Biology DAT Ch. 1-5 Flashcards
Matter
Anything that takes up space and has mass
Element
Purest substance that has physical/chemical properties, cannot be broken down
Atom
Smallest unit of matter with chemical properties
Molecule
one or two atoms joined together
Intramolecular forces
attractive forces holding atoms within a molecule
Intermolecular forces
forces that exist between molecules & affect physical properties of the substance
Monomers
single molecules that can be polymerized
Polymers
substance made up of monomers
Carbohydrates
Carbon, hydrogen, and oxygen (CHO). Come in forms of monosaccharides, disaccharides, and polysaccharides
Monosaccarides
carbohydrate monomers with the empirical formula (CH2O)n. n indicating the number of carbons.
Ribose
5 carbon monosaccarides
Fructose
6 carbon monosaccarides
Glucose
6 carbon monosaccarides
Disaccharides
Two monomers joined together by a glycosidic bond. This bonds is created by dehydration reaction.
Dehydration (condensation) reaction
Water molecule leaving, thus covalent bond is formed
Hydrolysis reaction
Water molecule added and covalent bond is broken
Sucrose
glucose + fructose
Lactose
galactose + glucose
Maltose
glucose + glucose
Starch
energy storage for plants and is a (alpha) bonded polysaccharides.
Glycogen
energy storage for humans and is a (alpha) bonded polysaccharide. Is much more branched than starch.
Amylose
linear starch
Amylopectin
branched starch
Cellulose
structural component of plant cell well, its b (beta) bonded polysaccharides. Linear strands are packed rigidly in parallel.
Chitin
component of fungi cell wall and insect exoskeleton, bonded by b (beta) polysaccharides, with nitrogen added to each monomer
Polysaccharides
multiple monomers bonded by glycosidic bonds in a long polymer
Proteins
contain hydrogen, carbon, oxygen, and nitrogen (CHON). These combine to form amino acids, which link up to form polypeptides.
Polypeptides
(proteins) polymers of amino acids linked by peptide bonds through dehydration and hydrolysis reactions. It forms an amino acid chain with two end terminals on opposite sides.
Amino acids
20 different, each have a different R-group
N-terminus
(amino terminus) the polypeptides side that ends with the last amino acid’s amino group
C-terminus
(carboxyl terminus) the polypeptide side that ends with the last amino acid’s carboxyl group
Protein structure
primary, secondary, tertiary, and quaternary structure
Protein classification
globular, fibrous, intermediate
Protein denaturation
temperature change, pH change, and salt concentration
Protein functions
storage immunity receptors enzymes hormones motion structure
Protein composition
conjugated (amino acids + other components) and simple (amino acids)
Primary structure
sequence of amino acids
Secondary structure
alpha and beta pleated sheets formed by hydrogen bonding due to intermolecular forces between polypeptide backbone
Tertiary structure
3D structure due to interactions between R-groups. Hydrophobic and hydrophilic. Disulfide bonds are created by covalent bonding between R-groups of two cysteine amino acids.
Quaternary structure
multiple polypeptides chains coming together to form one protein
Storage
reserve of amino acids
Hormones
provide signaling throughout the body to regulate physiological processes
Receptors
Proteins in cell membrane which bond to signal molecules to trigger changes inside the cell
Motion
movement generated for a cells or of an entire organism
Structure
Provide strength and support to tissues
Immunity
Prevention and protection against foreign invaders
Enzymes
acts as a biological catalyst, binding to the substrate (reactants) to convert them into products
Catalyst
increases reaction rate by lowering activation energy, it reduces energy in the transition state. They do not shift chemical reaction & do not affect spontaneity
Transition State
unstable intermediate between reactants and products
Active site
site on enzyme where substrate binds, it is specific
Specificity constant
measures how efficient the substrate binds with the enzyme and converting it to a product
Induced fit theory
the active site changes shape to fit the substrate when it binds, also known as “lock and key” model
Ribozyme
RNA molecule that acts as an enzyme
Cofactor
non-protein molecule that helps enzymes perform its reaction
Coenzyme
An organic cofactor such as vitamins. (inorganic=metal ions)
Holoenzymes
cofactor + enzyme
Apoenzymes
enzyme + NO cofactor
Prosthetic groups
cofactor tightly or covalently bonded with its enzyme
Competitive inhibition
competitive inhibitor competes with substrate for the active site binding. Adding more substrate would increase enzyme reaction rate.
Km = increases
Vmax = stays the same
Noncompetitive inhibition
noncompetitive inhibitor does not compete for active site but instead binds on allosteric site, thus modifying the active site. Adding more substrate would NOT increase enzyme reaction rate.
