FINAL Flashcards
What are the seven properties of life?
cellular organization, reproduction, growth and development, metabolism, homeostasis, response to environment, evolutionary adaptation
What are the core themes of Biology?
Interactions, Matter and energy, Information, and Evolution
Why does DNA have thymine instead of uracil?
Uracil is more energy efficient, but thymine is more stable
How does energy enter and leave ecosystems?
enters as light and leaves as heat
What is light microscopy?
passing a beam of light through a specimen
What is electron microscopy>
passing electrons over or through a specimen
What is resolution?
Minimum distance two objects can be separated and still be distinguishable
What is magnitude?
ratio of an objects image to its real size
What is contrast?
difference in brightness between light and darkness
What is the cytoplasm?
Interior of a cell containing organelles
What is cytosol?
jelly-like substance that suspends the organelles
What are ribosomes?
complexes of proteins and rRNA that are responsible for protein synthesis
What are free ribosomes?
ribosomes suspended in the cytosol
What are bound ribosomes?
ribosomes attached to the ER or Nuclear Envelope
What is the endomembrane system?
Nucleus, ER, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane
How is the endomembrane system connected?
physical continuity or the transfer of vesicles
What is the nucleus?
Contains the genetic information of the cell in the form of chromosomes.
What is the nuclear envelope?
a double membrane, each being a lipid bilayer. lined by nuclear laminate (protein filaments) that provide structure. contains pores for transfer of molecules
What is the nucleolus?
location of rRNA transcription and ribosome assembly
What is the smooth ER?
involved in lipid synthesis, drug detoxification, calcium storage.
What is the rough ER?
covered in ribosomes, responsible for synthesis of proteins to be exported. involved in glycosylation and membrane synthesis
What is the Golgi apparatus?
sorts molecules and releases vesicles for transport elsewhere in the cell. alters the structure of macromolecules
What are lysosomes?
membranous sacs fwith an acidic interior containing hydrolytic enzymes
What are vacuoles?
large vesicles with an internal solution differing in composition from cytoplasm.
What is the mitochondria?
site of cellular respiration
What is a chloroplast?
site of photosynthesis, producing sugars from carbon dioxide, water and light
What does the endosymbiont theory describe?
the origins of mitochondria and chloroplasts
What does the endosymbiont theory describe?
Early prokaryotes engulfed an oxygen-using prokaryote and a photosynthetic prokaryote, that over time became the mitochondria and the chloroplast
What supports the endosymbiont theory?
The fact that both mitochondria and chloroplasts contain their own DNA and ribsosomes, which are more similar to that of prokaryotes than eukaryotes
What is the cytoskeleton?
Dynamic network of fibres extending throughout the cytoplasm
What does the cytoskeleton consist of?
Microtubules, microfilaments, and in some cells, intermediate filaments
What does the cytoskeleton do?
Provides mechanical support, structure, and anchorage of organelles. also involved in cell mobility
What are types of cell junctions?
Plasmodesmata, Gap junctions, tight junctions
what are plasmodesmata?
channels connecting plant cells, allowing the transfer of compounds between cells
What are gap junctions?
the animal cell equivalent of plasmodesmata
what are tight junctions?
tight seals between cells that prevent the passage of extracellular fluid
What are Desmosomes?
fasten cells together, anchored by intermediate filaments
What is the plasma membrane?
selectively permeable phospholipid bilayer
What are membrane proteins?
proteins attached to the plasma membrane
What are integral proteins?
proteins that penetrate the hydrophobic interior of the bilayer, include transmembrane proteins
What are peripheral proteins?
proteins that are loosely bound to the surface of the membrane and often associate with integral membrane proteins
How is the fluidity of the plasma membrane determined?
by composition of the plasma membrane
What happens when more unsaturated lipid tails are present?
increased fluidity due to kinks (cis not trans double bonds)
What is the role of cholesterol in the plasma membrane?
