BIO130

Prokaryotic Cell

A cell that lacks a nucleus and is generally single-celled. Genetic material is confined to the DNA of nucleoid in the center of the cell. These cells also tend to contain a bacterial flagellum, pills, cell wall, capsule, and plasma membrane. (Examples: Eubacteria and Archaea)

Eukaryotic Cell

A cell that can either be single-celled or multicellular found in plants, fungi, animals, and humans. These cells contain mitochondria and a variety of other intricate organelles to carry out many functions.

Animal vs. Plant cells (eukaryotic)

Plant cells contain cell walls, chloroplasts, and vacuoles. These organelles allow for them to partake in photosynthesis transforming Carbon Dioxide into Oxygen to create energy for the organism.
Animal Cells lack a cell wall but usually have either flagellum or cilia protruding from the cell membrane. Animal Cells also have a cytoskeleton

Cell wall

tough protective outer coat (optional in prokaryotic cells but necessary for eukaryotic plant cells)

Capsule

(only found in certain prokaryotic cells) Polysaccharide layer protection from engulfment

Plasma membrane

surrounds all cells

DNA of nucleoid

Compact structure of DNA and proteins

Ribosome

Aid in Protein Synthesis

Bacterial Flagellum

A tail-like structure protruding from prokaryotic and some eukaryotic animal cells whose main function is for locomotion

Pilus

Small tail like structures that are similar to cilia found only in prokaryotic cells that can either be used for locomotion or sexual conjugation

Cytoplasm

fluid inside the cell

Cytoskeleton

a microscopic network of protein filaments and tubules in the cytoplasm of many living cells, giving them shape and coherence.

three parts of cytoskeleton

microtubule, microfilament, intermediate filament

microtubule

straight, hollow tube of proteins that gives rigidity, shape, and organization to a cell

microfilament

Long, thin fibers that function in the movement and support of the cell

intermediate filament

Threadlike proteins in the cell's cytoskeleton that are roughly twice as thick as microfilaments

microvilli

projections that increase the cell's surface area

lysosome

An organelle containing digestive enzymes that aids in "cleaning" the cell

Smooth endoplasmic reticulum (ER)

organelles that create lipids or fat

Mitochondria

Powerhouse of the cell, organelle that is the site of ATP (energy) production

Chromatin

Clusters of DNA, RNA, and proteins in the nucleus of a cell

Nuclear pore

passageway for molecules into and out of the nucleus

Nuclear Envelope

A double membrane that surrounds the nucleus in the cell

Nucleolus

Found inside the nucleus and produces ribosomes

Rough endoplasmic reticulum (ER)

An endomembrane system covered with ribosomes where many proteins for transport are assembled

Golgi Complex

A cell organelle that helps make and package materials to be transported out of the cell.

Chloroplast

a plastid that contains chlorophyll and in which photosynthesis takes place.

Vacuole

An organelle mainly found in plant cells that functions for storage an functions like the animal lysosome for degradation

Endosymbiotic Theory/Endosymbiont Theory

Describes how a single "composite" cell of greater complexity could evolve from two or more separate simpler cells living in a symbiotic relationship with one another

Proof for Endosymbiotic/Endosymbiont Theory

Mitochondria and chloroplasts have their own DNA, RNA, ribosomes, and protein

neutrophil

hunt and kill bacteria

phagocytosis

cell eating

19th and 20th Century Approach to Studying Diversity

Using large collections

Late 20th and 21st century approach

Model organisms

Model organisms

species that have been studied extensively over a long period of time and thus serve as models for deriving fundamental biological principles

General Attributes of a Model Organism

1. Rapid Development with Short Life Cycles
2. Small adult (reproductive) size
3. Readily available (collections or wide-spread)
4. Tractability - ease of manipulation or modification
5. Understandable Genetics

Model System Examples (Prokaryotes)

E. coli, a heterotrophic eubacterium found in the human gut

Synechocystis, a free living phototrophic cyanobacterium (Also a eubacterium)

Model System Examples (Eukaryote)

Yeast - (Saccharomyces cerevisiae), a minimal eukaryotic model

Arabidopsis - a model flowering plant species

Caenorhabditis elegans - a nematode worm (with 959 body cells)