Km = stays the same
Vmax = decreases
Allosteric site
other site on enzyme that is not the active site
Enzyme kinetics plot
can be used to visualize how inhibitors affect enzymes
Michaelis Constant (Km)
substrate concentration at which velocity is 50% of vmax
Vmax
maximum reaction of velocity
Saturation
occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration
Lipids
Carbon, hydrogen, and oxygen (CHO), they have long hydrocarbon tails making them very hydrophobic
Triacyglycerol
a lipid molecule with a glycerol backbone and 3 fatty acids linked by ester linkages
Ester linkages
links glycerol back bone and the 3 fatty acids
Glycerol backbone
3 carbon and 3 hydroxyl groups
Saturated fatty acids
no double bonds and as a result pack TIGHTLY (solid at room temperature)
Unsaturated fatty acids
double bonds by monounsaturated fatty acids and polyunsaturated fatty acids
Cis-Unsaturated fatty acids
have kinks that cause the hydrocarbon tails to bend, thus do not pack tightly
Trans-Unsaturated fatty acids
have straighter hydrocarbon tails so they pack more tightly (unhealthy)
Phospholipids
lipid molecule that have glycerol backbone, one phosphate group, and 2 fatty acids, causing it to be amphipathic, thus spontaneously assembling into a lipid bilayer
Cholesterol
lipid molecule that has 4 fused hydrocarbon rings. It is amphipathic. It is the most common precursor to steroid hormones. It helps with membrane fluidity
Steroid hormones
cholesterol is its precursor, 4 hydrocarbon rings
Cholesterol is starting material
material for vitamin D and bile acids
Membrane fluidity
temperature: increase of temp = increase of fluidity
cholesterol = holds membrane together at HIGH temp and keeps membrane fluid at LOW temp
degree of unsaturation
Lipoproteins
allow the transportation of lipid molecules into the blood stream due to out coat of phospholipids, cholesterol, and proteins
Low-Density Lipoproteins (LDLs)
“Bad Cholesterol”
low protein density, delivers cholesterol to peripheral tissues, and vessel blockage can occur
High-Density Lipoproteins (HDLs)
“Good Cholesterol”
high protein density, delivers and takes cholesterol away from peripheral tissues to the liver to make bile (reduces blood lipid levels)
Waxes
Hydrophobic protective coating, simple lipids that have long fatty acids connected to monohydroxy alcohols through ester linkages
Carotenoids
Pigments, lipid derivatives containing long carbon chains with conjugated double bonds and 6 membered rings at each end.
Nucleic acids
Carbon, hydrogen, oxygen, nitrogen, and phosphorus (CHONP). Nucleotide monomers that build into DNA or RNA polymers.
Nucelosides vs Nucleotides
Nucleoside
- ribose sugar and nitrogenous base
Nucleotide
- ribose sugar, nitrogenous base, and phosphate group
Deoxyribose sugar
contain hydrogen at the 2’ carbon
Ribose sugar
contain hydroxyl group at the 2’ carbon
Purines
A, G (two rings)
Pyrimidines
C T and U (one ring)
Phosphodiester bonds
connect the phosphate group of one nucleotide at the 5’ carbon to the hydroxyl group at the 3’ carbon. A series of phosphodiester bonds create the sugar-phosphate backbone with a 5’end free phosphate and a 3’end free hydroxyl.
Nucleic acids polymerizaion
proceeds as nucleoside triphosphate are added to the 3’ end of the sugar-phosphate backbone
DNA
double stranded, antiparallel double helix, two complementary strands with opposite directionalities (5’ and 3’ end) twist around each other.
RNA
single stranded after being copied from DNA during transcription, U replaces T and binds to A.
Modern Cell Theory
- All lifeforms have one or more cells.
- The cell is the basic structural, functional, and organizational unit of life.
- All cells from from other cells (cell division).
- Genetic information is stored and passed down through DNA
- An organism’s activity is dependent on the total activity of its independent cells.
- Metabolism and biochemistry (energy flow) occurs within cells
- All cells have the same chemical composition within organisms of similar species.
Central Dogma of Genetics
information is passed through DNA –> RNA –> Protein
exceptions: reverse transcriptase and prions
RNA world hypothesis
states that RNA dominated Earth’s primordial soup before there was life. RNA developed self-replicating mechanisms and later could catalyze reactions such as protein synthesis to make more complex macromolecules. Since RNA is reactive and unstable, DNA later became way of reliably of storing genetic information.
A-T bond
2 hydrogen bonds
G-C bond
3 hydrogen bonds
Cell membrane
is made up of phospholipids, cholesterol, and proteins
Membrane proteins
are either integral or peripheral membrane proteins
Integral (transmembrane) proteins
Transverse the entire bilayer, thus it is amphipathic. Assist in transport and cell signaling.
Peripheral membrane proteins
is found outside the bilayer, thus it is hydrophilic. Assist with cell recognition, receptor, adhesion.
Receptor
Trigger secondary responses within cell for signaling
Adhesion
attaches cells to other things (e.g. other cells).
Cellular recognition
proteins which have carbohydrate chains (glycoproteins). Used by cells to recognize other cells.
Glycoproteins
any of a class of proteins that have carbohydrate groups attached to the polypeptide chain. They form hydrogen bonds with the water molecules surrounding the cell and thus help to stabilize membrane structure.
Fluid Mosaic Model
describes how the components that make up the cell membrane can move freely within the membrane (fluid). Thus, the cell membrane contains many different kinds of structures (mosaic).
3 types of transport across the cell membrane
Simple diffusion, facilitated diffusion, and active transport.
Simple diffusion
flow of small, uncharged non-polar substances (e.g. O2 and Co2) across the cell membrane from high to low without using energy.
Osmosis
simple diffusion that involved water molecules
Facilitated transport
integral proteins allow larger, hydrophilic molecules to cross the cell membrane; uniporters, symporters, or antiporters, channel proteins, carrier proteins, passive diffusion, porins and ion channels
Channel proteins
Integral protein open tunnel from both sides of bilayer
Carrier proteins
Integral protein that binds to a molecule on one side to change the shape to bring it to the other side
Passive diffusion
performed by channel proteins,, bring molecules down their concentration gradient without energy use (similar to simple diffusion but a protein channel is used). E.g. porins and ion channels
Active transport
substances that travel against their concentration gradient and require the consumption of energy by carrier proteins.
