WEEK 1 Flashcards
prokaryotes
single celled, no nuclei, includes eubacteria and archea (also called bacteria and arcbacteria)
eukaryotes
have nuclei, can be single or multicellular, includes plants, funghi, animals, humans
Example of a single celled eukaryote
yeast
Features of the prokaryotic cell
capsule - polysaccharide layer for protection from engulfment (optional)
cell wall - tough, protective outer coat (optional)
plasma membranes - surrounds all cells
DNA nucleoid - compact structure of DNA (NO NUCLEUS, but is still found in specific part of cell)
Which features are optional in prokaryotic cell (which ones are not present in all p. cells)?
Capsule and cell wall, flagellum and pilus
Ribosome
protein synthesis
flagellum
locomotion (not in all prokaryotes)
Pilus
two types:
- one for locomotion
- one for sexual conjugation
Eukaryotic cell
- 1000 times bigger than prokaryotic cell, which means it requires cytoskeleton for support
- has membrane bound organelles
- has mitochondria (powerhouse of cell, ATP generation)
- has nucleus
- has plasma membrane like prokaryotic
Features that plant cells have but animal cells don’t…
cell wall - for protection
chloroplast - for photosynthesis
vacuole - two types for storage and degradation (there are similar structures in animal cells but they’re called something else)
Two lines of evidence that show eukaryotes evolved from prokaryotes
fossil record - eukaryotes appear in record 1 billion years later after prokaryotes
structural similarity - share many complex traits that could not have evolved independently
Endosymbiont Theory
- Eukaryotic ancestor is a heterotrophic (cannot produce own food must take organic matter from environment) anaerobic (derived energy from food matter without molecular oxygen) cell
- mitochondrial ancestor was a free living, aerobic prokaryote able to use oxygen to help generate ATP that was engulfed by the larger heterotrophic aerobic cell and resisted digestion in cytoplasm
FECA
First Eukaryotic Common Ancestor
- gave shelter to mitochondrial ancestors in exchange for oxygen generated ATP
- nuclear membrane developed as symbiosis occurred
LECA
Last Eukaryotic Common Ancestor
- does not contain chloroplasts (last common ancestor between us and plants)
What was the key step in producing FECA?
Prokaryotic ancestors somehow acquired ability to form internal membranes and compartments. The key step towards FECA was the development of these membranes into closed internal compartments (which then allowed for production of nucleus to hold DNA).
Are internal membranes exclusively a eukaryotic trait?
No, some bacteria can have extensive internal membrane networks but they are NOT closed—they do not have membrane bound organelles like eukaryotes
Evidence for endosymbiont theory
- Some prokaryotes form simple internal membranes
- There are carnivorous single-celled eukaryotes which can phagocytosize (engulf) things - shows that the mechanism is plausible
- Mitochondria and chloroplast still have evidence of their own DNA - genome is circular and looks prokaryotic
- Both mitochondria and chloroplast have double membranes and their own ribosomes (remnant structures)
Where did Margulis propose chloroplasts came from?
Cyanobacteria. An early heterotrophic eukaryote acquired ability to photosynthesize.
Archea are prokaryotes but are in some ways…
more similar to eukaryotes.
How does the double membrane of mitochondria and chloroplast provide evidence for endosymbiont theory?
The internal and external membrane have different compositions. Possible that one originated from original anaerobic host cell and other from the host cell itself.
Cyanobacteria, Methanococcus, Methanobacteria
- capable of photosynthesis (PROKARYOTE)
- lives at hydrothermal vents at bottom of ocean (ARCHEA)
- lives in low pH, anaerobic conditions (cow stomach) (ARCHEA)
Difference between 19th/20th century method and 20th/21st century method of studying diversity?
Older approaches - collect more stuff and organize
Newer approaches - model organisms
Model organisms
- studied extensively over a long period of time
- have rapid development with short life cycles
- small adult size (can fit in lab)
- readily available
- tractability (ease of modification/manipulation)
- understandable genetics (DNA is not too complicated)
Central dogma
DNA –(transcription)–> RNA —-(translation)–> PROTEIN
How is the central dogma slightly more complicated
There are many different types of RNAs some of which have nothing to do with making proteins and even STOP you from making proteins.
Types of RNAs
mRNA - messenger RNA, codes for proteins
tRNA - transports amino acids, used in protein synthesis
rRNA - part of the ribosome
Genome
complete set of DNA sequences in a cell or organism
Transcriptome
complete set of RNA sequences in a cell or organism
Proteome
complete set of proteins in a cell or organism
Interactome
complete set of protein interactions in a cell/organism
Metabolome
complete set of small, molecule metabolites in a cell/organism (deals with nutrients and wastes (ATPS, lipids, etc)).
Phenome
complete set of phenotypes for the cell/organism
Brief summary of steps in protein synthesis in eukaryotes
- segment of DNA is transcribed (RNA is made)
- mRNA processing
- nuclear export (goes into cytoplasm)
- translation
- protein folding
DNA
Deoxyribonucleic acid
RNA
Ribonucleic acid
Components of DNA and RNA? What’s the difference between the two?
- Pentose sugar
- nitrogenous bases (varies)
- Phosphate group (backbone)
DNA is missing the hydroxyl group on the 2’ carbon (IT STILL HAS OXYGEN)
Where does the carbon numbering start on the ring?
Outside on the carbon that attaches to the phosphate group — that one is the 5’. The base attaches to the 1’
Purines
Guanine and Adenine
- have two rings
Pyramidines
Cytosine, Uracil, Thymine
- each only has one ring
interactions between molecules…
are usually noncovalent interactions
nucleotide
nucleoside with phosphates—can be monophosphate, diphosphate, triphosphate. A nuceloside is just a sugar and a base covalently bonded.
Common component of all amino acids
An alpha carbon that has a carboxyl group, an amino group, and an R group attached
Number of naturally existing amino acids
20
What differentiates between amino acids?
R groups
What part of the amino acid is NOT involved in peptide bond formation?
The R group
How are peptide bonds formed?
Carboxyl reacts amino to form water and strong covalent peptide bond. The peptide bond exists between the carbon of the carboxyl group and the nitrogen of the amino group of the other amino acid. OH from carbxyl and proton from amino form water.
What kind of reaction is peptide bond formation?
Condensation (also known as dehydration synthesis)
More amino acids are added onto…
carboxyl end (c-terminus) until AA chain is complete
What are amino acids in a polypeptide chain called?
Residues
What structure does the polypeptide chain form?
twists in on itself to form cylindrical structure because of hydrogen bonding between oxygen of carbonyl group on residue “n” and the hydrogen of amine group on residue n+4 (ex. 1 and 5, 2 and 6, 3 and 7, 4 and 8, etc). Because the h-bonding only occurs every 5 residues, the structure doesn’t appear until the chain is at LEAST 5 residues.
What stabilizes the alpha helix?
hydrogen bonds between carbonyl oxygen and amine group
Difference between Thymine and Uracil?
One of the hydrogens on Uracil is replaced with a methyl group in Thymine.
