What is Life Flashcards
All living things.. (9)
- composed of common set of chemical compounds
- made up of cells
- use molecules obtained from environment to make news molecules
- extract energy from environment to use it to do work
- regulate internal environment
- contain genetic information
- use universal molecular code to build proteins from genomic information
- grow and change
- exist in population that evolve over time
What are prions
prions are misfolded proteins which transmit their misfolded shape onto normal variants of the protein
Characteristics of prions (3)
- no DNA
- survive being boiled
- treated with disinfectants
Prions are
non living
Characteristics of viruses (2)
- Contain genetic material (DNA/RNA)
- Replicate and evolve
Viruses are
not living (need host to replicate + no metabolic processes)
What are the 3 theories on how life began
- Prebiotic synthesis experiment model early earth
- Life came outside from earth
- RNA may have been first biological catalyst
- Prebiotic synthesis experiment model early earth
hot - early atmospheric gases struck by spark cause chemical reaction to make new compounds
cold - 27 years of gases -78c caused chemical reactions to speed and accumulate
- Life came outside from earth
meteorite carried different amino acid (L/D- isomers earth usually has L)
isotope ratio of carbon and hydrogen different in sugars
- RNA may have been first biological catalyst
catalytics RNAs - ribozymes
speed up reactions involve their own nucleotides
RNA catalyst for its own replication + protein synthesis
What does reverse transcriptase do in retroviruses
catalyse RNA –> DNA
What is a protocell
Molecules form a bilayer and polar heads are near water and non polar tails are interior
Prebiotic water filled structures
How did first cells with membrane come to exist
Fatty acids are amphipathic
Stabilise structure in aq. makes lipid bilayer - protocell
nucleic acids inside protocell would replicate using nucleotides from outside
limited replication
What is the cell theory (4)
- cells are fundamental unit of life
- all living organisms are composed of cells
- all cells from pre existing cells
- modern cells evolved from common ancestors
What do similarities among living organisms indicate?
- all live on earth has common ancestry
- evidence for origin of life 4 billion years ago
- organisms go through evolution from past years
- organisms are related sharing same genetic code/chemical composition/cellular structure
Describe evolution by Charles Darwin
Species change over time by natural reproduction of some individuals due to fitness
Descent with modification - divergent species share common ancestor
Definition of evolution by Charles Darwin
Changes of genetic composition of population over time
What is lysozyme protein held by
Water molecules
How did stromatolites form banded iron
oxygen from photosynthesis organisms react with iron in water
how did chloroplasts form
photosynthetic organisms symbiotic relationship with eukaroytes
what is cyanobacteria
group of bacteria forming oxygen
biofilms of cyanobacteria die and other take layers
thrive in salty ass water
effect of increase ozone (O3) on earth
life able to grow + adapt since lesson UV rays
effect of oxygen for animals
larger and more complex organisms + diversify
what is the cambrian explosion
the appearance of major animal groups and rapid diversification + little fossils form
what are stomatolites
evidence of early life
compare and contrast the features of DNA and RNA
DNA: deoxyribose nucleic acid double stranded no oxygen on 2-carbon RNA: ribonucleic acid single stranded OH on 2-carbon can have complementary binding to its own nucleotide - folded shape (mRNA/tRNA/rRNA) Uracil instead of Thymine
How do polynucleotides (RNA/RNA) form (DNA replication)
3’ OH on sugar forms a phosphodiester bond with phosphate group
Two phosphate groups released
Hydrolysis of pyrophosphate to its individual phosphates releases energy for polymerization
Nucleic acids elongate 5’ → 3’ for the sugar phosphate backbone
Include RNA molecule that function as primers to allow duplication of RNA
RNA regulate expression of genes (transcription), DNA used to amplify (translation)
Hydrogen bonds form between (A=T/C triplebond G)
Hydrogen bonds form due to the polar C=O/N-H so the hydrogen and oxygen has delta +/- → lots of hydrogen bonds provide large attraction but not strong so it can be broken/made
nucleic acids/nucleotides/polynucleotides/nucleoside? explain
sugar + phosphate group (no base) = nucleoside
nucleoside + base = nucleotide
nucleotide + nucleotide = polynucleotide
polynucleotide (2) = nucleic acid (DNA)
what’s the name of DNA nucleosides
DEOXY-adenosine etc
RNA doesn’t have
what are the pyrimidine bases
C/U/T
what are the purine bases
A/G
nucleotide components
base (ribose/deoxyribose) + pentose sugar + phosphate group
what are proteins for (8)
Structural Defence Hormones Muscles Transport Storage Enzymes Mucilage
amino acid components
basic amino group
r group side chain
carboxyl acidic group