Sodium-potassium pump
us a primary active transport that uses ATP hydrolysis to pump molecules against their concentration gradient. It establishes membrane potential.
Secondary active transport
uses free energy released when other molecules flow down their concentration gradient (gradient established by primary active transport) to pump the molecule of interest across the membrane.
Cytosis
refers to the bulk transport of large, hydrophilic molecules across the cell membrane and requires energy (active transport mechanism).
Endocytosis
cell membrane wrapping around an extracellular substance, internalizing it into the cell via vesicle or vacuole. Phagocytosis, pinocytosis, and receptor-mediated endocytosis.
Phagocytosis
cellular eating around solid objects
Pinocytosis
cellular drinking around dissolved materials (liquids)
Receptor-mediated endocytosis
requires binding of dissolved molecules to peripheral membrane receptor proteins, which initiates endocytosis.
peripheral membrane receptor proteins
initiates endocytosis, binds to dissolved molecules for receptor-mediated endocytosis
Exocytosis
opposite of endocytosis, releasing material to the extracellular environment through vesicle secretion
Organelles
cellular compartments enclosed by phospholipids bilayers (membrane bound) located in the cytosol.
Cytosol
aqueous intracellular fluid
Cytoplasm
cytosol + organelles
Prokaryotes
do not have organelles but have other adaptation such as keeping their genetic material in a region called the nucleoid.
Nucleus
primarily functions to protect and house DNA. DNA replication and transcription occurs here (DNA –> mRNA).
Nucleoplasm
is the cytoplasm of the nucleus
Nuclear envelope
membrane of the nucleus. Two phospholipids bilayers (outer and inner) with a perinuclear space in the middle
Nuclear pores
holes in the nuclear envelope that allows molecules to travel in and out of the nucleus
Nuclear lamina
provides structural support for the nucleus, as well as regulating DNA and cell division
Nucleolus
is a dense area that is responsible for making rRNA, and producing ribosomal subunits.
ribosomal subunits
rRNA + proteins
Ribosomes
not an organelle but work as small factories that carry out translation (mRNA –> protein). Composed of ribosomal subunits.
Eukaryotic ribosomal subunits
(60s + 40s) to assemble in the nucleoplasm and form a complete ribosome in the cytosol of 80s.
Prokaryotic ribosomal subunits
(50s + 30s) to assemble in the nucleoid and form the complete ribosome in the cytosol 70s.
Free-floating ribosomes
ribosomes make proteins that function in the cytosol
Rough ER
ribosomes make proteins that are sent out of the cell or to the cell membrane. Rough ER is continuous with the outer membrane of the nuclear envelope. Proteins synthesized by the embedded ribosomes are sent into the lumen for modifications (glycosylation).
Smooth ER
Not continuous. Its main function is to synthesize lipids, detoxify cells, and produce steroid hormones.
Golgi apparatus
made up of cisternae (flattened sacs) that modify and package substances. Vesicles come from the ER and reach the cis face of the Golgi and leave from the trans face.
Lysosomes
membrane-bound organelles that break down substances taking through endocytosis. They contain acidic digestive enzymes that function at low pH. They carry out autophagy and apoptosis.
Autophagy
breakdown of the cell’s own machinery for recycling
Apoptosis
programmed cell death
Transport vacuoles
transport material between organelles
Food vacuoles
temporarily hold endocytosed food and later fuse with lysosomes
Central vacuoles
large in plants and have a specialized membrane called tonoplast that helps maintain cell rigidity by exerting turgor. Functions in storage and material breakdown.
Storage vacuoles
stores pigments, starches, and toxic substances
Contractile vacuoles
found in single-celled organisms and works to actively pump excess water out
Endomembrane system
works to modify, package, and transport proteins and lipids that are entering and exiting the cell. Nucleus, ER, golgi, lysosomes, vacuoles, and cell membrane.
Peroxisomes
contain an enzyme called catalase that performs hydrolysis, and break down stored fatty acids and help with detoxification. These processes generate hydrogen peroxide , which is toxic because produces ROS.
Reactive oxygen species (ROS)
damage cells through free radicals
Catalase
enzyme that breaks down hydrogen peroxide into water and oxygen.
Mitochondria
powerhouse of the cell, generates ATP for energy use through cellular respiration
Chloroplast
found in plants and some protist, carries out photorespiration
Centrosomes
found in animal cells containing a pair of centrioles, oriented at 90 degree angles to one-another. They replicate during the S phase of the cell cycle so that each daughter cell after cell division has one centrosome.
Microtubule organizing centers (MTOCs)
present in eukaryotic cells and organize microtubule extension during cell division.
Cytoskeleton
provides function and structure within the cytoplasm; microfilaments, intermediate filaments, and microtubules
Microfilaments
smallest, are composed of 2 actin filaments. Involved in cell movement and can quickly assemble and disassemble.
Microfilament functions
cyclosis, muscle contraction, and cleavage furrow
Cyclosis
cytoplasmic streaming, stirring of the cytoplasm, organelles and vesicles travel on microfilament tracks
Cleavage furrow
during cell division, actin microfilaments form contractile rings that split the cell.