Acts as a buffer to control membrane fluidity in fluctuating temperatures
What is the electrochemical gradient?
the diffusion gradient of an ion, influenced both by [ion] and membrane potential
What is tonicity?
the ability of a solution to make a cell lose or gain water
what is passive transport?
diffusion of molecule across a biological membrane down its electrochemical gradient
What is facilitated diffusion?
Passive transport aided by highly selective transport proteins
What is active transport?
uses energy to transport a compound against its electrochemical gradient
What is cotransport?
coupling the transport of the diffusion of one molecule down its electrochemical gradient with the transport of another molecule against its electrochemical gradient. (NaK pump)
What is symport?
cotransport where both molecules are going in the same direction
what is antiport?
cotransport where the molecules are going in opposite directions
What is a channel protein?
a hydrophilic channel. not active transport
what is a gated channel?
a channel that is not active until it receives a signal
what is a carrier protein?
a protein that can be used for active or passive transport. moves molecules through a change in its shape
What is bulk transport?
the endo/exocytosis of macromolecules across the membrane via vesicles
What are designer endosymbionts?
the introduction of a prokaryote into a eukaryote to try to foster a mutually beneficial symbiotic relationship
What is the magnification and resolution of light microscopy?
1000x, 200nm
What is the resolution and magnitude of electron microscopy?
1e6x-1e8x, 0.05-2nm
What is the ER made up of?
flattened sacs called cisternae?
What is the internal compartment of the ER called?
ER lumen
What is the transitional ER
produces tranport vesicles and moves products to other regions of the cell
What are the sacs of the Golgi apparatus called?
cisternae, 4-8 of them
How is the Golgi apparatus directional?
cis face oriented towards ER to receive vesicles, trans face sorts molecules and releases them to go elsewhere in the cell
What is phagocytosis?
The endocytosis of large particles coupled with digestion
What is autophagy
the recycling of the cells organic material
What are food vacuoles?
formed by phagocytosis
what are contractile vesicles?
pump excess water out of cell. found in aquatic, unicellular cells
What are hydrolytic vacuoles
similar to lysosomes, found in plants and fungi
What are small vacuoles?
storage of organic compounds like toxins
what are central vacuoles?
found in plants cells, stores inorganic ions and contributes to cell growth and structure
What is a system?
the matter under study. everything else is the surroundings
What is the first law of thermodynamics?
energy cannot be created or destroyed
What is the second law of thermodynamics?
entropy of the universe increases for every transfer or transformation
What is entropy?
how dispersed energy is
Can the entropy of a system decrease?
yes, but it needs energy to do so
What is Gibb’s Free Energy?
How much of a system’s energy can do work
What is the energy of activation?
the energy required to start a reaction
What does exergonic mean?
decrease in free energy
What does endergonic mean?
increase in free energy
What are enzymes?>
biological catalysts. increase reaction rate by decreasing EA without affecting change in energy
What are enzyme inhibitors?
molecules that prevent the function of certain enzymes
what are competitive inhibitors?
inhibitors that bind to the active site
what re non-competitive inhibitors?
molecules that bind away from the active site
What is energy coupling?
pairing exergonic and endergonic reactions together so that the energy released from one reaction is used by the other reaction
Is bond breaking endo or exothermic
endothermic
Is bond formation endo or exothermic?
exothermic
Where does glycolysis occur?
in the cytosol
How many ATP are produced per molecule of glucose?
30-32
What is the net reaction of glycolysis?
Glucose + 2 NAD+ + 2 ADP + 2 phosphate -> 2 ATP + 2 NADH + 2 H+ + 2 H2O + 2 pyruvate
What is pyruvate oxidation?
connects glycolysis to the CAC
Where does pyruvate oxidation occur?
in the mitochondria in eukaryotes and the cytosol in prokaryotes
What is the net reaction of pyruvate oxidation per 1 pyruvate?
pyruvate + NAD+ + CoA -> NADH + H+ + CO2 + acetyl CoA
What is allosteric regulation?
