Module 1- What is Life? Flashcards
What are the nucleic acids in DNA?
thymine, adenine, guanine, cytosine
What are the nucleic acids in RNA?
uracil, adenine, guanine, cytosine
Which nucleic acids are pyrimidines?
1 ringed nucleic acids
uracil, thymine, cytosine
Which nucleic acids are purines?
2 ringed nucleic acids
adenine, guanine
How many hydrogen bonds between nucleic acids?
Thymine + adenine = 2 hydrogen bonds
Guanine + cytosine = 3 hydrogen bonds
How are nucleotides connected?
Carbon 3 on deoxyribose is bondedd with phosphate group
3’-5’ on one strand and opposite way in parallel stand
Formed by condensation reaction (water is formed)/ dehydration reaction (hydrogen is lost)
What are some functions of non-coding regions on DNA?
regulation gene expressions, protection of end of chromosomes (telomeres), DNA profiling (satellite DNA), non-coding RNA genes (genes for tRNA)
Sense and anti-sense strand?
Antisense strand = 3’-5’, strand that is transcribed into RNA, complimentary to RNA strand
Sense strand = 5’-3’, strand that is NOT transcribed into RNA (coding strand, same as RNA strand)
What are the types of RNA?
mRNA (messenger) = transcript copy of a gene that translates to a specific polypeptide
tRNA (transporter) = carries amino acids (codons) to ribsomes for synthesis
rRNA (ribosomal) = primary component of ribosomes and is responsible for catalytic activity
Base structure of amino acids?
Basic amino group on left side and carboxyl group on right, and R-group (side chain group)
How are proteins bonded?
Amino acids are linked together by peptide bonds
OC-NH bond
Formed by condensation reaction (water is formed) and/or dehydration reaction (hydrogens are lost)
N-terminus is where amino group is located
C-terminus is where carboxyl group is located
How are R-groups differentiated?
Polar R-groups (uncharged) are hydrophilic (e.g. serine)
Non-polar groups (charged) are hydrophobic (e.g. glycine, alanine)
Charged R-groups are hydrophilic (acidic/basic amino acids)
Structures of proteins
Primary structure - sequence of amino acids
Secondary structure - alpha helix or beta sheets (both have hydrogen, electrostatic bonds of amino acids)
Tertiary structure - 3D structure of protein, determined by interaction of side groups (disulfide bridges, hydrogen bonds, ionic interactions) (configuration which least free energy)
Quaternary structure - connection of more than 1 polypeptide or prosthetic groups (inorganic molecule, e.g. iron in haemoglobin)
Examples of monosaccharides, disaccharides and polysaccharides
Mono = glucose, fructose, galactose
Di = maltose (glucose + glucose), lactose (glucose + galactose), sucrose (glucose + fructose)
Poly = starch, glycogen, cellulose, pectin
General formula of carbohydrates
(CH2O)n
Forms of carbohydrates
Straight chain form turns to cyclic form (e.g. in glucose, C1 bonds with C5)
Forms either alpha or beta cyclic form
Alpha - hydrogen group is on top in C1
Beta - hydrogen group is on bottom in C1
Significance between glucose and galactose?
Glucose and galactose are stereoisomers that only differs on carbon-4
both beta in C1
alpha for glucose
beta for galactose
How do monosaccharides bond?
