unit test #2 Flashcards
macromolecules definition + examples
large molecule made up of many smaller molecules (ex. large sugars, lipids)
monomer definition
individual subunit of molecule
polymer definition
chain of monomers linked together with bonds
what are the monomer and polymer of carbohydrates
monomer: monosaccharide
polymer: polysaccharide
what are the monomer and polymer of proteins
monomer: amino acids
polymer: polypeptides
what are the monomer and polymer of lipids
monomer: fatty acid + glycerol
polymer: lipid
what are the monomer and polymer of nucleic acid
monomer: nucleotide
polymer: nucleic acid
versatility of carbon
- 4 valence electrons
- almost infinite amount of possible molecules can be made
- carbon chains can be any length
what are functional groups
- elements that commonly stay together that can attach to carbon, forming “clusters”
- ex. H, O, S, N
what are 4 functional groups
hydroxyl, amine, carboxyl, methyl
how does metabolism work
includes pathways where a molecule can turn into another molecule in a series of small steps
- can be a chain or cyclic
anabolism/condensation reaction
build molecules by making bonds
- includes formation of macromolecules
disaccharide definition
two monosaccharides bonded together
formula for anabolic reaction
small molecule -OH+ H-small molecule –energy–> large molecule + H2O
difference b/w alpha glucose and beta glucose
alpha: bond on right side has H on top, OH at bottom
beta: bond on right has OH on tip, and H on bottom
catabolism/hydrolysis reactions
breaks down molecules by breaking bonds
- hydrolysis of macromolecules into monomers
formula of catabolic reactions
large molecule + H2O –energy–> small molecule-OH + H-small molecule
structure of monosaccharides
- contains 3-7 carbon atoms
- can be pentose (pentagon shape) or hexose (hexagon shape)
- typically ring shape, may be chain
monosaccharides in glucose
- small + soluble (like all), easily transported
- chemically stable, good for storage
- glucose in cell=creates osmotic problems, stored as glycogen/starch instead
- releases energy when oxidized
monosaccharide definition
a sugar that cannot become a simpler one
- single monomer for polysaccharide
polysaccharide definition
polymers of 2+ monosaccharides
structure of polysaccharides
- very long, may be branched
- contains glycosidic bonds (1,4 or 1,6)
- stores energy as a-glucose
- no fixed size
structure of polysaccharides (cellulose)
- 710,000 beta glucose monomer
- 1,4 glycosidic bonds oriented n alternating directions
- straight, unbranched chains
- not soluble in water
properties/function of polysaccharides (cellulose)
- high tensile strength (ability to be stretched)
- bundles of microfibrils compose cell wall, preventing it from bursting
structure of polysaccharides (amylose)
- thousands of alpha glucose
- 1,4 glycosidic bonds oriented in same direction
- curved, unbranched chains
- hydrophilic, however too large to be soluble in water (doesn’t affect osmotic balance)
properties/function of polysaccharides (amylose+amylopectin)
- only made by plant cells
- molecules vary in size, easy to add/remove glucose units
- useful for glucose/energy storage, glucose can be converted to starch for storage then hydrolyzed when needed (amylopectin more ideal, more free ends)
structure of polysaccharides (glycogen)
- 10,000 alpha glucose
- chain of 1,4 glycosidic bonds w 1,6 bonded branches
- curved and branched chains
- lower solubility. than glucose, doesn’t affect osmotic balance
properties/functions of polysaccharides (glycogen)
- compact, easy to add/remove
- good for storage since doesn’t affect osmotic balance (insoluble)
- stored in liver and muscles of human
structure of polysaccharides (amylopectin)
- 100,000 alpha glucose
- oriented in same way throughout
- curved + branched chains
- hydrophilic, but too big to be soluble in water (doesn’t affect osmotic balance)
state changes of oils
- liquid at room temp
- melts at 20C
state changes of fats
- melts b/w 20-37C
- solid at room temp
- liquid at body temp
state changes of wax
- melts at 37C
- liquid at high temp
ester linkage
connection b/w hydroxyl group of alcohol covalently linked to carboxylic acids (condensation reaction)
what is a triglyceride
glycerol + 3 fatty acids that form 3 water molecules and ester linkage
H/OH areas of bonds are hydrophobic/hydrophilic while triglycerides are hydrophobic/hydrophilic
hydrophilic, hydrophobic
forming phospholipids
glycerol backbone+ 2 fatty acids + phosphate group (hydrophilic)
- creates hydrophilic head, hydrophobic tail
length of fatty acids
- 14-20 carbons long
saturated fatty acids
- only single bonds
- contains as many H as possible
unsaturated fatty acids + monounsaturated/polyunsaturated
- has 1+ double bonds
- fewer H atoms than possible
monounsaturated: 1 double bond
polyunsaturated: 2+ double bonds
structure/properties of cis-isomers
- very common in nature
- H atoms are on the same side of C chain
- bend in fatty acid chain (caused by double bond)
- loosely pack, lower melting point
structure/properties of trans-isomers
- rare in nature
- H atoms on different sides of C atoms
- straight fatty acid chain
- closely packed, higher melting point
adipose meaning
body tissue used for strange of fat (triglycerides)
why are triglycerides ideal for storage?
