Chapter 4 – Origin of Cells and Their General Features

Bio 190A

The reducing atmosphere hypothesis

proposes that the early Earth atmosphere facilitated the redoc reactions required to form organic molecules; experimental work has supported this hypothesis

The Miller-Urey experiment

showed organic molecules could be formed from simple precursors (H₂O, H₂, CH₄, and NH₃)

The extraterrestrial hypothesis

proposes that the organic molecules (organic carbon, amino acids, and nucleic acid) were carried to the surface of the Earth in meteorites

The deep-sea vent hypothesis

proposes that the key organic molecules may have originated at deep-sea vents, where superheated water containing many dissolved gases and metal ions mixes with cold seawater

What is found near modern deep-sea vents?

Complex biological communities

Note that these three hypotheses are

not mutually exclusive

How many stages led to the formation of living cells?

4

Stage 1

make monomers

Stage 2

make polymers

Stage 3

boundary encloses polymer

Stage 4

cellular characteristics evolve

Scientists hypothesize that the second stage in the origin of life was

the formation of organic polymers (DNA, RNA, proteins)

Experimental evidence supports the hypotheses that polymers may have formed on

clay surfaces or in the prebiotic soup

Protocell

used to describe an aggregate of prebiotically produced molecules within a boundary

Protocells are envisioned as

possible precursors of living cells, given the following characteristics: a boundary separated internal contents from the external environment, polymers inside the protocell contained information, polymers inside the protocell had catalytic functions, and protocells eventually developed the capability to self-replicate

Liposomes

vesicles surrounded by a lipid bilayer; researchers have hypothesized that protocells may have existed as them

RNA

may have been the first macromolecule found in protocells

Unlike other polymers, RNA exhibits 3 key functions:

1. RNA had the ability to store info in its base sequence

2. Due to base pairing, its nucleotide sequence had the capacity for self-replication

3. RNA can perform a variety of catalytic functions; ribosomes are catalytic RNA molecules

Chemical selection occurs

when a chemical within a mixture has special properties or advantages that cause it to increase uib number

RNA world

a hypothetical period on early Earth when both in info needed for life and the catalytic activity of living cells were contained in RNA molecules

Why might the RNA world evolve into the modern RNA/DNA?protein world?

Incorporation of DNA may have allowed RNA to take on the roles (different binding and catalytic functions), DNA is more stable than RNA, and, due to the different chemical properties of the amino acids, proteins have greater catalytic ability than RNA

Microscope

a magnification tool that allows visualization of cellular structures

Resolution

a measure of the clarity of an image (the ability to observe two adjacent objects as distinct from one another)

Contrast

relative differences in lightness, darkness, or color between adjacent regions in a sample (can enhance with dyes)

Magnification

the ratio between the size of an image produced by a microscope and the object’s actual size

Light microscopes

use light for illumination; light resolution is 0.2 μm

Electron microscopes

use a beam of electrons for illumination; resolution in 2nm (100x better than light microscopes)

Transmission electron microscopy (TEM)

a beam of electrons is transmitted through a sample; gives best resolution

Scanning electron microscopy (SEM)

A beam scans surface to make 3D image

Cell structure and function are primarily determined by 4 factors:

Matter, energy, organization, and information

Matter

each type of cell synthesizes a unique set of molecules/macromolecules that contribute to cell structure

Energy

needed to build molecules and carry out many other cellular functions

Organization

the interior environment of a cell is highly organized; protein-protein interactions create intricate structures within cells

Information

each species has a unique genome

Genome

entire complement of genetic material

Based on cell structure, cells are categorized as either

prokaryotic or eukaryotic

Bacteria and archaea have ___ cells

prokaryotic

Prokaryotic cells are

reatively simple; they do not have a nucleus

Eukaryotic cells contain

a nucleus and other membrane-bound organelles

Eukaryotic cells exhibit extensive

compartmentalization

The shape, size, and organization of cells vary among

species and cell types in multicellular organisms

Plant cells contain___ similar to those in animal cells

organelles

Additional structures found in plant cells (but not in animal cells) include

chloroplasts, a central vacuole, and a cell wall

Liquid-liquid phase separation

aggregated solutes(such as proteins and RNA molecules) separate from the bulk solvent and form a droplet; another mechanism of compartmentalization

