BIO1MGC exam

hierarchical organisation

different phases of things that build up a larger thing. eg. muscle organs are made of muscle tissues made of muscle cells.

exergonic reactions

products have less energy than reactants. releases energy (still requires activation energy). spontaneous, favourable, exothermic. can drive endergonic reactions.

endergonic reactions

products have more energy than reactants. energy is required. non-spontaneous, unfavourable, endothermic.

catabolic reactions

exergonic reactions that break down complex macromolecules from our food into smaller, simpler units. pays for anabolism.

anabolic reactions

endergonic reactions used to build up the complex molecules that we need, using smaller components as materials.

alleles

gene variants (only mutations of germ cells cause evolution). alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

step 2 of evolution

determination of which variants are passed on through natural selection, gene flow, genetic drift, etc.

step 1 of evolution

random generation of genetic variants.

nitrogenous base pairs

A-T (or U for RNA)

G-C

purines

A, G

pyrimidines

T, C, U

primary protein structure

sequence of chain of amino acids

secondary protein structure

local folding of polypeptide chain into either alpha helix or beta pleated sheets. interactions of adjacent amino acids.

tertiary protein structure

3D folding pattern of a protein due to side chain interactions. vital for function.

quaternary protein structure

association of several protein chains into a closely packed arrangement. a protein consisting of more than one amino acid chain has a quaternary structure. produces dimers.

type of bonds in proteins

hydrogen bonds, ionic bonds, disulphide linkages, hydrophobic interactions.

prokaryotes

small, simple, unicellular, contain circular DNA, lack membrane bound organelles, don’t have a nucleus.

eukaryotes

large, complex, unicellular or multicellular, contain linear DNA and membrane bound organelles.

phospholipids

amphipathic lipids. polar, hydrophilic heads. non-polar, hydrophobic tails.

micelles, liposomes and bilayer sheets.

formed spontaneously when phospholipids are added to water.

mRNA

messenger RNA.

* product of DNA transcription.
* acts as messenger of information between DNA sequences and final protein sequences following translation.
* synthesised and processed in nucleus
* provides instructions for protein synthesis

rRNA

ribosomal RNA.

* components of the ribosomes.
* catalyse the formation of the peptide bonds.
* also used for molecular sequencing.
* carry out protein synthesis

tRNA

transfer RNA.

* binds to specific amino acids to deliver them to the ribosome during protein translation.
* has an anticodon that determines specificity

autotroph/producer

an organism that can produce its own food using light, water, CO2, or other chemicals.

heterotroph

an organism that eats other plants or animals for energy and nutrients.

endosymbiosis evidence for mitochondria and chloroplasts

both organelles show similarity to bacteria.


1. split and divide in similar ways to bacteria
2. contain their own ribosomes and DNA
3. have an inner membrane similar to bacterial plasma membranes

septate & coenocytic hypha

hypha are the branching filaments of fungus. septate hypha involve cross walls, whereas coenocytic hypha involve one massive cell that’s multicellular (increased SA).

features of ATP that make it good

high energy content, easy to transport, easy to regenerate, ubiquitous.

cofactors

cofactors provide structural integrity by stabilising bonds, allowing substrates to fit into active sites.

coenzymes

organic cofactors. often vitamins and contain a nucleotide. they’re also carriers of electrons, and they fit into the active site of the enzyme, changing the shape of the active site.

fermentation products

w/o oxygen, fermentation replaces aerobic respiration. pyruvate turns into lactate or ethanol, allowing the regeneration of NAD+.

aerobic respiration

pyruvate is metabolised into Acetyl CoA.

oxidative phosphorylation products

produces 24-28 ATP. prior to this, 4 ATP is produced (2 during glycolysis, 2 during citric acid cycle).

chemiosmotic theory

refers to the flow of protons generating ATP. an energy coupling mechanism.

uses energy stored in the form of a H+ ion gradient across a membrane to drive cellular work.

electron carriers

vital for electron transport chain. NAD+ traps e- through oxidised food, causing NADH to form. this brings e- to the ETC.

electrons are passed through the ETC along 4 protein complexes, generating ATP through creating a proton gradient. as an e- goes down the chain, NADH becomes NAD+ again.

process of proton gradient

NADH moves down the 4 protein complexes, donating e-, which push protons across the membrane from the matrix inside the mitochondria to the intermembrane space b/w the inner and outer membrane of the mitochondria.

this generates a proton gradient w/ more protons in the intermembrane space than the matrix. when protons flow back into the matrix, this generates ATP, as the protons must move via proton channels (ATPase).