- chemically stable
- not soluble in water (doesn’t affect osmotic balance)
- releases 2x as much energy as carbs/sugars
- poor conductors of heat (insulation)
- liquid at room temp (shock absorber)
structure of steroids
- 4 rings of carbon atoms (17 C atoms in total)
- 3 cyclohexane rings, 1 cyclopentane ring
how many amino acids are there
20
components of an amino acid
- central carbon
- carboxylic group
- amine group
- R-group
central carbon in amino acids
- alpha carbon
- creates 4 bonds with other atoms
- centre of AA
carboxylic group in amino acids
- can donate a proton (H+)
- acidic
- RS of AA (when drawing)
amine group in amino acids
- can accept a proton
- basic
- LS of AA (when drawing)
R-group in amino acids
- every AA has unique R-group, giving AAs unique batteries
- ex. some polar, non-polar, neg/pos charged, contain sulfur etc
- connected to bottom of central carbon
an amino acid is a monomer/polymer
monomer
dipeptide meaning
chain of 2 amino acids
oligopeptide meaning
chain of <20 amino acids
polypeptide meaning
chain of many AAs (>20)
- main components of proteins
how are polypeptides built
- ribosomes act as catalyst b/w AAs to build chains (polypeptides)
- condensation rxn
polypeptide structure
- repeating N-C-C backbone structure
- amino terminal on LS
- carboxyl terminal on RS
can plants synthesize amino acids
yes, they can synthesize all 20 amino acids
can animals synthesize amino acids
no, they can synthesize 11 AAs(non-essential) and rest must be obtained from food (essential)
number of possible peptide chains
- AAs can be linked together infinite amount of times (20 AAs and any length)
- creations based on instructions in genetic code
are there infinite peptide chain variations in organisms
no, although there are infinite possibilities in creation of peptide chains, organisms only make small amount
proteome meaning
all proteins made by cell/tissue/organism
genome meaning
all genes of cell/tissue/organism
variability of proteomes
- different specialized cells make different proteins
- cell makes diff proteins during diff times of cycle
- can be identified through gel electrophoresis
largest protein in body
titin, a part of muscle (34,350 amino acids)
A-amylase protein
digests starch in saliva (496 amino acids)
beta-endorphin protein
natural painkiller secreted by pituitary gland (31 amino acids)
insulin protein
monitors blood sugar levels (51 amino acids)
conformation of protein
- refers to 3D structure of protein (folding)
- determined by AA sequence (R-groups) and interacting polypeptides
- protein folding must occur for protein to be functional
proteins - primary structure
the amino acid sequence
proteins - secondary structure
- hydrogen bonding b/w amino acid back-bones
- polypeptides fold into repeating pattern (alpha helix or beta pleated sheets)
proteins - tertiary structure
- 3D folding of polypeptide due to R group interactions
proteins - quaternary structure
- not all proteins reach this stage
- interaction of 2+ polypeptide chains in tertiary structure
protein structure in hair
- made of protein called keratin which forms helical shape with sulfur bonds
- more sulfur bonds = curlier hair
how is 3D conformation of proteins stabilized
the bonds/interactions b/w R-groups of amino acids