Muscles contraction
actin have directionality, allowing myosin motor proteins to pull on them for muscles contraction
Intermediate filaments
structural support, keratin and lamins in nuclear lamina
Microtubules
largest, structural integrity to cells, they are hollow and have walls made of tubulin protein dimers
Centrioles
hollow cylinders made of 9 triplets of microtubules (9x3 array)
Cilia and flagella
have 9 doublets of microtubules with two singles in the center (9+2 array) and are produced by a basal body
Basal body
formed by the mother centriole and produce cilia and flagella
Mother centriole
older centriole after S phase replication
Extracellular matrix (ECM)
provides mechanical support between cells
Proteoglycan
type of glycoprotein that have a high proportion of carbohydrates
Collagen
most common structural protein and organized into collagen fibrils (secreted by fiboblasts)
Integrin
transmembrane protein that facilitates ECM adhesion and signals to cells how to respond to the extracellular environment (growth, apoptosis, etc.)
Fibronectin
protein that connects integrin to ECM and helps with signal transduction
Laminin
influence cell differentiation, adhesion, and movement, it is a major component of the basal lamina.
Cell walls
are carbohydrate-based structures that act like a substitute ECM because they provide structural support to cells that either do not have or have minimal ECM. Present in plants (cellulose), fungi (chitin), bacteria (peptidoglycan), and archaea.
Glycocalyx
glycolipid/glycoprotein coat found mainly on bacterial and animal epithelial cells. Helps with adhesion, protection, and cell recognition.
Cell-matrix junctions
ECM –> cytoskeleton
focal adhesions and hemidesmosomes
Focal adhesions
ECM connects via integrins to actin microfilament inside the cell
Hemidesmosomes
ECM connects via integrins to intermediate filaments inside the cell
Cell-cell junctions
connect adjacent cells
Tight junctions
form water-tight seals between cells to ensure substancecs pass through cells and not between them
Desmosomes
provide support against mechanical stress. connects neighboring cells via intermediate filaments
Adherens junctions
similar in structure and function to desmosomes, but connects neighboring cells via acting filaments
Gap junctions
allow passage of ions and small molecules between cells
Middle lamella
plant cell, sticky cement similar in function to tight junctions
Plasmadesmata
plant cell, tunnels with tubes between plant cells, allows cytosol fluids to freely travel between plant cells.
Isotonic solutions
same solute concentration as the cells placed in them
Hypertonic solutions
have higher solute concentration than the cells placed in them, causing water to leave the cell and it shrinking
Hypotonic solutions
have a lower solute concentration than the cells place in them, causing water to enter the cell (cell swells up), lysis is the bursting of a cell when too much water enters
Metabolism
refers to metabolic pathways (a series of chemical reactions) that are happening in an organism.
Catabolic
breaking down larger molecules for energy
Anabolic
using energy to build larger macromolecules
To break down carbohydrates for energy, cells must…
utilize aerobic or anaerobic cellular respiration
Adenosine triphosphate (ATP)
is an RNA nucleoside triphosphate. It contains adenosine nitrogenous base linked to a ribose sugar and 3 phosphate groups. It is the cellular energy currency because of the high energy bonds between the phosphates groups. These bonds release energy by hydrolysis, breaking the bonds.
Reaction coupling
the process of powering energy-requiring reactions with energy releasing reaction. It allows unfavored reaction to be powered by a favorable one, making the net Gibbs free energy negative, exergonic, spontaneous
Mitochondria structure
inner (with cristae) and outer membrane, intermembrane space, and matrix
Endosymbiotic theory
states that aerobic bacteria were internalized as mitochondria while the photosynthetic bacteria became chloroplasts. Size similarities and the fact that mitochondria and chloroplasts contain their own circular DNA and ribosomes.
Aerobic cellular respiration
is performed to phosphorylate ADP into ATP, by breaking down glucose and moving electrons around. It involves 4 catabolic processes: glycolysis, pyruvate manipulation, krebs cycle, and oxidative phosphorylation.
Glycolysis
Glucose –> 2 ATP + 2 NADH + 2 Pyruvate
Takes place in the cytosol and does NOT require oxygen
Substrate-level phosphorylation
the process used to generate ATP in glycolysis, transferring a phosphate group to ADP directly from a phosphorylated compound.
Glycolysis phase 1
Hexokinase uses one ATP to phosphorylate glucose into glucose-6-phosphate, which cannot leave the cell.
Glycolysis phase 2
Isomerase modifies glucose-6-phosphate fructose-6-phosphate.
Glycolysis phase 3
Phosphofructokinase uses a second ATP to phosphorylate fructose-6-phosphate into fructose-1,6-biphosphate.
Glycolysis phase 4
Fructose-1,6-biphosphate is broken into dihydroxyacetone phosphate (DHAP) and
glyceraldehyde-3-phosphate (G3P), which
are in equilibrium with one another.
Glycolysis phase 5
G3P proceeds to the energy payoff phase so DHAP is constanly converted into G3p to maintain equilibrium. 1 glucose molecule will produce 2 G3P that continue into the next steps.
Glycolysis phase 6
G3P undergoes a series of redox reactions to produce 4 ATP through substrate-level-phosphorylation, 2 pyruvate and 2 NADH.
Pyruvate manipultions
2 pyruvate –> 2CO2 + 2NADH + 2 acetyl CoA
Pyruvate dehydrogenase
is an enzyme that carries out the pyruvate manipulation; decarboxylation, oxidation, and Coenzyme A
Pyruvate dehydrogenase phase 1
Decarboxylation: pyruvate molecules move from the cytosol into the mitochondrial matrix (except for prokaryotes), a carboxyl group is removed from pyruvate, releasing carbon dioxide.