Joined by glycosidic bonds
Forms a ether bond and forms water as by-product (condensation/dehydration)
Requires an enzyme to form linkage (e.g. glycotransferase for sucrose, or with pectin where each linkage requires different enzyme)
Structures of polysaccharides
Glycogen (storage polysaccharide found in liver of animals) - branched structure of alpha 1-4 and 1-6 glycosidic linkage (more branched than amylopectin)
Cellulose - linear structure of beta 1-4 glycosidic linkage (beta linkage causes it to be indigestible)
Starch - Amylopectin and Amylose
Amylopectin = branched structure of alpha 1,4 and 1-6 (not as branched as glycogen)
Amylose = linear (helical) structure of alpha 1,4 glycosidic linkage (harder to digest and less soluble, due to small uptake of space = storage in plants)
Chitin - chain of glucose with acetyl group (acetyl group is on opposite ends in each atom, intertwining)
Basic monomer of lipids
Base unit for lipids are long fatty-acid chains (they are straight chains with a -COOH group at one end)
Unsaturated = double bond included (causes a kink, thus can line up in room temperature + weaker bonds and are liquid) Saturated = single bonds (straight chains, usually solid in room temperature)
Examples of common lipids
Wax = 2 chains of fatty acids joined by an ester linkage (O=C-O)
Triglyceride (fats) = 3 chains of fatty acids joined by glycerol (head group)
Lipids are good energy reserves (e.g. canola oil, produced in seed whilst germinating, oil is used as energy)
Structural component of phospholipids
Hydrophilic head = glycerol, phosphate, choline
Hydrophobic tail = fatty acid tail
Which molecules can pass through phospholipid membrane?
Water, gases (co2, o2, n2), small uncharged polar molecules (urea, ethanol)
Transportation in phospholipids
Proteins can create pores in membrane (due to polarity) Facilitated diffusion (along help with protein) - carrier-mediated transport and channel-mediated transport Movement of molecules in facilitated diffusion and simple diffusion are down the electrochemical gradient (e.g. carrier = for fructose (large molecules), channel = aquaporins for water)
Active transport - use of proteins to pump molecules in or out using ATP
Types of active transport
Primary active transport - Na/K pump
pumps 3 Na out (high conc of Na outside cell)
and pumps 2 K in (high conc of K inside)
Secondary active transport - relies on products of primary active transport to drive the mechanism, only pumps molecules inside
e.g. pumping glucose inside cell, Na is energy source
What is the typical size of prokaryotes?
1μm (can be up to 1μm)
1μm = 0.001 mm
Cell structure of prokaryotes
Ribosomes - production of proteins
Pili - adhesion to other cells/communication/exchange genetic material
DNA (plasmid)
Rotary motor + flagellum - movement
Outer capsule, cell wall and plasma membrane - structure, permeability
(cell wall = made of peptidoglycagen)
(outer capsule = made of sugars, used to survive extreme environments or invading immune system)
Resting spores
Certain prokaryotes (mostly from domain of bacteria) can create resting spores/endospores
Allow prokaryote to remain in a ‘dormant’ state and surviving tough environments that then ‘wake up’ when environment is more suitable
Prokaryotic flagellum
just made out of one protein (flagellin) that is helically coiled
very simple structure compared to eukaryotic flagellum
Prokaryotic ribsomes
70S (50s + 30s)
~55 proteins
3rRNA
Eukaryotic ribosomes
80S (60s + 40s)
~80 proteins
4 rRNA
Antibioctics/medications for prokaryotes
Drugs tend to target prokaryotic ribosomes to inhibit protein translation + production OR cell wall
e.g. Tetracyclines - targets small subunit of ribosome (tRNA cant bind to ribosome, disrupting protein production)
Chloramphenicol - targets large subunit (preventing peptide bond being formed between amino acids)
Cell division in prokaryotes
Prokaryotes divide by binary fission
Double strand of DNA attaches to cell wall where cell wall + plasma membrane needs to elongate
Replicated genomes pull away from each other causing a cleavage
Daughter cells can pinch away from each other
Prokaryotic diversity
Prokaryotics have lots of spontaneous mutations causing a large biochemical diversity
(considered highly evolved as they were in beginning of time where they were responsible for Earth’s gases of today)
Prokaryotic domains
Bacteria and Archaea
Archaea is more closely related to eukaryotes