Drosophila, Mouse, and Zebra Fish

The Central Dogma/Information Flow in the cell

DNA--\>RNA--\>Protein

DNA --\> RNA

Transcription

RNA--\>Protein

Translation

DNA goes to mRNA

which goes to protein

DNA goes to tRNA

which goes to transport AA's for protein synthesis

DNA goes to rRNA

which goes to part of the ribosome

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome//intermediate between a gene and its polypeptide

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

rRNA

ribosomal RNA; type of RNA that makes up part of the ribosome

genome

complete set of DNA or DNA sequences in an organism

interactome

complete set of interactions in a cell or organism

metabolize

complete set of small molecule metabolites

phenome

complete set of phenotypes

DNA, RNA, and proteins are all:

Linear chains of information

Info in nucleic acid sequence is translated into

an AA sequence via a genetic code which is essentially universal among all species

Nucleic acids are:

1) genetic material in a cell (organism's blue prints)
2)DNA
3)RNA

DNA

deoxyribonucleic acid

RNA

Ribonucleic acid

Three parts of a nucleic acid

pentose sugar (scaffold for base), nitrogenous base (varies), phosphate group (backbone, 1P, 2P's, 3P's)

Purine

two rings: guanine, adenine

Pyrimidine

One ring: Cytosine, Thymine, Uracil

DNA

deoxyribose, GCAT

RNA

ribose, GCAU

How do RNA and DNA differ?

RNA lacks a methyl group in uracil and contains a 2' OH group on one of its sugars

DNA contains a 2' H its sugar and a methyl group on Thymine

Nucleoside Monophosphate

Sugar+base+1P

Nucleoside Diphosphate

Sugar+base+2P

Nucleoside Triphosphate

Sugar+base+3P

Nucleoside

Base+Sugar

Nucleotide

Base+Sugar+at least one P

cytosol

soluble phase of the cytoplasm caused from overcrowded nature of eukaryotic cells

mitosis

Duplicated chromosomes condense into compact structures that are segregated by an elaborate microtubule containing apparatus

Mitotic Spindle

allows each daughter cell to receive an equivalent array of genetic material

Conjugation

Piece of DNA is passed from one cell to another

Biofilms

they live in complex multi species communities

archaea

more closely related to eukaryotes than bacteria that consist of extremophiles, methanogens, halophiles, acidophiles, thermophiles, and hyperthermophiles

extremophiles

inhospitable environments

methanogens

convert CO2 and H2 into methane

Halophiles

live in extremely salty environments

Acidophiles

acid loving prokaryotes

Thermophiles

heat loving prokaryotes

Hyperthermophiles

prokaryotes found around hydrothermal vents

Nitrogen fixation (What cyanobacteria use)

conversion of nitrogen gas into reduced forms of nitrogen

Metagenome

collective genome

Differentiation

specialized cells are formed by this process

Ribozymes

RNAs having a catalytic role are called RNA enzymes

ATP

Adenosine Triphosphate (Energy)

Guanosine Triphosphate (GTP)

energy/binds to a variety of proteins and acts as a switch to turn on their activities

Gene expression

production of a functional product using the information encoded in a gene

Transcription

synthesis of RNA from a DNA template

Central Dogma

concept of a DNA-based gene encoding an RNA based message that is then translated into a protein

Translation

How proteins are synthesized in the cytoplasm by a complex process

Interactions between individual molecules are usually mediated by\____attractions

non-covalent

Examples of non-covalent interactions between individual molecules

1. Electrostatic attractions
2. Hydrogen bonds
3. Van der Waals attractions
4. Hydrophobic Interactions
Individually, very weak forces--BUT can sum to generate strong binding between molecules

DNA is synthesized from

deoxyribonucleoside triphosphate otherwise known as dNTP's

RNA is synthesized from

ribonucleoside triphosphates or NTPs

Nucleotides are linked by

phosphodiester bonds (have phosphorus in them)

A-T requires how many bonds

2 H-bonds

G-C requires how many bonds

3 H-bonds

Forces that keep two strands together

Hydrogen bonds, Van Der Waals attractions, Hydrophobic Interactions

DNA is strictly speaking

two molecules non-covalent attractions between them or one molecule composed of two strands

One complete turn of a molecule of DNA

10.5 base pairs

Major groove

The wider of the two grooves in a DNA double helix