non polar means
hydrophobic
polar, uncharged means
hydrophilic
charged means
hydrophilic
peptide bond formation type of reaction
condensation
definition of primary structure
sequence of amino acids in straight chain
definition of secondary structure
consist of regular and repeating patterns in polypeptide chain - involved hydrogen bonding
- alpha helix
- B-pleated sheets
what is an alpha helix
R groups extend outwards of the helix
Hydrogen bonding between C=O and N-H of amino acids throughout segments
Coiling right hand
what is b pleated sheets
Two or more polypeptide aligned side by side/completely extended
Hydrogen bonding between C=O and N-H on separate polypeptide cains
definition of tertiary sturcture + types of bonds
3D structure formed from the interaction of R groups with itself and environment Covalent disulfide bridges Hydrogen bonds Ionic bonds Hydrophobic/van der waals
definition of quarternary structure
Contains two or more polypeptides folded and bind together and interact
what are carbohydrates for (5)
Source of chemical energy Form structural components Abundant organic compounds in nature (CH2O)n Subunit is a monosaccharide
glycosidic bonds reaction?
condensation reaction between monosaccharides
examples of monosaccharides
glucose
galactose
fructose
glucose + glucose ->
maltose
galactose + glucose ->
lactose
fructose + glucose ->
sucrose
polysaccharides (3)
starch
glycogen
cellulose
describe glycogen
Water insoluble
Highly branched polymer of glucose
Store glucose in liver in form of glycogen
describe starch
A-1,4 and a-1,6 glycosidic bonds
Amylose unbranched
Amylopectin branched
Energy storage in plants
cellulose
More stable due to b-glycosidic bonds
Structural for cell wall - can withstand harsh conditions
Linear polysaccharide
describe lipids
Insoluble in water
Dissolve readily in organic solvents
Composed of C,H,O
Differ from carbohydrates due to smaller proportion of oxygen
Contain other elements (P/N)
Unsaturated = double bond form a kink = liquid in r.t.p
Saturated = single bond throughout = solid in r.t.p
purpose of lipids
Insulation
Phospholipid membrane
Energy reserve
Buoyancy
what is triglyceride made of
3 fatty acids + glycerol
what are the fundamental elements of biomolecules
C,H,O,N
general formula for carbohydrates
(CH2O)n
size of prokaryotes
1-10um
size of eukaroytes
10-100um
characteristics of prokaryotes
Capsule Cytoplasm Nucleoid Cell membrane Flagellum Pili (protein hairlike structures) Cell wall (peptidoglycan)
characteristics of eukaryotes
Compartmentalisation is important to cell Nucleus (DNA held inside) Endoplasmic reticulum Mitochondria Vacuole Golgi apparatus (cell membrane + cytoplasm)
ribosomes present in prokaryotes
70S (50 + 20)
2 rRNA molecules
describe the great oxygenation event
High levels of methane/CO2/ammonia gas + radiation
cyanobacteria form oxygen to allow ozone layer
how do prokaryotes divide
binary fission exponentially
describe binary fission in prokaryotes
replication of circular DNA at origin of replication
cell elongates and FtsZ protein migrate to middle of cell
duplicated chromosome move to opposite ends
FtsZ proteins form ring at midpoint - directs formation of septume
cell wall and plasma membrane accumulate there
septum complete - cell pinched into two daugher cells
ribosomes are used as
drug targets
antibiotic targets ribosomes - inhibit protein synthesis to make bad protein
difference between archaea and bacteria
Morphologically (physically) are similar
Achaean genes new - more closely related to eukaryotes
Archaea and eukarya millions of years apart
RNA polymerase in Archaea has multiple - bacteria has one
Genetic transcription and translation more similar to eukaryotes than bacteria
Features of archaean lipids and membrane unusual and lack of peptidoglycan wall
More archaea are extremophiles
Many are thermophilic/acidophilic
Maintain internal pH of 5.5-7 sitting in pH 2-3
Pyrolobus fumarii found in deep sea hydrothermal vents 106 degrees - metabolically inactive below 90 degrees
No production of resting spores - no long term state of immortality
No archaean pathogens - no disease affecting humans
Bacteria causes many diseases
what are prokaryotes used for
recycling and nitrogen fixing bacteria and GM bacteria and primary producers
2 features of prokaryotes
small genome and rapid cell division
metabolically diverse and found everywhere
when did eukaryotes evolve
2.1 billion years ago
how did eukaryotes come about
through spirally coiled photosynthetic algae
what is linker DNA
double stranded DNA which holds two nucleosome cores
describe nucleus
Surrounded by double membrane/nuclear envelope
Presence of nuclear pores (50 nm)
Allows movement of ribosomes in and out
Nucleolus: subregion containing ribosomal genes
definition of chromosome
threadlike structure containing protein
what is nucleosome
histone + DNA packing protein
what is heterochromatin
highly condensed - gene poor
euchromatin
easily condensed - gene rich
Describe the structure and function of the mitochondrion.
