without nutrients

when conditions improve: endospore rehydrates → metabolism resumes → normal bacterial growth returns

fimbriae

short, numerous, hairlike structures that help bacteria attach to surfaces or other cells

pili

generally longer than fimbriae and less numerous. help bacterial surfaces to attach to one another and facilitate DNA transfer (s*x _)

taxis

Not all prokaryotes are stationary. About half are capable of _, which is directed movement toward or away from a stimulus. The cell detects something in its environment and changes its movement accordingly.

chemotaxis

a type of taxis that moves a prokaryote towards or away from a chemical stimulus

Positive _ move toward a beneficial chemical.

Negative _ move away from a harmful (toxic) chemical.

Allows microorganisms to actively seek favorable environments

(bacterial) flagellum

one of the most common physical tail-like cellular structures used for prokaryotic movement is the _.

These are DIFFERENT from eukaryotic _.

Prokaryotic _ are:

• Thinner

• not usually enclosed by an extension of the plasma membrane

• Built from different proteins (42 total)

• powered different from eukaryotic _

• Rotate, vs eukaryotic _ that bend.

motor, hook, and filament

components of the bacterial flagellum include:

motor

The _ of a bacterial flagellum rotates the structure.

hook

The _ of a bacterial flagellum connects components.

filament

The _ of a bacterial flagellum extends outwards and interacts with the surrounding environment

analogous structures

structures that perform similar functions but did not evolve from the same ancestral structure (i.e bacterial, archaeal, and eukaryotic flagellum)

homologous structures

structures that evolved from the same ancestral structure but perform different functions

Ex: some flagellar proteins are _ to proteins already used for secretion and ion transport

42, 21, 19

For bacterial flagellum, there are _ different kinds of proteins. Of all flagellum, _ proteins are required by all species. _ are modified versions of proteins that perform other functions in bacteria. This shows that evolution didn’t invent every component from scratch, but instead proves exaptation.

exaptation

a structure that evolved for one function becomes useful for another function. In other words, existing molecular components could be modified and combined to produce a new function.

nucleus, mitochondria, golgi apparatus, ER

prokaryotic cells lack membrane-bound organelles including:

genome

the complete set of genetic information in an organism

Prokaryote: one main circular chromosome (can have multiple or be linear, though rare)

Eukaryote: several linear chromosomes (at least one, but can come circular, such as inside the mitochondria) most located in nucleus

nucleoid

The chromosome in prokaryotes is located inside the _. This is the region of the cytoplasm containing the prokaryotic chromosome.

plasmid

a small, independently replicating DNA molecule separate from the main chromosome.

Usually only contain a few genes, that can sometimes provide useful traits (i.e antibiotic resistance).

ribosomes

molecular machines that build proteins by translating the chain of amino acids the mRNA brings to them

Prokaryotic _ are slightly smaller, and differ in their RNA and protein composition from eukaryotic _.

phototroph

an organism that obtains energy from light

chemotroph

an organism that obtains energy from chemical compounds

autotroph

organism that obtains carbon from inorganic sources (CO2) to build organic molecules

Inorganic sources lack C-H bonds

heterotroph

an organism that obtains carbon from at least one organic compound (like glucose, or food)

obligate aerobes

an organism that requires O2 for cellular respiration

obligate anaerobes

an organism that is harmed or killed by oxygen

Instead, obtain energy exclusively through fermentation or anaerobic respiration

fermentation

a metabolic process where microorganisms like bacteria and yeast break down carbohydrates into acids, alcohol, or gases without using oxygen

anaerobic respiration

Cellular respiration involves transferring electrons through an electron transport chain. In _, something other than O2 is the final electron acceptor (i.e Nitrate, Sulfate)

another molecule accepts electrons

aerobic respiration

Cellular respiration involves transferring electrons through an electron transport chain. In _, O2 is the final electron acceptor

O2 accepts electrons

facultative anaerobe

an organism that uses oxygen when oxygen is available, but can switch to fermentation or anaerobic respiration when oxygen isn’t available. This flexibility helps them survive changing environments.

nitrogen fixation

Nitrogen is required to make amino acids and nucleic acids. But atmospheric nitrogen exists primarily as N2. Most organisms cannot directly use this. A solution to this issue is _, which is a conversion of atmospheric N2 into ammonia (NH3) or related usable nitrogen compounds.

Some cyanobacteria and methanogens (archaea that produce methane) can perform _. This nitrogen can then be incorporated into amino acids, nucleic acids, and other organic molecules.

Important as plants can’t use atmospheric N2 directly, but can use nitrogen compounds produced through microbial (prokaryote) processes.

Problem: requires enzymes that are damaged by oxygen (which is produced by photosynthesis!)

anabaena

a cyanobacterium that forms long chains of connected cells. Different cells specialize in different things, and cooperate Most perform photosynthesis, and a few perform nitrogen fixation.

heterocysts

specialized cyanobacterial cell that performs nitrogen fixation. They have a thickened cell wall that limits oxygen entering the cell. After performing fixed nitrogen, the cells that produce oxygen and carbohydrates (photosynthetic cells) and _ exchange resources.

metabolic cooperation

different cells or organisms perform different metabolic processes and exchange the products, allowing a group to accomplish things that an individual cell couldn’t accomplish as efficiently.

biofilm

a community of microorganisms attached to a surface and embedded in a matrix they produce (i.e plaque on teeth).

Formation process: bacteria communicate using signaling molecules. nearby cells are recruited. The cells then produce polysaccharides and proteins, creating a sticky matrix. The bacteria become attached to the surface and one another, eventually forming a structured microbial community.

Have channels, allowing nutrients entrance into interior cells and waste out of the biofilm.

They can damage infrastructure, contaminate medical devices, and cause chronic infections (resiliant).

binary fission

prokaryotes reproduce through _, where a single cell divides into 2 cells. Process:

1. DNA is replicated

2. The cell grows

3. The copies of DNA separate

4. The cell divides

5. Two daughter cells result

1 → 2 → 4 → 8 → 16 → 32… (exponential growth)

Can’t grow forever due to limited nutrients, toxic metabolic waste, competition, predators, and other environmental limitations.

adaptive radiation

diversification of a lineage into many forms adapted to different environments

horizontal gene transfer

movement of genetic material between organisms that are not parent and offspring. allows prokaryotes to acquire useful genes, even from distantly related species.

transformation

cells pick up loose/naked DNA from the environment

conjugation

2 cells physically connect and transfer DNA (often a plasmid) through a pilus

transduction

a bacteriophage (virus) transfers DNA between bacteria unintentionally