The binding of a regulatory molecule to a protein at one site that affects the function at another site
What is feedback inhibition?
form of allosteric regulation where the regulatory molecule is an end product of the same metabolic pathway
How is work performed using atp hydrolysis?
through changes in protein shape or a phosphorylated intermediate
What is the difference between aerobic and anaerobic respiration?
aerobic respiration consumes O2 as a reactant whereas anaerobic respiration replaces oxygen with another inorganic molecule
What types of bonds are oxidized to produce energy?
C-H bonds are oxidized to products with C-O bonds
How are electrons passed through to oxygen?
Through electron carriers
What is a dehydrogenase?
an enzyme that transfers 2 electrons and 1 proton from an organic compound to NAD+, producing NADH
What is substrate-level phophorylation?
formation of ATP from ADP and a phosphorylated intermediate
What is the net reaction of the CAC?
acetyl-CoA + 3 NAD+ + FAD + ADP + phosphate + H2O -> 2 ATP + 2 FADH2 + 6 A
How is the synthesis of ATP powered?
through the transfer of electrons from NADH and FADH2 to O2
What are the two stages of oxidative phosphorylation?
the electron transport chain and chemiosmosis
What is the electron transport chain?
th transfer of electrons to O2 through a series of redox reactions through multi protein complexes, tightly bound to non-protein prosthetic groups
What is a prosthetic group?
a non-protein molecule that binds to a protein and aids its function
What is the proton-motive force?
The free energy required to move protons across a membrane. result of [] and electrochemical differences
AZ What is chemiosmosis?
An energy coupling mechanism that uses energy stored in the form of a proton gradient across a membrane to drive cellular work
AAÀZŹAZZZZ Z QZ What does chemiosmosis do?
Provides the energy for ATP production through ATP synthase
What is the efficiency of cellular respiration?
~34%
What is the main key step in the regulation of cellular respiration?
PFK. allosterically regulated by ATP (inhibitor), AMP (activator), and citrate (inhibitor)
Why is anaerobic respiration less efficient than aerobic respiration?
Other molecules are less effectively oxidizing agents than O2
What is fermentation?
skips ETC, relies soly on substrate level phosphorylation. turns pyruvate into ethanol or lactate. Recycles NADH to NAD+ via electron transport to pyruvate
What is photosynthesis?
The conversion of light energy into chemical energy in the form of organic compounds
What are the two stages of photosynthesis?
the light reactions and the Calvin cycle
What are the Stroma?
the fluid within the chloroplast that surrounds the thylakoids
What are the thylakoids?
Thylakoids are membrane bound compartments consisting of the thylakoid membrane surrounding the thylakoid space
What are the Grana?
stacks of thylakoid sacs
What kind of energy is light?
electromagnetic energy
What are electromagnetic waves?
disturbances in the electric and magnetic fields
What is the electromagnetic spectrum?
The entire range of electromagnetic energy
what is a photon?
a discrete quantity of light with a specific quantity of energy
What are pigments?
substances that absorb visible light of specific wavelengths
What is the absorption spectrum?
A graph showing the ability of a pigment to absorb different wavelengths of light
What is chlorophyll a?
the primary light capturing pigment
what is chlorophyll b?
an accessory pigment
What are Carotenoids?
accessory pigments that broaden the spectrum of light that can drive photosynthesis and play a role in photo protection
Why do leaves change color in the autumn?
chlorophyll pigments degrade, leaving carotenoids
Where are the pigments located?
In the thylakoid membranes
Where do light reactions occur?
In the thylakoid membrane
What is cell signalling?
How a cell responds to its environment and to other cells
What is reception?
the detection of a signal
What is transduction?
The conversion of a signal to a form that can bring about a cellular response
What is the response?
How the cell reacts to the signal
What recieves a signal?
a receptor protein. Usually surface, but some are intracellular
What is a ligand?
