Week 1 Flashcards
give 4 ways in with cells differ from each other
size, shape, chemical requirements, and function
two examples of how cells differ in shape
- nerve cells are extended and branched to transmit electrical signals
- paramecium is shaped like a submarine and covered with cilia, whose coordinated beating sweeps the cell forward
cell specialisation
- in multicellular organisms, division of labour allows for efficiency
- this does not occur in single celled organisms
- some cells become so specialised that they cease to proliferate
what do all living cells share?
- a similar basic chemistry; composed of the same sorts of molecules which participate in the same types of chemical reactions
- genetic information carried in genes
define a living cell
a self-replicating collection of catalysts
viruses and reproduction
- do not have ability to reproduce by their own efforts
- parasitise reproductive machinery of the cells they invade to make copies of themselves
where have all living cells evolved from?
the same ancestral cell, which existed between 3.5 and 3.8 billion years ago
- mutation
- sexual reproduction
- natural selection
3 major domains of the tree of life
eukaryotes (smallest domain), bacteria, and archaea
how is the tree of life organised?
analysis of the genome
which cells are larger; eukaryotes or prokaryotes? what about their genomes?
eukaryotic cells, and also have much larger genomes
most of the earth’s biomass is stored in
plants
which domain of life is most diverse and why?
bacteria
- small
- have been around for longest
- reproduce very quickly (so evolve fast)
draw and label a bacterial cell
- cytoplasm
- plasma membrane
- outer membrane
- cell wall
which domain is most poorly understood?
archaea
describe archaea
- differ from bacteria by chemistry of their cell walls, types of lipids that make up the membrane, and range of chemical reactions they can carry out
- archaea live everywhere, including extreme environments
- predominant form of life in soil and seawater
- play a major role in recycling nitrogen and carbon
- genomes closely related to eukaryotes
nucleus
- information store of cell
- enclosed in 2 concentric membranes (nuclear envelope)
- contains molecules of DNA
mitochondria
- enclosed in 2 membranes, with inner membrane invaginated
- generate chemical energy for the cell via cell respiration
- harness energy from oxidation of food molecules to produce ATP
- contain own DNA and reproduce by dividing
chloroplasts
- two surrounding membranes and stacks of membranes containing chlorophyll (green pigment)
- carry out photosynthesis
- contain own DNA and reproduce by dividing
endoplasmic reticulum
- irregular maze of interconnected spaces enclosed by a membrane
- site where most cell-membrane components, as well as materials destined for export from the cell are made
Golgi apparatus
- stacks of flattened, membrane-enclosed sacs
- modifies and packages molecules made in the ER that are destined to be secreted from the cell or transported to another cell compartment
lysosomes
small organelles in which intracellular digestion occurs, releasing nutrients from ingested food particles into the cytosol and breaking down unwanted molecules for recycling within cell or excretion
peroxisomes
small, membrane-enclosed vesicles that provide an environment for a variety of reactions in which hydrogen peroxide is used to inactivate toxic molecules
transport vesicles
ferry materials between one membrane-enclosed organelle and another
draw diagram for continual exchange of materials in a cell
pg 24
endocytosis
portions of plasma membrane tuck inward and pinch off to form vesicles that carry material captured from the external medium into the cell
exocytosis
vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium
cytosol
concentrated aqueous gel of large and small molecules; site of many chemical reactions
cytoskeleton
- responsible for directed cell movements
- composed of three major filament types; actin filaments, intermediate filaments, and microtubules
- role in cell division
actin filaments
thinnest filaments; particularly abundant in muscle cells, where they serve as a centre part pf the machinery responsible for muscle contraction
microtubules
thickest filaments; form of minute hollow tubes; help pull chromosomes apart during mitosis
intermediate filaments
thickness between actin filaments and microtubules; serve to strengthen most animal cells.
motor proteins
use energy stored in molecules of ATP to move along cytoskeleton filaments
protozoans
free-living, motile, unicellular eukaryotes
Didinium
- large, carnivorous protozoan with a diameter of 150 micrometers
- uses beating cilia to swim at high speed
- when it encounters prey (usually another protozoan) it releases numerous small, paralysing darts from its snout
- attaches to and devours the other cell, inverting like a hollow ball to engulf its victim
model organisms
representatives species studied by biologists
E. coli
- small, rod shaped
- lives harmlessly in the gut of humans and other vertebrates, but will also grow and reproduce in simple lab nutrient broths
what knowledge has come from studying E.Coli?
- how cells regulate gene expression
- how cells replicate their DNA and how they make proteins from DNA
- ‘recombinant DNA’ revolution, enabling us to manipulate genes and DNA in the laboratory
- harnessed as a biological factory for producing large quantities of therapeutic proteins, including insulin
S. Cervisiae
- small, single-celled fungus that is more closely related to animals than plants
- rigid cell wall, relatively immobile, many organelles (nucleus, GA, ER, mito) but no chloroplasts
- can grow and divide almost as rapidly as bacteria
- carries out basic tasks that every eukaryotic cell must perform and can even mate w opposite sex
what knowledge has come from studying Baker’s yeast?