Double membrane
Inner and outer membranes
Inner membrane is highly convoluted - high surface area for protein complex → ATP synthesis/reactions
Carry anaerobic respiration in eukaryotic cells
reactions in the mitochondria matrix
TCA cycle and B-oxidation occur in the matrix
Describe the structure and function of the chloroplast.
Cells contain one or many chloroplasts per cell
Surrounded by two membranes - out and inner to form thylakoids
Photosynthetic pigments located in thylakoids
Chloroplasts responsible for photosynthesis - light energy → chemical energy
why do mitochondria and chloroplast have double membrane
- nucleus formed from invagination of plasma membrane around the nucleoid of an ancient prokaryote
- mitochondria arise from primary endosymbiosis from purple bacteria
- chloroplasts arise from primary endosymbiosis from photosynthetic cyanobacteria
evidence of endosymbiotic from mitochondria/chloroplasts
- organelles morphologically similar
- outer membrane/inner membrane
- semi-autonomous - retain own genome
- make their own stuff (protein/ribosomes)
- metabolism like existing prokaryotic organisms
- some chloroplasts have bacterial peptidoglycan
definition of primary endosymbiosis
engulfing and absorbing of a prokaryotic cell by a eukaryotic cell
steps of primary endosymbiosis
Aerobic bacteria enters in the eukaryote as a prey/parasite → becomes a cell living in a cell (endosymbiont)
Endosymbiont releases oxygen to allow the cell to survive - eventually turns into a mitochondrion
Eukaryotic cell may go on to obtain more endosymbionts (cyanobacteria) which will become chloroplasts
Outer membrane disappears
definition of secondary endosymbiosis
engulfing and absorbing of a eukaryotic cell (undergone primary endosymbiosis) by a eukaryotic cell
how many genomes do plants and animals have
plants - 3 (+ chloroplasts)
animal - 2
definition of endomembrane system
system of compartments that include all membrane bound components of cell except for mito/chloro/microbodies
describe the endoplasmic reticulum
Cisternae (enclosed membrane) → internal compartments and channels
Changing in structure and function
Rough endoplasmic reticulum
Ribosomes attached
Protein synthesis
Smooth endoplasmic reticulum
Synthesis for glycoproteins/carbohydrates/lipids
Biomolecules secreted throughout the cell
describe the golgi apparatus
collection/packaging/distribution of molecules, then secreted
Biochemically modified (addition of sugars etc)
Polysaccharides formed
Consists of Golgi stacks (flattened sacs of membrane)
Receive vesicles from ER
Golgi polar structures
Vesicles arrive at cis face
Vesicles leave at trans face
Many molecules (hormones/digestive enzymes) exit the Golgi in secretory vesicles (exocytosis)
describe the lysosomes
Break down material ingested by endocytosis or recycle old organelles
Surrounded by single membrane
Acidic interior - hydrolytic enzymes
describe the plant vacuole
Surrounded by single membranes (tonoplast)
Contain hydrolytic enzymes
Storage of nutrients/pigments/maintenance
Maintain cell turgor pressure
describe microbodies
Surrounded by single membrane
Found in animal and plant cells
Contain enzymes from free ribosomes in cytoplasm (not in RER)
Neutral pH
Oxidative enzymes release hydrogen peroxide
Enzyme catalase breaks down hydrogen peroxide
Peroxisomes (break down amino acids) and glyoxysomes (break down fatty acids)
describe cytosol
Site of numerous biochemical processes
Space between organelles and endomembrane
Protein biosynthesis - protein synthesis begins in the cytosol and proteins made passed to nucleus/mitochondria etc
Cytoskeleton
Glycolysis reaction starts in the cytosol → mitochondria
what is cytosol
fluid in cytoplasm, cytoplasm is the entire content within cell membrane
describe cytoskeleton
Composed of protein (made in cytosol)
Act as form of structural elements within cytoplasm in cell (actin/microtubules)
what are cytoskeleton components
microtubules + actin filaments
describe the microtubules and actin filaments in cytoskeleton
Tubulin makes up microtubules (25nm diameter)
Actin makes up actin filaments (7nm diameter)
Form stiff structures don’t branch or contract