An alternate name for signal molecules
What do receptors do?
They bind to signal molecules
What are G protein coupled receptors?
receptors that work in conjunction with a G protein to bring about cellular response
What is the G protein
a protein that binds GDP and GTP
What is the G protein associated with in an active state?
GTP
In what ways are G proteins and G coupled receptors specific?
G coupled receptors only for specific signal molecules and G proteins only interact with specific G coupled receptors and enzymes
How does G coupled reception work?
A single molecule binds to the receptor inducing a change in shape, Receptor interacts with the G protein causing the replacement of GDP with GTP. Protein diffuses across the membrane and interacts with its target enzyme. Either activates or inhibits enzyme function. G protein has enzymatic activity and will hydrolyze GTP to GDP, inactivating the G protein , which will reset the signalling complex.
What is an RTK?
a receptor tyrosine kinase
How many signal transduction pathways can RTKs activate
up to 10
What happens when signal molecules bind to RTK?
They dimerize
What does dimerization of RTKS do?
Activates the kinase activity. transfers phosphates from ATP to its own tyrosines. The phosphorylated receptor is fully active.
What are relay proteins?
Proteins that pass the message through the cell
What are ligand gated ion channels?
Receptors that also function as ion transporters?
What happens with Ligand gated ion channels in an inactive state?
There is a gate covering the channel, preventing the diffusion of ions across
What happens with ion gated channels when they are activated?
The ligand bind to the channel, causing a change in shape, opening the channel for facilitated ion diffusion
What is a voltage gated ion channel?
A channel activated by electrical current. Useful in the nervous system
What are HKs?
Histidine Kinases
What is the difference between between HKs and RTKs?
HKs transfer the phosphate group to a histidine which then transfers the phosphate to an aspartate on another protein called a response regulator, which is then activated and brings about a cellular response
What are intracellular receptors?
Receptors located within the cytoplasm?
What kinds of molecules do the ligands for intracellular receptors have to be?
non-polar, or small molecules that can cross the cell membrane
What do intracellular receptors usually function as?
Transcription factors
What are transcription factors?
Proteins that bind to DNA and influence the rate of transcription for a gene or for a class of genes
What are the advantages of multi-step transduction pathways?
Increased amplification of signal, more opportunities for regulation
What are scaffold proteins?
Proteins with many Relay molecules attached
Why are scaffold proteins useful?
They allow for many relay proteins to be in close proximity, increasing the efficiency and amplitude of signal transduction. Similar in concept to a multi enzyme complex
What is the role of protein phosphatase in many single transduction pathways?
Termination through dephosphorylation
What is a phosphorylation cascade?
A transduction through which kinases activate other kinases and so forth, bringing about a cellular response
What are second messenger?
small hydrophilic non-protein relay molecules
What Is useful about second messengers?
Due to their size, they diffuse easily through the cytoplasm
What is cAMP
cyclic adenosine monophosphate
What is cAMP synthesized by?
adenylyl cyclase (substrate is ATP)
How is cAMP synthesis regulated?
By G proteins
What is phosphodiesterase?
The enzyme that converts cAMP to AMP
What does cAMP do?
allosterically regulates other proteins, such as protein kinase A
What does protein kinase A do?
Goes around and phosphorylates other proteins to bring about a cellular response.
What function does calcium serve in the cell?
as a second messenger?
How is calcium as a second messenger initiated?
by G protein coupled receptors or RTKs
How does calcium interact with proteins?
it acts as an allosteric regulator
What is IP3?
inositol triphosphate (another second messenger
How does signal transduction involving calcium ions work?
The signal is received, and IP3 is released, which then diffuses through the cytosol, interacts with a Calcium ligand gated channel and allows Calcium to exit the ER. Calcium then activates various proteins leading to a cellular response
What is the proteome?
The complete set of proteins in the cell.
How is cell signalling specific?