Pyruvate dehydrogenase phase 2
Oxidation: two-carbon molecule is converted into an acetyl group, giving electrons to NAD+ to convert it into NADH
Pyruvate dehydrogenase phase 3
Coenzyme A: CoA binds to the acetyl group, producing acetyl CoA
Krebs cycle
2 acetyl CoA –> 4 CO2 + 6 NADH + 2 FADH2 + GTP
Occurs in the mitochondrial matrix
Krebs cycle phase 1
Acetyl CoA joins oxaloacetate (4 carbon) to form citrate (6 carbon)
Krebs cycle phase 2
Citrate undergoes rearrangements producing 2 CO2 and 2 NADH
Krebs cycle phase 3
After the loss of 2 CO2, the resulting 4 carbon molecule produces 1 GTP through substrate level phosphorylation
Krebs cycle phase 4
The molecule will now transfer electrons to 1 FAD+, which is reduced into 1 FADH2
Krebs cycle phase 5
The molecule is converted back to oxaloacetate, thus gives electrons to produce 1 NADH
Oxidative phosphorylation
Electron carriers (NADH + FADH2) + O2 –> ATP + H2O
ETC goal
regenerate electron carriers and create an electrochemical gradient to power ATP production. The mitochondrial inner membrane is the ETC for eukaryotes while cell membrane is for prokaryotes
Oxidative-reduction (redox) reactions
four protein complexes I-IV are responsible for moving electrons through a series in the ETC.
Electrochemical gradient
As the series of redox reactions occurs, protons are pumped from the mitochondrial matrix to the intermembrane space, making it highly acidic
Complex I
NADH is more effective and drops electrons off, regenerating NAD+
Complex II
FADH2 drops electrons off at this second protein, regenerating FAD+, this results in less pumping of protons due to the bypassing of complex I
Chemosmosis goal
Use the proton electrochemical gradient (proton-motive force) to synthesize ATP
ATP synthase
is a channel protein that provides hydrophilic tunnel to allow protons to flow down their electrochemical gradient (back into the mitochondrial matrix). The spontaneous movement of protons generates energy that is used to convert ADP + Pi –> ATP, a condensation reaction that is endergonic, +∆G
NADH produces
3 ATP (NADH from glycolysis produces less)
FADH2 produces
2 ATP
Glycolysis stage
Net products: 2 ATP & 2 NADH
Net yield ATP: 2 ATP & 4-6 ATP
2 pyruvate oxidations stage
Net products: 2 NADH
Net yield ATP: 6 ATP
2 Krebs cycles stages
Net products: 2 GTP, 6 NADH, 2 FADH2
Net yield ATP: 2 ATP, 18 ATP, 4 ATP
Total net ATP yield during aerobic respiration
36-38 ATP
Fermentation
does not require energy, anaerobic pathway, only relies on glycolysis by converting the produced pyruvate into different molecules in order to oxidize NADH back to NAD+, thus glycolysis can continue to make ATP. Occurs in the cytosol.
Two types of fermentation
Lactic acid and alcohol fermentation
Lactic acid fermentation
uses the 2 NADH from glycolysis to reduces the 2 pyruvate into 2 lactic acid, thus NADH is oxidized back to NAD+ so that glycolysis may continue, this happens in muscle cells and occurs in red blood cells, which do not have mitochondria for aerobic respiration
Cori cycle
is used to convert lactate back into glucose once oxygen is available again, it transports the lactate to liver cells, where it can be oxidized back to into pyruvate, it can then be used to form glucose, its an ideal energy generation
Alcohol fermentation
uses 2 NADH from glycolysis to convert the 2 pyruvate into 2 ethanol, NADH is oxidized back to NAD+ so that glycolysis may continue, this process has an extra step; decarboxylation of pyruvate into acetaldehyde, which is only then reduced by NADH into ethanol.
pyruvate -CO2-> acetaldehyde -NAD+-> ethanol
Obligate aerobes
only perform with oxygen present
Obligate anaerobes
can only undergo anaerobic respiration or fermentation, oxygen is poison to them
Facultative anaerobes
can perform either anaerobic or aerobic respiration or fermentation but prefers oxygen because it generate the most ATP
Microaerophiles
can only undergo aerobic respiration but cannot handle too much oxygen it can be harmful
Aerotolerant organisms
only undergoes anaerobic fermentation but oxygen is not toxic
Alternative sources of energy generation
fats, carbohydrates, and proteins
Glycogenolysis
when carbohydrates enter during glycolysis. It describes the release of glucose-6-phosphate from glycogen, a highly branched polysaccharide of glucose. Disaccharides can undergo hydrolysis to release two carbohydrate monomers, which can enter glycolysis.
glyogen –> glucose-6-phosphate
Glycogenesis
the reverse process - the conversion of glucose into glycogen to be stored in the liver when energy and fuel is suffiecent
Fats
are present in the body as triglycerides, lipase are required to first digest fats into free fatty acids and alcohols, these digested pieces the can be absorbed by enterocytes to reform triglycerides.
Lipolysis
process of digesting fats into free fatty acids and alcohols
Enterocytes
absorb digested pieces in the small intestine to reform triglycerides
Adipocytes
cells that store fat (triglycerides) and have hormone sensitive lipase to help release triglycerides back into circulation as lipoproteins or as free fatty acids bounded to albumin
Lipase
enzyme that helps release triglycerides back into circulation as lipoproteins or free fatty acids
Albumin
a protein that is bound to free fatty acids
Chylomicrons
are lipoprotein transport structures formed by the fusing of triglycerides with proteins, phospholipids, and cholesterol. They leave enterocytes and enter lacteals.