Polar and dynamic structures (one side negative/positive/one way)
polymerise/depolymerise to satisfy cell needs (forming polymer)
Cell movement generated by motor proteins (by actin filaments + microtubules)
what are microtubule associated proteins
kinesin and dynein
describe kinesin and dynein in microtubules
Kinesin motor move towards + end of microtubules
Dynein motors move towards - end of microtubules
May consume ATP for movement
what does myosin do
pulls organelles along actin filament
responsible for cytoplasmic streaming (plant) and muscle contraction (mammals)
3 things to remember about membranes
- always enclose a space
- membranes never open ended unless damaged cell
- phospholipid bilayer
describe phospholipid bilayer
semi permeable
selective
water passed by osmosis
difference between simple and facilitated diffusion
both passive diffusion facilitated sometimes use some carrier protein etc for fac.
describe primary active transport
Na/K pump (antiporter)
ATP required against gradient
2K in cell
3Na out of cell
describe secondary active transport
cotransporter (symport)
Using the electrochemical gradient formed from primary active transport
Coupling molecules
why do cells need to divide
Cellular maintenance
Growth and development
Cell division rates are highly variable
yes
what is the cell cycle of eukaryotes
G1
S phase - dna synthesis
G2
M - mitosis
describe g1 phase
Unreplicated DNA (spent most time here) G0 = resting phase g1 cyclin
describe s phase
DNA replication 5-6 hours
s cyclin
describe g2 phase
Preparation for mitosis 3-4 hours
g2-m cyclin
describe m phase
Nuclear division 2 hours → cytokinesis = 2 daughter cells
m cyclin
describe the cell cycle
4 steps
- Internal signal trigger events to progress a cell through phases of cell cycle
Cyclins and cyclin-dependent kinase (Cdk)
If they come together → form activated complex
Phosphorylate target - phosphate group from ATP to protein substrate
= Phosphorylated protein (active) + ADP
Regulation of cell cycle - R (restriction points) regulated by different cyclin-cdk complex
- Cyclins are transient proteins (proteins can form and broken easily) during cell cycle
RB protein stop movement of cell out of G1 to S
Synthesis of G1/S cyclin
DNA → mRNA → G1/S cyclin + CDK (active complex)
Deactivates RB by phosphorylating it stop blocking cell into moving into S phase
Breakdown of cyclin - If checkpoints not meant = cyclin-Cdk interact with signalling pathways to prevent progression
describe the cell cycle
4 steps
- Internal signal trigger events to progress a cell through phases of cell cycle
Cyclins and cyclin-dependent kinase (Cdk)
If they come together → form activated complex
Phosphorylate target - phosphate group from ATP to protein substrate
= Phosphorylated protein (active) + ADP
Regulation of cell cycle - R (restriction points) regulated by different cyclin-cdk complex
- Cyclins are transient proteins (proteins can form and broken easily) during cell cycle
RB protein stop movement of cell out of G1 to S
Synthesis of G1/S cyclin
DNA → mRNA → G1/S cyclin + CDK (active complex)
Deactivates RB by phosphorylating it stop blocking cell into moving into S phase
Breakdown of cyclin - If checkpoints not meant = cyclin-Cdk interact with signalling pathways to prevent progression
look at page 37 cell cycle graphs ok
ok
what is the cell cycle in prokaryotes
B phase - gap phase
C phase - replication
D phase - division
conditions for C phase in prokaryotes
A lot of DnaA-ATP
Little of DnA-ADP
DnaA-ATP responsible for C phase → high affinity for DnaA binding region at the origin of replication (oriC region) in bacterial genome
Can bind and unwind
conditions for D phase in prokaryotes
Little of DnaA-ATP
A Lot of DnA-ADP
Cell cycle progression in bacteria regulated by initiation DNA replication DnaA-ATP - define oriC region/DnaA-ATP
(single origin of replication)
DnaA is a protein that activates initiation of DNA replication in bacteria, bound to ATP
how does DnaA-ATP –> DnaA- ADP
DnaA-ATP opens and pulls apart DNA
Helicase pulls apart DNA → attract DNA polymerase III
DNA polymerase replicate DNA
ATPase converts DnaA-ATP → DnaA-ADP
dna synthesis is semi conservation because?