- however most are relatively weak (ex. hydrogen bonds), can be disrupted/broken
what happens when the 3D conformation of proteins is disrupted
- change to conformation leads to denaturation, loss in function
- minimal disruption: protein may be able to regain original shape (renaturation)
denaturation meaning
breaking of the many weak linkages/bonds (ex. hydrogen bonds) within protein
- leads to loss of folded structure and function
effect of heat on proteins
- causes vibration in molecules, breaking intermolecular bonds
- 3D conformation changes
- soluble proteins become insoluble as hydrophobic AAs become exposed to water (eggs)
- proteins vary in heat tolerance (ex. proteins in thermus aquaticus, a projaryotic cell living in hotspring works best at 80C)
effect of pH on proteins
- extreme changes: can change charges in R-groups, breaks down existing/creates new ionic bonds, 3D conformation changes
- soluble proteins become insoluble
- proteins vary in tolerance (ex. pepsin in stomach works best at pH of 1.5)
catalyst during reaction
- increases rate of rxn
- not changed or used up during rxn, can be reused
what are enzymes
- biological catalysts
- made by living organisms to speed up biochemical reactions
- converts substrates into products
what would happen without enzymes
reactions would occur so slowly that it would be unable to sustain life
substrate meaning
substance on which an enzyme can act
how are enzymes used
- specific enzyme–> specific rxn
- needs reactions: enzyme is produced
- preventing reaction: enzyme is not produced/temporary block from enzymes working
what is activation energy
- used to break bonds in substrate
- released when new bonds form
transition state with enzyme vs. without enzyme
with: bonds are weakened by catalyst, less activation energy needed to break. not necessarily faster rxns, but more rxns can happen at once
without: more energy needed to reach transition state
enzymes are ____ proteins
globular
what is the active site
special region on enzyme where substrate binds
- chemical properties of active site and substrate match
- very specific size, shape in order to fit substrate
importance of 3D structure of enzymes
- crucial to function
- folding brings AAs close together meaning 3D structure is very important
collision theory
used to explain why different reactions happen at different rates
1. particles must collide
2. particles must have sufficient energy
3. particles must collide at the correct orientation
induced fit binding model
- substrates and enzymes more randomly
- when they get close, chemical properties of enzymes attracts substrate
- substrate binds to active site
- interaction causes substrate and enzyme to slightly change 3D conformation (induced fit binding)
- products detach from active site, enzymes conformation returns to normal, catalyzes another rxn
what happens when substrate binds to active site
enzyme/substrate complex, enzyme slightly changes shape, enzyme/product complex, products leave enzyme
why is induced fit bonding and conformational changes important
- must happen because of alterations of bond angles/lengths
- adding another substrate will result in conformational change
- easier for bonds to break/reform
what is substrate-active site collision? where do they occur?