Cell signalling is specific due to the different proteomes of different cells
What is pinocytosis?
“cellular drinking” non-specific intake of small solutes by forming a vesicle covered in protein “fuzz”
What is phagocytosis?
“cellular eating” the intake of a large food molecule by the extending of pseudopodia and the forming of a food vacuole
What are sister chromatids?
two duplicated copies of a chromosome joined by protein
What are homologous chromosomes?
Chromatin with the same genes at the same loci but with different alleles
What are non-sister chromatids?
Chromatids of homologous chromosomes
What is the centromere?
Where sister chromatids are held together most tightly
What is the cell cycle?
The sequence of events from cell organ to division
What is the G1 phase?
cell growth occurs
What is the S phase?
The phase where DNA replication occurs
What is the G2 phase?
Another period of cell growth
What is the Mitotic phase?
Where mitosis and cytokinesis occur
What is the G1 checkpoint?
Where the cell determines if it has everything it needs and has undergone the right amount of great to divide
What is the G2 checkpoint?
Where DNA is checked to make sure it was properly replicated
What is the M checkpoint?
Checks if sister chromatids are attached to kinetochore microtubules
What is the G0 phase?
A non-dividing phase that occurs if a cell doesn’t pass the G1 checkpoint
What are Cyclin Dependent Protein Kinases?
CDK. Kinases that are only active when bound to cyclin
What is cyclin?
a protein whose [] fluctuate throughout the cell cycle
What is the maturation protein factor?
MPF. A Cyclin-CDK complex involved in the G2 checkpoint. As cyclin [] increase, MPF activity increases
How is the cell cycle regulated?
By cyclins
How is cell division regulated?
By growth factors, density dependent inhibition, and anchorage dependence
What are growth factors?
proteins that are released by some cells that signal other cells to grow
What is density dependent inhibition?
If cells become too crowded then they stop dividing due to the binding of cell-surface proteins to adjacent cells
What is anchorage dependence?
in animal cells, division only occurs if the cell is on a solid surface
What is Mitosis?
The division of cells into two genetically identical cells
What happens in the interphase of mitosis?
Chromosomes duplicate (uncondensed)
What happens during the prophase of mitosis?
Chromosomes condense, the nucleolus disappears and the mitotic spindle forms
What is the mitotic spindle?
A microtubule network that is essential for the movement of chromosomes
What happens during the pro metaphase of mitosis?
The nuclear envelope degrades, the kinetochore forms, and microtubules attach to the kinetochore
What is the kinetochore?
proteins associated with the centromeres of the sister chromatids and allow for the attachment of the mitotic spindle
What happens during the metaphase of mitosis?
chromosomes align along the centre of the cell
What happens during the anaphase of mitosis?
The cohesions between sister chromatids are cleaved, they separate and the cell elongates
What happens during the telophase of mitosis?
nuclei form and nucleoli reappear
What is cytokinesis?
The pinching of the plasma membrane by contractile actin filaments associated with myosin
When is a chromosome considered distinct?
Once they are fully separated from each other, no matter how much chromatid there is
What is asexual reproduction?
The process through which a single parent produces offspring with identical genomes. Accomplished through mitosis
What is sexual reproduction?
two parents parents produce offspring with unique combinations of genes from both parents. Involves meiosis and fertilization, along with gametes and somatic cells
What is meiosis?
The division of 1 parent cell to 4 genetically different daughter cells
What occurs during meiosis 1?
The division of 1 diploid cell to two haploid cells
What occurs in meiosis 2?
the separation of sister chromatids in the two cells from meiosis 1, and the formation of 2 daughter cells from each
Why occurs during prophase 1?
Chromosomes condense, meiotic spindle forms, nuclear envelope breaks down, crossing over occurs, kinetochore forms, microtubules attach
What happens during metaphase 1?
homologous chromosome pairs align at metaphase plate
What happens during anaphase 1?
cohesion cleaved along chromosome arms. Cell elongates
What occurs during telophase 1?
nuclei form. Cell splits
What occurs during prophase 2?