Differences between Archaea and Bacteria
Archaea:
•archaea genes are more recent/new to science
- comparison of nucleic acid sequences are different to bacteria (allowing to construct phylogenetic trees that differ to bacteria + eukaryotes)
- genetic transcription + translation differ to bacteria (more similar to eukaryotes) allowing them to have their own domain
- archaea lack a peptidoglycan cell wall
- many Archean are extremophiles
Archaea + Bacteria:
•morphologically they look similar
Bacteria:
•create resting spores (archae do not)
•can be pathogens (no archaean pathogens as of now)
Use of bacteria in industry
use in recycling, GM plants, nitrogen-fixing bacteria, pharmaceuticals
- recycling - bacteria cleans up waste in water
- agriculture - nitrogen-fixing bacteria convert nitrogen to ammonia in roots
- pharmaceuticals - E. coli is used to mass produce insulin
- GM plants - Agrobacterium tumefaciens (plasmid is used to insert desired gene)
Angrobacterium tumefaciens for GM plants
plasmid from bacteria is extracted and restriction site is cut out
desired gene is inserted using restriction enzyme and DNA ligase
plasmid is introduced into the plant
desired product is made in plant/carried out
Significance of cyanobacteria
primary producers that have big impact on earth
- great oxygenation event
- related to evolution of chloroplasts
Structure of nucleus (eukaryotes)
command centre of the cell (holds genetic information) surrounded by double membrane (nuclear envelope) has nuclear (annular) pores (50nm in size) for mRNA to exit Nucleolus = subregion of nucleus that holds ribosomal genes (for transcription) (darker part of nucleus)
Chromosome structures
long strands of nucleotides wrapped around histone proteins
(8 subunits of histones)
histones are positively charged + DNA is negatively charged
Nucleosome
1 histone protein and 2 nucleotides wrapped around
Heterochromatin
nucleosomes grouped up together
Structure of mitochondria
•two membranes (outer and inner membrane)
inner membrane folds (increasing SA) = cristae
has ribosomes too
•matrix = inside space of the inner membrane
Structure of chloroplasts
•two membranes (outer and inner membrane)
inner membrane forms internal network of thylakoids/lamellae
•photosynthetic pigments are found in thylakoids
- granum = stack of thylakoids
- stroma = outside space (cytosol/cytoplasm)
Examples of accessory pigments
- chlorophyll B (catches photons in plants)
- phycoerythrin
- phycocyanin
Origins of mitochondria and chloroplasts
Mitochondria:
•arose from primary endosymbiosis of a purple bacteria + nucleoid cell (engulfed)
Chloroplasts:
•primary endosymbiosis of photosynthetic cyanobacteria + nucleoid cell
Origin of nucleus
May have formed from invaginations (pocket forming) of plasma membrane around the nucleoid of an ancient prokaryote
Endosymbiosis and origins of organelles
cyanobacterium/bacteria is engulfed but did not digest/die
outer membrane of organelle disappears and genes are transferred to the nucleoid cell
Evidence of endosymbiotic origin
- mitochondria/chloroplasts appear morphologically similar to bacteria
- surrounded by outer membrane whilst inner membrane folds/invaginates
- semmi-autonomous (have their own genome)
- own machinery for synthesizing proteins (self-sustainable)
- metabolism is similar to prokaryotes
•chloroplasts in some organisms still have peptidoglycan cell wall between inner + outer membranes
Secdonary emdosymbiosis (eukaryotes)
occurs when a chloroplast is derived from a eukaryotic cell (not prokaryotic)
- product of primary endosymbiosis is engulfed by another eukaryotic host
- genes from chloroplast+nucloid is transferred to new host’s nucleus
- old nucleus + membranes of cell breaks down
- another membrane froms around chloroplast
Differentiating from primary + secondary endosymbiosis
Primary:
•3 genomes in eukaryotic cell
•2 cell membranes
Secondary:
•plastid has 3-4 membranes
•nucleomorph = nucleus from engulfed cell morphs into new nucleus
Partitioning and division of labour
Related to respiration
Glyoxysome and mitochondria share very similar process and produce similar products
both are independent metabolisms and allow more efficiency (more glucose can be produced)
Animal and Plant Cell (genome differences)
Animal = 2 genomes (nucleus and mitochondria)
Plant = 3 genomes (nucleus, mitochondria + chloroplast)
Which organelles make up the Endomembrane system?