the coming together of substrate and active site
- reactions occur in water
how does the collision theory apply to substrate-active site collision
- particles moving randomly = occasional collision
- faster molecules = more chance of collision
- angles align = substrate is able to bond to site
variations in enzyme and substrate moleucles
substrate: smaller, moves more to make up for lack of movement of enzyme
enzyme: large, cannot move, sometimes embedded in membrane
what is enzyme-substrate specificity
- shape + chemical properties of active site only allow for specific substrate to bond
- some enzymes can bond to group of substrates
graph of pH on enzyme activity
- peak in graph at optimum pH (usually 7)
- 0 enzyme activity at extremely high/low pHs
what happens when pH is too low/high for enzyme activity
disrupts ionic bonds between AAs, affecting protein solubility
- can change shape of active site, meaning it’s unable to bind to substrate
- enzymes become denatured
- may be reversible
graph of temp on enzyme activity
- gradual increase until optimum temperature
- steeper decrease after optimum temp (as enzymes experience denaturalization)
what happens when temp is too low/high for enzyme activity
low: not enough thermal energy for activation of reaction
high: denaturalization
graph of effect of substrate concentration on enzyme activity
- starts at 0, and increases rapidly until it reaches a plateau
what happens when substrate concentration is too high for enzyme activity
- not enough enzymes to catalyse all the substrates (reaching plateau at max efficiency)
- competition for activation sites
properties of ATP + functions
soluble in water: moves freely in solutions and cytoplasm, cannot pass bilayer
stable at pH: close to neutral: matches pH of cytoplasm
structure of ATP + function
chain of 3 phosphates: last phosphate bond can be broken (hydrolysis) to release just enough energy for cell processes
hydrolysis in ATP function
- powers mechanical, transport, and chemical reactions
- energy is release when bond b/w last 2 phosphates is broken
- catalyzed by enzyme called atpase
- exergonic reaction (releases energy)
how is ATP an energy store, how much does it store
- removing 1 phosphate group form each molecule in 1 mole of ATP releases 30.5J on energy
why is internal temp of mammal different form outside temp
- processes release heat energy to create optimal environment for reactions to occur
how is ATP a useful energy carrier
- cycled, can be reused through phosphorylation
- packages energy released into useful amounts
- can attach to other molecules to drive processes
phosphorylation meaning
attachment of a phosphate group to a molecule or ion
life processes in cells that require ATP
- synthesizing macromolecules (DNA, RNA, proteins)
- active transport
- movement within cell (cytokinesis, chromosomes, muscle contractions)
how is ADP created
- as ATP is used, phosphate is removed, creating ADP
what does ADP stand for
adenosine diphosphate
how is phosphate re-attached to ADP/ATP
phosphorylation occurs to re-attach phosphate and make more ATP
- process uses energy which is released by cellular respiration
cellular respiration meaning
the controlled release of energy from organic compounds in cells
what is the equation for cellular respiration
C6H12O6 (glucose) +6O2 –> 6CO2 + 6H2O +energy
what organisms use cellular respiration
all living organisms use cellular respiration in different ways
- all organisms break down carbon compounds in oxidation rxn to produce ATP
what is anaerobic respiration
- cellular respiration that doesn’t need oxygen
- can produce alcoholic/acidic waste products (harmful)
equation for anaerobic respiration
glucose –> lactate + energy
glucose –> ethanol + CO2+energy
what is aerobic respiration
- cellular respiration that needs oxygen
- produces CO2 as waste
- gas exchange and cellular respiration are closely linked
aerobic respiration in humans
- oxygen used
- sugars/lipids used as substrates
- 30-32 ATP/ glucose
- CO2+ water is waste
- happens in cytoplasm and mitochondria
anaerobic respiration in humans
- no oxygen used
- glucose/other sugars used as substrates
- 2ATP/glucose
-lactate(lactic acid) as waste - occurs in cytoplasm only
why do humans sometimes used anaerobic respiration
- very quick, rapid generation of ATP maximizes power of muscle contractions
what happens to humans after using anaerobic respiration
- rxn produces lactate which humans have tolerance limit of
- after anaerobic respiration, body will require more oxygen to break down lactate for several mins
- demand for oxygen after anaerobic respiration is called oxygen debt
how can rate of cell respiration be measured
- oxygen uptake (most common)
- CO2 production
- consumption of glucose/other respiratory substrates
what is a respirometer
- any device used to measure respiration rate
- measures consumption of oxygen
what are the parts of a respirometer
- sealed container w organism/tissue
- sealed container with bead w/ same volume as organism
- alkali to absorb CO2
- capillary tube containing fluid connected to both containers
how does a respirometer work
- aerobic respiration turns 6O2 into 6 CO2, but CO2 is absorbed by alkali
- the liquid in the capillary tube is pulled to the side that uses oxygen
what is the general theory regarding temperature and rate of respiration
as the temperature increases, the rate of respiration increases
autotrophic meaning
organisms that makes energy-rich molecule
heterotrophic
organisms that obtain energy rich molecule
how do autotrophs use photosynthesis
they “fix CO2” to produce carbon based molecules (sugars, amino acids)
what are the 3 groups of photosynthetic organisms? what domain has no photosynthesizers?