The chromosomes condense, the spindle forms, and the nuclear envelope degrades
What occurs during metaphase 2?
Chromosomes line up along the centre of the cell
What occurs during anaphase 2?
The sister chromatids separate at the centromere and move to opposite poles along the spindle fibres
What occurs during telophase 2?
The cells divide and the result is 4 haploid gametes
What is crossing over?
The exchange of DNA of the non-sister chromatids of homologous pairs during the prophase of meiosis 1
Why is crossing over good?
It increases genetic variability
What is the independent assortment of chromosomes?
alignment of each pair of homologues is independent of other pairs of homologues?
How many possibilities does independent assortment of chromosomes produce?
2^n possibilites (n=haploid #)
What is Random Fertililzation?
Any sperm and egg can fuse to form zygotes
How many possibilities does random fertilization produce?
2^n*2^n possibilites (n=haploid #)
What is genomics?
The study of whole sets of genes and their interactions
What is high-throughput sequencing?
Tech that rapidly determines all nucleotides in a DNA sequence
What is genome assembly?
The aligning and merging of short DNA reads to construct a full original sequence
What is bioinformatics?
The use of computers to address bio problems
What is genome size?
The number of base pairs in a genome
What is genome density?
The number of genes per Mbp
How do prokaryote and eukaryote genome size and density compare?
Eukaryotes have much greater genome size whereas prokaryotes have much greater genome density
What is alternate splicing?
Changes in the way introns are removed from pre-mRNA
How is alternate splicing beneficial?
It increases protein diversity without increasing the number of genes. Only in eukaryotes
What is non-coding DNA for?
Regulatory sequences, tandem repeat DNA, introns, etc…
How much DNA is coding?
approx. 1.5% of the genome
How much DNA is gene-related?
approx. 25% of the genome?
How much DNA is non-coding?
over 70%
How much of bacterial genomes are coding?
> 90%
How do transposons move?
Via a DNA intermediate. Cut and Paste mechanism of movement.
How do retrotransposons move?
Via a RNA intermediate. The overall amount of DNA in the genome increases
Which are more common: Retrotransposons or Transposons?
Retrotransposons are more common in eukaryotes
How do tandem repeats occur?
DNA polymerase error during replication leading to addition or deletion
What can lead to alterations in chromosome structure?
Translocations and fusions
What are multigene families?
Collections of two or more genes, all coming from a common ancestor
What is exon shuffling?
The mixing and matching of exons within a gene or between non-allelic genes through meiotic recombination errors
What is ancient DNA?
DNA isolated from ancient samples. Can be sequenced. Ex. Wolly Mammoth
What is Primase?
Adds RNA primer to DNA
What is the purpose of RNA primer?
Provides the 3’ end for DNA synthesis
What is Helicase?
An enzyme that breaks dsDNA apart
What is topoisomerase?
An enzyme that breaks the phosphodiester bond in a strand in order to relieve super coiling from helicase
What are repair enzymes?
Enzymes that look for mismatched DNA
Why is linear DNA problematic?
the 5’ of the strand where the primer was cannot be replicated as there is no 3’ end for the polymerase to attach to
What happens to DNA after repeated replications?
It is shortened
What is the leading strand?
The strand that can be seamlessly synthesized due to DNA coming being opened up 3’ end first
What is the lagging strand?
The strand that is disjointedly synthesized due to DNA coming out of the replication bubble 5’ to 3’
What are telomeres?
repetitive DNA that “caps” the end of chromosomes and allows for the replication of DNA without the erosion of chromosomes
What is telomerase?
An enzyme that synthesizes telomeres in certain cells
How do telomeres protect against cancer?
The prevent the cancer cells from replicating continuously
How have some cancers bypassed telomeres?
They activate telomerase
What is the template for telomerase?
RNA