Lacteals
small lymphatic vessels that take fats to the rest of the body.
Proteins as an energy source
is less desirable because the processes to get them into cellular respiration take considerable energy and proteins are needed for essential functions in the body
Oxidative deamination
removal of NH3, then proteins can be broken down into amino acids, then shuttled to various parts of cellular respiration
Ammonia
is toxic, so it must be converted into uric acid or urea depending on the species and excreted from the body. Humans convert ammonia into urea which is then excreted as urine.
Free fatty acids
undergo beta-oxidation to be converted into acetyl-CoA, it requires an initial investment of ATP, but then is cleaved to yield two-carbon acetyl CoA molecules (that can be used in the Krebs cycle) and electron carriers (NADH or FADH2)
Glycerol
molecule that travels to the liver, it can undergo a conversion to enter glycolysis or make new glucose via gluconeogensis at the liver
Heterotrophs
get energy from what they eat
Autotrophs
make their own energy (food)
Photosynthesis
creates chemical energy that is transferred through food-chains, reduces atmospheric carbon dioxide, and releases oxygen.
6CO2 + 6H2O –> C6H12O + 6O2
photosynthesis + solar energy—>
chemical energy
Photons
are light energy that are used to synthesize sugars (glucose) in photosynthesis.
Carbon fixation
is the process of taking inorganic carbon (CO2) and converts it into organic glucose. Photosynthesis takes electrons from photolysis and excites them using solar energy, thus these electrons are using to power carbon fixation
Photolysis
splitting of water molecules
Epidermis
out layer of the cells that provides protection and prevents water loss
Palisade mesophyll cells
right below the upper layer of the epidermis, has most of the chloroplast here
Spongy mesophyll cells
bottom of the leaf, has moderate chloroplast here, the leaf has a lot of space here due to gas movement.
Stomata
are pores underneath the leaf for gas to enter and exit
Guard cells
surround the stomata and control their opening and closing
Choloroplasts
similar to mitochondria but found in plants and photosynthetic algae (not in cyanobacteria)
Parts of a chloroplast
outer membrane, intermembrane, inner membrane, stroma (fluid material fills are inside inner membrane, calvin cycle), thylakoids (within stroma, light dependent reactions occur, granum is the entire stack, lamella is the junction in between), thylakoid lumen (interior of the thylakoid and H+ ions accumulate)
Light dependent reactions
located in the thylakoid membrane, harnesses light energy to produce ATP and NADPH that is later used in the Calvin cycle
Photosystems
contain pigments such as chlorophyll and carotenoids that that absorb photons
Reaction center
special pair of chlorophyll molecules in the center of these proteins: photosystem II (680) and photosystem I (700) that are used in photosynthesis
Non-cyclic photophosphorylation
is carried about by light dependent reactions
Non-cyclic photophosphorylation step 1
water is split, passing electrons to photosystem II and releasing protons into the thylakoid lumen
Non-cyclic photophosphorylation step 2
Photons excite in the reaction center of photosystem II, passing electrons to a primary electron acceptor
Non-cyclic photophosphorylation step 3
The primary electron acceptor sends the excited electrons into the electron transport chain (ETC). During redox reactions within the ETC, protons are pumped from the stroma to the thylakoid lumen. The electrons are then deposited into the photosystem I
Non-cyclic photophosphorylation step 4
Photons excite pigments in the photosystem I, energizing the electrons in the reactions center to be passed to a primary electron acceptor
Non-cyclic photophosphorylation step 5
the electrons are sent to a short ETC that terminates with NADP+ reductase, and anzyme then reduces NADP+ to NADPH using electrons and protons.
Non-cyclic photophosphorylation step 6
The accumulation of protons in the thylakoid lumen generates an electrochemical gradient that is used to produce ATP using ATP synthase (chemiosmosis), as H+ moves from the thylakoid lumen back into the stroma
Cyclic photophosphorylation
happens when photosystem I passes electrons back to the first ETC, causing more proton pumping and more ATP production, while not NADPH is generated
The Calvin cycle
known as the light independent reactions, it does not directly use light energy, but it can only occur of the light dependent reaction is providing ATP and NADPH. It takes place in the chloroplast stroma of plant mesophyll cells, it fixes CO2 that enters the stomata.
6CO2 + 18 ATP + 12 NADPH + H+ –> 18 ADP + 19 Pi + 12 NADP+ + 1 glucose
The Calvin cycle step 1
Carbon fixation: carbon dioxide combines with 5-carbon ribulose -1,5-bisphosphate (RuBP) to form 6-carbon molecules, which quickly break down into 3-carbon phosphoglycerates (PGA). This reaction is catalyzed by RuBisCo.
The Calvin cycle step 2
Reducation: PGA is phosphorylated by ATP and
subsequently reduced by NADPH to form
glyceraldehyde-3-phosphate (G3P).
The Calvin cycle step 3
Regeneration: Most of the G3P is converted
back to RuBP.
The Calvin cycle step 4
Carbohydrate synthesis: some of the G3P is
used to make glucose.