System of compartments that include all membrane bound organelles (EXCLUDING MITOCHONDRIA, CHLOROPLASTS AND MICROBODIES)
INCLUDES:
•Rough and Smooth endoplasmic reticulum
•nuclear envelope
•golgi apparatus
Function of rough endoplasmic reticulum
- Has ribosomes attached
- provides a surface for synthesis of proteins, glycoproteins, carbohydrates and lipids
- delivers products in vesicles to golgi apparatus
Function of smooth endoplasmic reticulum
- no ribsomes attached
* related to detoxification metabolism (lots of smooth ER in livers)
Role of endoplasic reticulum (ER)
- considered the heart of the endomembrane system
- contains CISTERNAE (membrane that forms channels and internal compartments)
- products are secreted through endomembrane system
Function of Golgi apparatus
•reponsible for collection, packaging and distribution of products from endomembrane system
•edits and cuts sugars
(biochemical modifications)
•polysaccharides production
•consists of Golgi stacks (flat stacks of membranes)
- receives vesicles from ER
- are polar structures
How does Golgi apparatus work?
Vesicles arrive at the cis face (receiving)
Vesicles leave at trans face (shipping)
vesicles leave to plasma membrane for secret (EXOCYTOSIS)
•vesicle fuses with plasma membrane and secretes product
•forms lysosomes if molecules are for internal use
Function of lysosomes
‘recycle bins’ of animal cells
(single membrane)
- contains enzymes that are very acidic (hydrolytic enzymes)
- break down materials through endocytosis (ingestion) or recycle old organelles (autophagy)
requires lots of ATP to keep it from exploding
Function of plant vacuoles
(plant equivalent of lysosomes)
surrounded by a single membrane (tonoplast)
- contains hydrolytic enzymes
- also stores nutrients, pigments and maintains cell turgor pressure
Function of microbodies
Similar to lysosomes but enzymes derive from free ribosomes (NOT ROUGH ER)
•neutral pH (oxidative enzymes that generate hydrogen peroxide then uses catalase to break down
two types of microbodies:
Peroxisomes = break down amino acids
Glyoxysomes = break down fatty acids
Origin of endomembrane system
Rough ER may have fromed due to invaginations of ribosome-bearing plasma membrane
Then evolved into full endomembrane system
Function of cytosol
- site for biochemical reactions
- many biochemical intermediates are transported or altered during transition
- biosynthesis of proteins (by polysomes)
(polysomes = group of ribosomes)
Cytoskeleton definition
- composed of proteins
* structural function within the cytoplasm of cell
Composure of cytoskeleton
Composed of actin, microtubules
Tubuliln = microtubules Actin = actin filaments
Stiff, non branching structures
Structure of Actin
Actin:
•actin filaments and intermediate actin
•two molecules intertwining with each other (actin filament)
•rigid, polar structure (one growing end and one degrading end)
•plays a role in movement, motor proteins (moved by MYOSIN)
Structure of microtubules
- circular, hollow round structure
- composed of tubulin (alpha) and subunits(beta) (interchanging)
- protofilament = 1 strand of tubulin and subunits
- 13 protofilaments per cylinder
- have polarity in both non-dividing cell and dividing cell
- grows at polar end
- contracted at negative end (polarity can block negative end, pushing out cell allowing structure of cell to be rigid)
Proteins on microtubules
Dyenin:
•protein that moves towards negative end of microtubule
Kinesin:
•protein that moves towards positive end of microtubule
(‘walks’ along microtubule carrying vesicles using ATP)
DNA replication is what type?
Semi-conservative
- one strand is original/parent strand
- second strand will be new/replicate
Difference between replication in prokaryotes and eukaryotes
Prokaryotes:
•single origin of replication along their DNA
Eukaryotes:
•multiple origins of replication along chromosomes
DNA Replication process
- DNA helicase unwraps DNA
- DNA polymerase III is on leading strand (continuous), adding complimentary nucleotide bases
- DNA primase adds a primers onto lagging strand
- DNA polymerase I fills in gaps
- DNA ligase joins fragments together in lagging strand (okazaki fragments)