ATPase

molecule imbedded in intermembrane of mitochondria. generates ATP by allowing protons to re-enter the matrix. the protons enter the rotor, which then changes its shape and spins, generating energy to convert ADP+Pi to ATP.

chlorophyll molecules

absorb photons from light, feed this energy into the ETC to generate a proton gradient (similar to mitochondria). however this gradient occurs across the thylakoid membrane.

have a cofactor of Mg at the centre, allowing the formation of a stable ring. when this Mg ring is excited by photons, energy is passed along through alternating single and double bonds. electrons go up a level and bounce around, producing energy.

rubisco

an important enzyme used in calvin cycle to catalyse the first major step of carbon fixation. needed to make glucose. catalyses fixation of CO2 from the atmosphere into the calvin cycle.

calvin cycle: phase 1

carbon fixation:

CO2 incorporated for transformation into sugar. rubisco fixes 3CO2 from atmosphere into 3 6-carbon RuBP, which then become 6 3-phosphoglycerate molecules.

no energy required.

calvin cycle: phase 2

carbon reduction:

each molecule of 3-phosphoglycerate becomes highly energised and becomes a new molecule. it then accepts a pair of e- from NADPH, causing loss of phosphate group, forming G3P (a sugar).

every 3 molecules of CO2 produce 6 molecules of G3P, though 5 move onto the next stage, only 1 going to storage. 6 NADPH are required.

calvin cycle: phase 3

regeneration of the CO2 acceptor:

5 G3P molecules continue around the cycle to be converted into 3 RuBP, which accepts CO2 from the atmosphere. 3 ATP is required to produce 3 RuBP.

cell signalling stages

reception

transduction

response

paracrine cell signalling

adjacent cells. signals released and transported.

autocrine cell signalling

one cell to itself.

juxtacrine cell signalling

adjacent cells. signals extended to connect w/ adjacent cell, requires contact.

endocrine cell signalling

across the body. signals released into blood and transferred to distant target cells.

agonist

type of activation: bind to receptor and activate receptor to lead to biological response. activation of receptor changes tertiary structure.

inverse agonist

bind to receptor (changing tertiary structure) and activate, but cause opposite activation response to agonist.

antagonist

bind to receptor, changing tertiary structure, and block binding of agonist. fail to trigger intracellular signalling events. block activity of receptor.

G-protein coupled receptors

contain 7 transmembrane domains connected by loops. these transfer the signal, binding the G-protein inside the cell. these receptors are a large diverse family, and receive many different signals.

adenylyl cyclase

protein embedded in plasma membrane that converts ATP into cyclic AMP (cAMP).

phosphodiesterase

metabolises secondary messengers eg. cAMP. breaks cyclic ring to convert cAMP to AMP. AMP can then be recycled.

secondary messengers

relay signals received by cell-surface receptors to effector proteins.

small molecules that are rapidly diffusible.

their effects are concentration dependent, and these messengers can be rapidly metabolised/destroyed. include cyclin nucleotides (cAMP), ions (Ca2+), inositol triphosphate and diacyl glycerol.

kinases

proteins that introduce phosphate groups into other proteins, catalysing protein phosphorylation. cause very rapid reaction, easily reversible, rapidly amplifying signal.

phosphatase

an enzyme that can catalyse de-phosphorylation, removing a phosphoryl group from a protein.

tyrosine kinase receptors

receptors on plasma membrane/cell surface. exist as monomers that dimerise when a ligand bonds. binding ligand causes activation of receptor, phosphorylating tyrosines, which are binding sites for intercellular proteins, amplifying signal.

cell communication gone wrong examples

loss of signal (type 1 diabetes), target can’t respond to signal (type 2 diabetes), too much signal (overproduction of adrenaline), multiple breakdowns in a pathway (cancer).

causes of hyperactivation

overexpression of receptor tyrosine kinases, sustained autocrine or paracrine production of activating ligands, activating mutations in receptor tyrosine kinases, Ras mutations and B-Raf mutations.

epidermal growth factor (EGF)

activates pathway by binding to receptor, activating MAPK pathway.

interphase general overview

the cell grows. chromosomes are duplicated, with DNA copied. approx. 24 hours total.

mitosis general overview

occurs in all eukaryotic organisms and somatic cells. new cells split from parent cells into daughter cells and are genetically identical.

cytokinesis general overview

the cell divides into two daughter cells, genetically identical to each other and to the parent cell.

phase 1 of mitosis: prophase

chromosomes condense

phase 2 of mitosis: prometaphase

further condensing. sister chromatids attach to spindle fibers.

phase 3 of mitosis: metaphase

chromosomes line up along equator of cell.

phase 4 of mitosis: anaphase

sister chromatids separate

stage 5 of mitosis: telophase

chromosome segregation complete

haploid

one copy of every chromosome

diploid

two copies of every chromosome

chromatin

entire complex of DNA and proteins, building material of our chromosomes.