RuBisCo
in addition to fixing carbon dioxide into RuBP, can also cause oxygen to bind to RuBP in a process called photorespiration
Photorespiration
occurs in the stroma, producing a 2-carbon molecule phosphoglycolate that is shuttled to peroxisomes and mitochondria for conversion into PGA. Fixed carbon is lost as carbon dioxide in the process, overall there is a net loss of fixed carbon atoms and no new glucose would be made.
C2 photosynthesis
aka photorespiration, since 2-carbon phoshoglycolate is produces
Hot and dry stomata
is close to prevent water loss, thus oxygen accumulates and CO2 is used up. RuBisCo binds oxygen and photorespiration occurs.
C3 photosynthesis
normal photosynthesis, where a 3-carbon PGA is produced
C4 photosynthesis
produces 4-carbon oxaloacetate, occurs in plants living in hot environments.
Spatial isolation
of CO2 to prevent photorespiration
Alternative photosynthetic pathways
C3, C4, and CAM photosynthesis
C4 photosynthesis step 1
PEP carboxylase fixes CO2 into a three carbon PEP molecule, producing oxaloacetate, which
is converted into malate in the mesophyll cell
C4 photosynthesis step 2
Malate is transferred to bundle sheath cells, which have lower concentrations of oxygen.
C4 photosynthesis step 3
Malate is decarboxylated to release CO2, spatially isolating where CO2 is fixed byRuBisCo. The only drawback is that pyruvate is also produced and needs to be shuttled back to mesophyll cells using ATP energy.
C4 photosynthesis step 4
Pyruvate is converted back into PEP.
CAM photosynthesis
uses temporal isolation of CO2 to prevent photorespiration in hot environments
CAM photosynthesis step 1
During the day, stomata are closed to prevent transpiration (evaporation of water from
plants).
CAM photosynthesis step 2
During the night, stomata are open to let carbon dioxide in. Just like in C4 photosynthesis, PEP carboxylase fixes CO2
into PEP, producing oxaloacetate and afterwards malate. However, malate is stored in vacuoles instead of being shuttled to bundle sheath cells.
CAM photosynthesis step 3
During the next day, the stomata are closed again and malate is converted back into oxaloacetate, which releases CO2 and PEP. Thus, CO2 accumulates in the leaf for use in the Calvin cycle through temporal isolation.
Photoautotrophs
can take light energy and convert it into chemical energy via Photosynthesis
Genome
all DNA in a cell
Chromosomes
separate DNA molecules that make up the genomes
Homologous chromosome pairs
two different versions of the same chromosome number. One from mom and one from dad.
Sister chromatids
identical, attached copies of a single chromosomes, forming dyads
Dyads
replicated chromosomes containing sister chromatids that look like an “X”
Centromeres
regions of DNA that connect sister chromatids in a dyad
Kinetochores
proteins on the sides of centromeres that help microtubules pull sister chromatids apart during cell division
Karyokinesis
division of the nucleus
Cytokinesis
physical division of the cytoplasm and cell membrane
Parent cell
one parent cell produces two daughter cells after division
Ploidy
describes the number of chromosomes sets found in the body.
Diploid
humans, contain two sets of chromosomes (46 chromosomes, 23 pairs) one from each parent
Haploid
gametes, only contain one chromosome set (23 chromosomes)
Sex chromosomes
one pair in the human body that determine sex
Autosomes
22 pairs in the human body that aren’t sex chromosomes
Gametes
haploid cells, egg and sperm
Germ cells
diploid cells that divide by meiosis to produce gametes
Gametocyte
eukaryotic germ cell that can either divide to form more gametocytes or produce gametes
Somatic cells
body cells excluding the gametes, diploid in humans
Cell cycle
is divided into interphase (G1, G0, S, and G2) and the M phase. 90% of the cell cycle happens during interphase. M phase is where karyokinesis and cytokinesis occur.
Go Sam Go Make Cake
Gap phase 1 (G1) Synthesis phase (S) Gap phase 2 (G2) Mitosis of M phase Cytokinesis of M phase
Gap phase 1 (G1)
cell grows in preparation for cell division and checks for favorable conditions. If favorable, the cell will enter S phase. If unfavorable it will enter G0 phase.
G0 phase
cells still carry out their functions but halt in the cell cycle, cells that do not divide are stuck here
Synthesis phase (S)
cell replicates its genome and centrosomes here and moves to G2 phase when completed.
Gap phase 2 (G2)
cell continues to grow and prepare for cell division by checking DNA for any errors after replication, also checking for mitosis promoting factor (MPF), which needs to be an adequate amounts for cell cycle continuation. Organelles replicated here.
Microtubules Organizing Centers (MTOCs)
made of protein tubulin, are responsible for forming spindle apparatus which guides chromosomes during karyokinesis, organizing microtubule extension
Microtubules in the spindle apparatus:
Kinetochore, astral, and polar microtubules
Kinetochore mircotubules
extend centrosomes and attach to kinetochores on chromosomes
Astral microtubules
extend from centrosomes to cell membrane to orient the spindle apparatus.
Polar microtubules
extend from the two
centrosomes and connect with each other. Pushes centrosomes to opposite ends of the cell.
Centrioles
Centrioles are hollow cylinders made of nine triplets of microtubules (9x3 array).
Centrosomes
organelles that contain a pair of centrioles oriented at 90 degree angles to one another (attached by interconnecting fibers), they replicate during the S phase of the cycle so that each daughter has one centrosome
Pericentriolar material
surrounds the centrioles and is responsible for microtubules nucleation (anchoring tubulin to start microtubule extension).