→ Daughter cell will get old strand from parental DNA and new strand
reference to replication origin on prokaryotes and eukaryotes
Prokaryote have single origin of replication along their DNA
Eukaryotes have multiple origins of replication along the chromosome
describe DNA replication
Leading strand (continuous) from 3’ to 5’
DNA polymerase works from 5’ to 3’
Lagging strand (discontinuous)
Primase makes short RNA primer on the lagging strand template (on empty space)
DNA polymerase add to 3’ on the RNA primer to form okazaki fragment (RNA primer 5’ + okazaki fragment 3’)
Primase will land on random bits of lagging strand
DNA synthesis requires a primer
RNA primer synthesised before DNA polymerase attachment
Primase makes RNA primer
DNA helicase unwinds DNA
DNA ligase removes RNA primer and patches up between okazaki fragments
Single stranded binding proteins prevent DNA from winding back together
describe chromosome/sister chromatids
G1 phase have single copy
S phase replication to form sister chromatids
End of S phase, chromosomes are held together by centromere
Before mitosis, DNA and histones form tightly packed structures
DNA double helix into nucleosomes (core of 8 histone molecules) - DNA wrapping around histones [10:1]
Nucleosomes wrap together to form super coles [50:1]
Chromatin forms loop domains on protein scaffold [250:1]
Condensed heterochromatin
Compacted chromosome
what do kinetochores do
Kinetochores (specialised protein structure) important for movement
Connect microtubules to centromere region
describe mitosis - IPMAT
Interphase
S phase - DNA replication
Prophase
Chromatin coils and supercoils to form visible chromosomes (paired sister chromatids)
Prometaphase
Nuclear envelope breaks down
Kinetochore and microtubules form and connect to poles
Cohesin holds sister chromatids together
Cohesin removed but held by by some cohesin in centromere
M cyclin + Cdk + APC + ATP → actives separase by phosphorylation
Metaphase
Centromeres align
Anaphase
Paired sister chromatids separate and move toward opposite poles
Daughter chromosomes separated
Telophase
Chromosome reach pole
Nuclear envelope forms
Decondensed chromatin
cytokinesis in plant vs animals
In animal cells: plasma membrane contractile ring forms to pulling two membranes together to form separate cells
In plant cells: cell plate forms from cell wall membrane - endomembrane form vesicles of carbohydrates to form cell plate
describe binary fission in prokaryotes
Double stranded circular DNA
DNA replication initiation (DnaA-ATP) in C phase
Daughter DNAs - DNA polymerase/helicase/ligase etc action
Cytokinesis
Forming of Z ring
FtsZ protein (filament temperature sensitive)
Forms protein fibres that constricts the cell
Similar to protein tubulin
Involved in division of chloroplasts/mitochondria
what does mutation in FtsZ protein do
Mutation in FtsZ alter bacterial shape and frequency and control chloroplasts division
- filament temp sensitive
- form protein fibres constricting the cell
- homologue of protein tubulin
- involved in division of chloroplasts/mitochondria
what does mutation in FtsZ protein do
Mutation in FtsZ alter bacterial shape and frequency and control chloroplasts division
- filament temp sensitive
- form protein fibres constricting the cell
- homologue of protein tubulin
- involved in division of chloroplasts/mitochondria