mitosis in plant cells

during cytokinesis in animal cells there is the formation of a cleavage furrow, pinching the cell in two. there is no furrow in plants, instead during telophase the vesicles move along microtubules in the middle of the cell, where they coalesce, producing a cell plate.

interphase stage 1: G1

chromosomes are decondensed. there is a checkpoint.

interphase stage 2: s phase

all DNA is copied. chromosomes are decondensed, enzymes are activated for replication process.

interphase stage 3: G2

chromosomes are starting to become condensed/two sister chromatids.

gametes

reproductive cell. sperm, eggs, pollen, etc.

locus

location where gene is found on chromosome

meiosis general overview

occurs in diploid, sexual organisms. creates haploid gametes with half the genetic complement of the parent cells. allows for a different combination of genetic material. we are diploid, carrying two copies of each chromosome (46 total), and when we reproduce, we produce gametes, which are haploid.

differences between mitosis and meiosis

* there are two cell divisions in meiosis, only one in mitosis
* meiosis produces 4 daughter cells, mitosis produces 2
* meiosis involves crossing over of DNA
* meiosis daughter cells are not identical to parent cells, as they have half the number of chromosomes.

law of segregation

two alleles for a heritable trait segregate during gamete formation and end up in different gametes.

pleiotropy

a single gene affects two or more traits in an organism.

epistasis

the expression of one or more other genes modifies the expression of another gene.

polygenic

a characteristic influenced by two or more genes.

incomplete dominance

neither allele is strong enough to be dominant. neither trait dominates. white chicken x black chicken = blue chicken.

codominance

inheritance in which two alleles of the same gene are expressed separately to yield different traits in an individual.

overdominance

the heterozygote has a phenotype that is more extreme than either parent. tomato plant with 4 tomatoes x tomato plant with 4 tomatoes = tomato plant with 7 tomatoes.

non-disjunction

when pairs of homologous chromosomes or sister chromatids fail to separate. eg. aneuploidy (monosomy or trisomy).

dna replication: first stage

helicase unwinds the parental double helix. molecules of single-strand binding protein stabilise the unwound template strands.

dna replication: second stage

the leading strand is synthesised continuously in the 5’ to 3’ direction by dna polymerase 3.

primase begins synthesis of the rna primer for the fifth okazaki fragment

dna polymerase 3 is completing synthesis of fragment 4. when it reaches the rna primer on fragment 3, it will detach and begin adding dna nucleotides to the 3’ end of the fragment 5 primer in the replication fork.

dna replication: third stage

dna polymerase 1 removes the primer from the 5’ end of fragment 2, replacing it with dna nucleotides added one by one to the 3’ end of fragment 3. after the last addition, the backbone is left with a free 3’ end.

dna ligase joins the 3’ end of fragment 2 to the 5’ end of fragment 1.

DNA packaging in chromosomes

the double helix dna is combined with histone proteins that wrap dna around themselves and are bound together. 8 histones bind to each other and dna to form nucleosomes, which wrap together in loops to form condensed dna in the form of chromatin, that then becomes chromosomes.

transcription stage 1: initiation

transcription factors bind to the DNA followed by RNA poly 2, which unwinds the DNA, activators initialise transcription.

transcription stage 2: elongation

the RNA polymerase 2 moves downstream, adding RNA nucleotides to create the mRNA 5’-3’. after trascription, the dna reforms a double helix.

transcription stage 3: termination

eventually, the rna transcript is released, and the polymerase detaches from the dna.

how mRNA is packaged before leaving the cell

5’ cap added to 5’ end and poly-A tail to 3’ end. this helps mRNA leave the nucleus, protects from degradation and helps ribosomes attach to 5’ end.

factors that affect gene expression

temperature, pH, water, solutes, toxins, pathogens.

also regulated by:

* access to dna
* rate of transcription
* processing of rna molecules
* stability of mRNA molecules
* rate of translation
* protein processing

factors that affect gene regulation

growth/development, environmental factors, homeostasis.

5’ end and 3’ end (how to identify)

the end of DNA with a free phosphate is the 5’ end. the end with the free sugar is the 3’ end.

sanger sequencing pros and cons

* one template at a time (slow)
* relies on dna polymerase
* very low error rate
* 800-1000 nucleotide reads
* automated sequencers can produce approx 80 Mb of dna sequence per run (not a lot)

plasmids

form of DNA in bacteria. mini genomes, can be swapped between bacteria, or different species. DNA is cloned into plasmids when the plasmids have selectable markers. they also require promoter regions and restriction sites.