M-phase
is the stage in the cell cycle where karyokinesis and cytokinesis occurs.
Mitosis
is a type of karyokinesis (nuclear division) that involves a diploid parent cell dividing into two diploid daughter cells.
Prophase
chromatin condenses into
chromosomes (X-shaped dyads). The nucleolus and nuclear envelope disappear. Spindle apparatus forms.
Metaphase
the spindle apparatus guides
the chromosomes to the metaphase plate (midpoint of cell) in single file.
Anaphase
kinetochore microtubules
shorten to pull sister chromatids apart. Now, the sister chromatids are considered separate
chromosomes. Chromosome number doubles.
Telophase
chromosomes have segregated
and nuclear membranes reform. In addition, nucleoli reappear and chromosomes decondense into chromatin.
Cytokinesis
is the physical separation of the
cytoplasm and cell membrane into two daughter cells.
Plant cell cytokinesis
cells, cytokinesis begins in telophase with the formation of a cell plate. The cell plate is
created by vesicles from the Golgi apparatus and ends up producing the middle lamella (cements plant cells together).
Animal cell cytokinesis
cytokinesis begins in late anaphase with the formation of a cleavage furrow. The cleavage furrow is a contractile ring of actin microfilaments and myosin motors that pinches the cell into two.
Cell cycle influences
cell division through limitations to growth and regulations to prevent cancerous growth.
Functional limitations
surface to volume ratio and genome to volume ratio
Surface to volume ratio
cell division occurs when volume is too large because cells rely on the surface area of their cell membrane for transport of material. Decrease in S/V leads to division.
Genomes to volume ratio
cell division occurs when volume is too large for cells to support with its limited genome. Decrease in G/V leads to division.
Cell specific regulations
cell specific checkpoints, cyclin-dependent kinases (CDKs), growth factors, density dependent inhibition, anchorage dependence.
Cell specific checkpoints
G1 restriction point (checks for favorable conditions to grow,
enters G0 phase if unfavorable), and end of G2 (checks accuracy of DNA replication and MPF levels), and M checkpoint (during metaphase, checks for chromosomal attachment to spindle fibers).
Cyclin-dependent kinases (CDKs)
phosphorylate certain substrates to signal cell cycle progression. Activated by cyclin, a protein that cycles through stages of synthesis and degradation.
Growth factors
bind to receptors in the plasma membrane to signal for cell division.
Density dependent inhibition
halting cell division when density of cells is high.
Anchorage dependence
dividing only when attached to an external surface.
Mitosis increases the number of
cells in an organism
Binary fission
used by archaea, bacteria, and certain organelles to reproduce. Organisms will replicate their genome while cell division is happening (no S phase for DNA replication). And no spindle
apparatus.
Meiosis
produces four haploid daughter cells from one diploid parent cell. It does this by repeating the steps of karyokinesis twice. Meiosis can be divided into meiosis I (homologous chromosomes separate) and meiosis II (sister chromatids
separate).
Meiosis I
(reductional division) produces two haploid daughter cells through separation of homologous chromosomes.
Prophase I
chromatin condenses into
chromosomes (X-shaped dyads). Also nucleolus and nuclear envelope will disappear. Homologous chromosomes pair
up and crossing over occurs.
Homologous chromosomes pair up and crossing over during:
Synapsis - the pairing up of homologous chromosomes to form tetrads (aka bivalents).
Synaptonemal complex - protein
structure that forms between
homologous chromosomes during synapsis.
Tetrads (bivalents) - pair of two
homologous chromosomes each with two sister chromatids.
Chiasmata - where chromatids
physically crossover during synapsis, causing genetic recombination.
Genetic recombination - exchange of DNA between chromosomes to produce genetically diverse offspring.
Metaphase I
tetrads randomly line up
double file on metaphase plate, also contributes to genetic diversity.
Anaphase I
kinetochore microtubules
shorten to separate homologous
chromosomes from each other. Will not begin unless at least one chiasmata has formed within each tetrad.
Telophase and Cytokinesis I
after tetrads have been pulled to opposite poles, nuclear membranes reform. In addition, nucleoli reappear and
chromosomes decondense into
chromatin. Cleavage furrow formed in animal cells and cell plate formed in plant cells.
Meiosis II
is very similar to mitosis because sister chromatids are separated. Two haploid cells divide into four haploid daughter cells.
Prophase II
chromatin condenses into
chromosomes (X-shaped dyads). Also nucleolus and nuclear envelope will disappear. Spindle apparatus forms. No crossing over.
Metaphase II
chromosomes line up single file at the metaphase plate just like in mitosis.
Anaphase II
kinetochore microtubules
shorten to pull sister chromatids apart. Sister chromatids become separate chromosomes and chromosomes number doubles
Telophase and Cytokinesis II
nuclear membranes reform, nucleoli reappear, and chromosomes decondense into chromatin. Four haploid daughter cells are produced in
total.
Mitosis chromosomes and chromatid numbers:
During the S phase of the cell cycle, a human’s 46 chromosomes are duplicated. Afterwards, there are still 46 chromosomes but also 92 chromatids.
Meiosis I chromosomes and chromatid numbers:
During S phase. This results in the same total numbers - 46 chromosomes and 92 chromatids. Each cell will have 23 chromosomes and 46 chromatids.
Meiosis II chromosomes and chromatid numbers:
sister chromatids are
separated, resulting in 23 chromosomes (23 chromatids) in each daughter cell. These cells are haploid.