- genetics of sexual reproduction
- cell division cycle
arabidopsis thaliana
- model plant
- can be grown indoors in large numbers
- thousands of offspring within 8-10 weeks
what knowledge has come from studying arabidopsis thaliana?
- understanding of the mechanisms that enable plants to grow toward sunlight, to flower in spring, and to coordinate development with season cycle
- insights into the development and physiology of crop plants
C. Elegans
- nematode worm
- develops with clockwork precision from a fertilised egg cell into an adult that has exactly 959 body cells, an unusual degree of regularity for an animal
- understanding of sequence of events of development
- understanding of apoptosis (programmed cell death for disposal of surplus cells)
Drosophila melanogaster
- fruit fly
- study of animal genetics
- genes for development similar to those of humans; human development and basis of genetic disease
- genetic analysis provided definitive proof that genes are carried on chromosomes
- shown how DNA directs development of zygote into adult
- mutants w body parts used to characterise genes needed to make normal adult
zebrafish
- developmental processes, particularly in vertebrates
- easily bred and maintained in lab
- transparent for first 2 weeks of life, allowing observation of how cells behave during development
- insights into development of heart and blood vessels
mouse
- mammalian genetics, development, immunology, cell biology
- possible to breed mice with deliberately engineered mutations in any specific gene, or with artificially constructed genes introduced into them
- test the function of any gene and determine how it works
why is it that many human cells can be studied in vitro?
when grown in culture, they continue to display the differentiated properties appropriate to their origin
organoids
- used to study developmental processes
- certain human embryo cells can be coaxed into differentiating into multiple cell types, which can self-assemble into organ like structures that closely resemble a normal organ
four types of weak interactions that help bring molecules together in cells
- electrostatic attraction: between oppositely charged molecules
- van der Waals: when two atoms approach each other
- hydrophobic force: generated by a pushing of non polar surfaces out of the hydrogen-bonded water network, where they would otherwise physically interfere with the highly favourable interactions between water molecules
application of hydrophobic interaction
promote molecular interactions in building cell membranes, constructed from lipid molecules with long hydrocarbon tails
define nucleotides
nitrogen-containing ring linked to a five-carbon sugar that has a phosphate group attached to it
bases
under acidic conditions, can bind an H+ and thereby increase the concentration of OH- ions in aqueous solution
pyrimidines
cytosine, thymine, uracil
derived from a six-membered pyrimidine ring
purines
guanine and adenine
bear a second, five-membered ring fused to the six-membered ring
base plus sugar (no phosphate group)
nucleoside
ATP
adenine, sugar, three phosphates linked in series by two phosphoanhydride bonds
rupture of these bonds releases free energy
structure of nucleic acids
long polymers in which nucleotide subunits are linked by covalent phosphodiester bonds between the phosphate group of one nucleotide and a hydroxyl group of the next
how are nucleic acid chains synthesised?
from energy-rich nucleotide triphosphate by a condensation reaction that releases pyrophosphate
distinguish between the roles of DNA and RNA
- DNA is more stable due to double helix so acts as a long-term repository for hereditary information
- RNA serves as more transient carriers of molecular instructions
draw the 5 bases
base/nucleoside names for the 5 bases
adenine - adenosine
guanine - guanosine
cytosine - cytidine
uracil - uridine
thymine - thymidine
AMP
adenosine monophosphate
dAMP
deoxyadenosine monophosphate
UDP
uridine diphosphate
how are phosphates usually bound sugars?
joined to the C-5 hydroxyl of the sugar
3 functions of nucleotides and their derivatives
- carry chemical energy in their easily hydrolysed phosphoanhydride bonds
- combine with other groups to form coenzymes
- used as small intracellular signalling molecules in the cell
between which carbons do phosphodiester bonds take place?
5’ and 3’ carbon atoms of adjacent sugar rings
3’ end
ends with OH (hydroxyl)
5’ end
ends with phosphate
A pairs with
T or U
G pairs with
C
describe the structure of the double helix
- strands antiparallel to each other (oriented with opposite polarities)
- anti-parallel sugar-phosphate sytands twist around each other to forma. double helix containing 10 base pairs per helical turn
why does twisting of the double helix take place?
renders conformation of DNA’s helical structure energetically favourable
do prokaryotes have cilia?
no
origins of mitochondria (endosymbiosis) - entangle - engulf - endogenies (E^3) model
- archaean cell was anaerobic
- bacterial ectosymbiont was aerobic
- surface protrusions on archaea expanded over time
- this led to enclosure of ectosymbiont by archaeal membrane fusion
- escape of endosymbiont into cytosol and formation of new intracellular compartments
- over time, this evolved into modern-day mitochondria
did prokaryotes or eukaryotes form first?
prokaryotes formed much earlier, and then eukaryotes
what is an alternative model for endosymbiosis?
some models are more predatory, where the aerobic bacterium is engulfed via a process similar to phagocytosis
common features of both types of endosymbiosis models
- ancient anaerobic archaeal cell
- ancient aerobic bacterium
- over evolutionary time, a symbiotic relationship
Asgard cell
- type of archaea belonging to the group Asgard
- has a cell body and protrusions with ectosymbionts on their surface
describe and draw the sequence of the tree of life
ancestral prokaryote (3.5-3.8b years ago)
bacteria and archaea separated
1b years later, the first single-celled eukaryote was formed
lines of evidence to support endosymbiont hypothesis
- mitochondria and chloroplasts still have remnants of their own genomes, which are circular. their genetic systems resemble that of modern-day prokaryotes
- mitochondria and chloroplasts have kept some of their own protein and DNA synthesis components and these resemble prokaryotes too. they have their own ribosomes and multiply by pinching in half — the same process used by bacteria. are also sensitive to similar antibiotics.