Example of a droplet organelle:

nucleolus

Due to differential gene regulation,

only a subset genes is expressed in any given cell types

Proteome

the complete protein composition of a cell or organism

The set of proteins made by a cell largely determines

the characteristics of that cell; protein profiles vary in many different ways

Nearly universal characteristic of cells

small size

Rate of transport in cells through their membrane is limited by

the surface area of the membrane

Which two areas increase differently as the radius of the cell increases?

internal cell volume (V) and membrane surface area (SA)

Why are cells small?

a large SA/V ratio is needed to support sufficient exchange

Cytosol

the region of the eukaryotic cell that is outside the cell organelles but inside the plasma membrane

Metabolism

the sum of all the chemical reactions in a cell/organism

Reactions are organized into two major categories:

catabolism (breakdown) and anabolism (synthesis)

Both catabolic and anabolic reactions occur in the

cytosol

Although many reactions occur within specific organelles, the cytosol is…

a central coordinating region for many metabolic activities

Ribosomes

some float freely within the cytosol; sites of protein synthesis

Cytoskeleton

a network of three different types of protein filaments (microtubules, intermediate filaments, actin filaments); each type is constructed form many protein monomers

Microtubules

long, hollow cylinders composed of tubulin subunits; they regularly grow and shorten (dynamic instability)

Intermediate filaments

can be built from several types f proteins; the proteins assemble in a staggered manner to form a twisted, rope-like structure

Actin filaments (microfilaments)

composed of actin subunits; two strands spiral around each other

ATP

primary energy currency of living cells

Motor proteins

a type of protein that use ATP as a source of energy to promote various types of movement

Motor proteins have three domains:

head, hinge, tail

Head

the site of ATP binding and hydrolysis

Hinge

bends in response to ATP binding/hydrolysis and drives movement

Tail

an elongated region attached to other proteins/molecules

Cells utilize motor proteins to drive different kinds of

movement (movement of cargo, movement of filament, bending of a filament [used by cilia and flagella])

Cilia and flagella

cell appendages that bend to produce different types of cell movement

Axoneme

the internal structure of both cilia and flagella

Axonemes contain

microtubules (organized in a 9 + 2 array), the motor protein dynein, and linking proteins

Basal bodies

microtubules extend from that are anchors to the cytoplasmic side of the membrane

Endomembrane system

a network of membranes that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane

Nuclear envelope

the double-membrane enclosing the nucleus

Nuclear pores

openings across the nuclear envelope that are formed by the proteins of the nuclear pore complex

Chromosomes

inside the nucleus; formed of chromatin

Chromatin

a complex of DNA and proteins

Nucleolus

a region of ribosome assembly

Nuclear matric

a network of filamentous proteins; supports the nuclear envelope

Chromosone territories

chromosomes are organized by the nuclear matrix into distinct, non-overlapping

Endoplasmic reticulum (ER)

a network of membranes that form flattened, fluid-filled tubules

Rough ER

studded with ribosomes; functions include protein sorting, insertion of membrane proteins, and glycosylation

Smooth ER

lacks ribosomes; functions include metabolism, detoxification, Ca²⁺ storage, and lipid synthesis and modification

Golgi apparatus

consists of a stack of flattened membranous sacs; each enclosed compartment is a cisterna

Golgi apparatus functions:

protein sorting, protein processing (including glycosylation and proteolysis), and secretion

Lysosomes

small organelles found in animal cells that break down macromolecules

Acid hydrolases

enzymes that catalyze hydrolysis reactions and function optimally at an acidic pH (~4.8); lysosomes contain many

Vacuoles

compartments that may contain diverse fluid or solid substances

Central vacuole of plant cells

provides storage and srtucture

Contractile vacuoles

provide water balance and maintain cell volume

Food vacuoles

contain degradative enzymes

Peroxisomes

small organelles found in all eukaryotic cells

Peroxisomes catalyze

a variety of reactions, including reactions that break down some nutrients (fats and amino acids) and toxins

Mitochondria and chloroplasts are considered

semiautonomous

The primary function of mitochondria is to

make ATP

Mitochondria do not create energy, rather they

convert chemical energy stored in the bonds of sugars, fats, and amino acids into chemical energy stored in the bonds of ATP

Mitochondria structures include

outer membrane, intermembrane, inner membrane (with folds called cristae), and the mitochondrial matrix

Photosynthesis

chloroplasts capture light energy and use some of that energy to synthesize organic molecules like glucose

Chloroplast structures include

outer membrane, intermembrane space, inner membrane, stroma, thylakoid membranes (stacked to form grana), and the thylakoid lumen