photosynthetic groups: plants, eukaryotic algae, some bacteria
no photosynthesizers: archaea
what will plants optimize to compete for light
- height vs. structure
- leaf size vs. water loss
- type of pigment to wavelengths of light
lianas in the forest ecosystem
- climb trees for support and to reach light, no need for a trunk
epiphytes in the forest ecosystem
- grows on the branches and trunks of tree, roots need minimal soil
strangler epiphytes in the forest ecosystem
- climb up tree trunks and outgrows the tree branch, eventually killing tree (roots fight, canopy is overtaken)
shrubs and herbs in the forest ecosystem
- can survive off of light that reaches forest group with their large leaves
chemoautotrophs meaning
autotrophs that don’‘t need light to produce their own food
what does every food chain begin with
a photosynthetic organism that transforms light energy into chemical potential energy (sugars) except for chemoautotrophs
photosynthesis meaning
a metabolic pathway where Co2+ water are used to produce carbs and oxygen is a waste gas
photosynthesis equation
6CO2 + 6H2O –sunlight–> C6H12O6 + 6O2
photolysis meaning
- the separation of molecules by the action of light
- ex. the splitting of water molecules during photosynthesis
photolysis equation
2H2O –>4e- + 4H+ +O2
what happens to O2 waste during photolysis
- builds up in chloroplast which causes concentration gradient
- O2 diffuses out of chloroplasts–>cytoplasm–>extracellular space –> air
high frequency radiation in organisms
- many waves/unit time = a lot of energy
- can cause DNA damage
low frequency radiation in organisms
- low energy
- too low to be useful in living organisms
what is a pigment
a substance that absorbs some wavelengths of visible light
how do different pigments absorb light energy
- black absorbs all light
- ex. green absorbs all light but green (which it reflects), looking green to our eye
how do plants absorb light energy
absorbs useful light that contains energy needed for photolysis
- photos contain energy specific to wavelength–> if pigment absorbs just right amount of energy, it will absorb proton
why do plants look green
- main pigment: chlorophyll
- good at absorbing red + blue, just right amount of energy to excite chlorophyll
- green light reflects off
what is the absorption spectrum
- shows absorbance of different light by photosynthetic pigments
what is the action spectrum
- range of wavelengths of light used in light-dependent reactions
comparing graphs of absorption spectrum of chlorophyl and action spectrum
- follows the same trend
- suggests that chlorophyl is the most important photosynthesis pigment
drawing the absorption and action spectrum
x axis: wavelength (400nm-700nm)
absorption y axis: % absorption (0-100)
action y axis: relative amount of photosynthesis as % (0-100)
do all plants have the same action/absorption spectrum
- no, accessory pigments allow some plants to use different wavelengths
- ex. some plants in low light conditions (underwater) can use green wavelengths
why do leaves change colour in the fall
- some leaves have accessory pigments that are hidden when chlorophyl is active
- cooler temps break down the chlorophyl before the accessory pigments
what are the limiting factors of photosynthesis
- concentration of CO2
- light intensity
- temperature
way to measure rate of photosynthesis
- oxygen production
- CO2 uptake
- change in biomass
equation to find rate of photosynthesis
rate = change/time
weather condition that makes CO2 a limiting factor for photosynthesis
- when it’s dry
- stomata swells up to slow down water loss, but also allowing less CO2 diffusion
what is CO2 enrichment
- purposefully increasing CO2 levels in greenhouses
- when temp +light intensity are at optimal levels, increase inCO2 leads to a higher rate of photosynthesis
what are FACE experiments
- “free air carbon dioxide enrichment experiments”
- tests if pollution could increase plant growth
- circle towers that release CO2 and air are built into semi natural vegetation to increase CO2 conc.
glycosidic bond meaning
C-O-C bond formed by condensation reaction between hydroxyl groups