- membranes in mitochondria and chloroplasts often similar to those in prokaryotes and appear to have been detached from engulfed bacterial ancestor.
general attributes of model organisms
- rapid development with short life cycles
- small adult (reproductive) size
- readily available (collections or wide-spread)
- tractability - ease of manipulation or modification
- understandable genetics
central dogma of molecular biology
DNA -(transcription)-> RNA -(translation)-> protein
tRNA
- transports amino acids
- protein synthesis
rRNA - ribosomal RNA
- part of the ribosome
- does catalytic work of making protein by creating peptide bonds
- has a structural role as part of RNA
refined central dogma
not all RNA is translated into protein - it has many other uses
draw a diagram for the elaborated central dogma information flow
genome
cell’s complete set of DNA, including mitochondria and chloroplasts
transcriptome
all the RNA in a particular cell at a particular point in time
genome vs transcriptome/proteome
transcriptome/proteome are much more dynamic
proteome
entire set of proteins in a cell at a particular point in time
how are the proteome and transcriptome related?
the proteome feeds information into the transcriptome
interactome
set of all protein-protein interactions taking place in a cell at a single point in time
metabolome
full set of small molecules that can be found in a cell at a certain point in time (anything that is generally smaller than a protein, like ATP, sugars, vitamins, some hormones)
example of metabolome affecting transcription
lac operon
phenome
comprised of everything (all the -omes), and together with the observable characteristics of what you’re looking at (cell, organ, etc)
describe the directionality of transcription and translation
- DNA, RNA, and proteins are synthesised as linear chains of information with a definite polarity
- info in RNA sequence is translated into an amino acid sequence via a genetic code which is essentially universal among all species
what are nucleic acids?
an organism’s blueprints - the genetic material in a cell
- DNA: deoxyribonucleic acid
- RNA: ribonucleic acid
three parts of a nucleotide
- pentose sugar - scaffold for base
- nitrogenous base
- phosphate group - backbone. There may be 1 (mono), 2 (di), or 3 (tri) phosphate groups
pyrimidines
UC The pyramids?
- single ring
- uracil
- cytosine
- thymine
purines
pure Animals Gobble
- double ring
- adenine
- guanine
where is the base attached?
1’
distinguish between ribose and deoxyribose in terms of functional groups
2’ carbon in ribose has a hydroxyl group - in deoxyribose it just has a hydrogen
nucleoside monophosphate
nucleoside vs nucleotide
nucleoside = base + sugar
nucleotide = base + sugar + phosphate
adenosine
sugar + adenine
guanosine
sugar + guanine
cytidine
sugar + cytosine
uridine
sugar + uracil
thymidine
sugar + thymine
nucleoside monophosphate
sugar + base + 1P
nucleoside diphosphate
sugar + base + 2P
nucleoside triphosphate
sugar + base + 3P
dNTPs
deoxyribonucleoside triphosphates
- DNA is synthesised from them
- N stands for A, C, T, G
NTPs
- N stands for A, C, U, G
- ribonucleoside triphosphates
- RNA is synthesised from them
nucleotides are linked by
phosphodiester bonds
overall charge on nucleic acids
negative all the way along
interactions between individual molecules are usually mediated by
noncovalent attractions:
1. electrostatic attractions (happen within and between large molecules) - weakened by water
2. hydrogen bonds - strongest in a straight line
3. van der Waals attractions - two atoms very close together, causing temporary dipole due to uneven distribution of electrons. not weakened by water
4. hydrophobic force - water pushing non-polar things away from itself. individually weak, but add up.
individually, very weak forces - BUT can sum to generate strong binding between molecules
Cell theory
- the cell is the basic organisational unit of life
- all organisms are comprised of 1 or more cells
- cells arise from pre-existing cells: the ability to reproduce is characteristic of living matter, which must be able to duplicate DNA, create proteins, etc
prokaryotic
- no nuclei
- single celled (but communities may exist)
- bacteria and archaea (domains)
eukaryotic
- nuclei with membrane
- single-celled (eg algae) or multicellular
- plants, fungi, animals, humans, protozoans
describe and draw a prokaryotic cell
- no membrane-bound organelles; localised DNA may be in nucleoid or not localised at all
- smaller size than eukaryotes (~1micrometer)
- less DNA than eukaryotes
draw and describe a eukaryotic cell (plant)
- nucleus
- several membrane-bound organelles
- larger size and more complex (~5micrometers)
draw and label a eukaryotic cell (animals)
what is the need for cytoskeletons in eukaryotic cells
simple diffusion is not enough to guide transport9
