Unit 2 review Flashcards
make up majority of cells dry weight. Will have components attached (functional groups) made of elements other than C and H
carbohydrates, lipids, proteins, nucleic acids
All have ratio of C:H:O as 1:2:1, have mono-, di-, and poly-, Function: to get you through until your next meal
carbohydrates
Fats, oils, waxes, phospholipids and steroids,
usually the smallest of the macromolecules
Lipids
what are lipids used as
long term energy storage (fats), water repellant for aquatic animals, insulation, cushioning for organs, hormones, and structural role in cells
of a substance able to be dissolved, especially in water
soluble
when are lipids soluble
NON-polar substances (a molecule where the electrical charges are distributed evenly across the molecule meaning there are no distinct positive or negative poles) - mostly due to non polar C-C and C-H bonds
complex lipids that make up cell membranes, major building blocks of all biological membranes, which protects the cell
phospholipids
A molecule that has both a hydrophilic (water loving) part called the head and hydrophobic (water fearing) part called the tail.
amphipathic (phospholipids are amphipathic with a hydrophilic head and two hydrophobic fatty acid tails)
what are the functions of proteins
enzymes, transport, structural, contraction, antibodies
what biological role do proteins have as structural
support
what biological role do proteins have as storage
store amino acids
what biological roles do proteins have in regards to enzymes
speed up chemical reactions
what biological roles do proteins have in regards to contractile
movement (muscle gets tighter or smaller)
what biological roles do proteins have for defense
protection against disease
what biological roles do proteins have for receptors
found in cell membranes and help transmit signals to other cells
what biological roles do proteins in regards to transport
help move substances into and out of the cell
what are proteins made of
amino acids
what are amino acids
organic compounds that have amino and carboxylic acid groups. They all have 3 groups in common around an alpha carbon. (amino group and carboxyl group connected to a side chain. 3 groups)
what is the primary structure of protein
amino acids
what is the secondary structure of proteins
alpha helixes and pleated/beta sheets
what is the tertiary structure of proteins
overall shape of single polypeptide chain (combo of pleated sheet and alpha helix)
what is the quaternary structure of a protein
the arrangement of multiple polypeptide chains to form a protein
what are nucleic acids
chemical compounds that serve as the primary information carrying molecules within cells
what are the two main types of nucleic acids
DNA and RNA
what is the concept that genetic info flows from DNA to RNA to protein
central dogma in biology
process by which chemical substances (nutrients) are acquired from the environment and used in cellular activities (work)
nutrition
must be provided to an organism from environment
essential nutrients
which category of essential nutrients: required in large quantities; play principal roles in cell structure and
metabolism. these are proteins, carbohydrates
macronutrients
which category of essential nutrients: required in
small amounts; involved in enzyme function
and maintenance of protein structure. These are manganese, zinc, and nickel for example
micronutrients
contain carbon and hydrogen atoms and are usually the products of living things (carbohydrates, lipids, proteins, and nucleic acids).
organic nutrients
atom or molecule that contains atoms other than carbon and hydrogen. metals and their salts, sulfate, ferric nitrate, sodium, gases, carbon dioxide, water
inorganic nutrients
must obtain carbon in an
organic form made
by other living
organisms (animals most microbes
heterotroph carbon source
– an organism that uses
CO2, an inorganic gas as its carbon source. not nutritionally dependent on other living things
Autotroph carbon source
which major nutritional type of energy source from electrons: gain energy from chemical compounds (may be auto- or hetero-)
chemotroph
chemotroph type that uses inorganic chemical
compounds (H2, H2S, etc.) “rock eaters”
lithotrophs
chemotroph type that uses organic chemical
compounds (sugars)
organotrophs
which major nutritional type of energy source from electrons: gain energy by absorbing light
phototrophs
use photosynthesis (light + water + CO2 = food)
photoautotrophs
Must obtain organic compounds
because they lack the genetic and
metabolic mechanisms to synthesize them
growth factors, essential amino acids, vitamins
Regulates molecules (except for water and gasses
like O2 and CO2 which can diffuse in and out
freely)
phospholipid bilayer of the cell (structure of the plasma membrane)
Serve as the gates to let desirable substances in
and push waste substances out
proteins -structure of the plasma membrane
The Movement of
Chemicals Across the Cell
Membrane
transport
does not require
energy; substances exist in a
gradient and move from areas of higher concentration to areas of
lower concentration
passive transport
diffusion of water
osmosis
requires a
carrier
facilitated diffusion
the net movement of anything generally from a region of higher concentration to a region of lower concentration
diffusion
excess hypertonicity (water leaves the cell)
can cause damage to the cell and destroy it. cells shrivel and may die.
excess hypotonicity (water rushes into the cell)
can cause damage to the cell and destroy it, cell may burst and die
transporters of a single substance, either in or out
uniporters
transporters of two substances at the same time
symporters
transporters of two substances, but in opposite
antiporters
Materials repelled by the membrane enter the
cell with help of membrane proteins. Do not require energy input to function moves down the concentration gradient. These helper membrane proteins are
channel proteins or carrier proteins
requires energy
and carrier proteins; gradient
independent
active transport
involves the use of chemical
energy, such as ATP, to drive the transport.
primary active transport
utilizes energy from a
proton motive force (PMF).
secondary active transport
An ion (charged) gradient that develops when the
cell transports electrons/protons
proton gradient
Uses energy from an energy-rich organic compound that is not ATP. also modifies the substance being transported during the process.
group translocation
aids in the uptake of sugar (the glucose can’t be removed once it is phosphorylated)
the phosphotransferase system in bacteria
bringing substances into the cell through a vesicle or phagosome
endocytosis
ingests non specific substances or
cells
phagocytosis
ingests liquids and the solutes within
pinocytosis
True or False: Receptor Mediated is a specific type
true
is defined not in terms
of increases in cell size but in terms of
an increase in the total number of cells
which occurs by cell division (in bacteria
usually via binary fission)
microbial growth
Cell duplicates its components and divides into two daughter cells via a septum which grows
between them to separate them, In actively dividing cells, DNA synthesis is continuous (vs. euk
cell cycle) and the chromosome is replicated shortly before division, The chromosome attaches to
the cell membrane and as it
grows it pulls the two
chromosomes into the daughter cells,
Binary Fission
which phase of growth: not increasing in number, rather they are metabolically active. growing in size, making new enzymes, using nutrients from the medium, producing energy. Bacteria use this time to get acclimated to the new environment.
Lag phase
which phase of growth: after adjustment, the MO grow at a logarithmic rate. Generation time is the time interval it takes for the number of MOs to double in number.
Log phase
can logarithmic growth go on forever?
NO! Medium contains a fixed amount of nutrients, space, oxygen, etc. (limiting
factors to a population)
As the bacterial number increases, they use up the resources of the medium
and are expelling waste into the medium
As the nutrients are used up the cells cannot make as much ATP and growth
slows and levels of
which phase of growth: rates of cell division equals the rate at which old cells die. less new cell growth due to used up nutrient supply. Increased death due to toxic waste materials and changes in pH and oxygen availability.
stationary phase
as the environment becomes less supportive and more toxic, most cells die. Cell number decreases at a log rate. Cells can undergo involution or a change in shape. Nutrient limitation will drive spore forming MO to form spores and metabolically active vegetative cells will die. 100 percent cell death is unlikely.
death phase
how do you measure bacterial growth
estimate the number of cells resulting from binary fission during a set period of time. expressed in terms of viable cells/mL of culture: standard plate count, direct microscopic or automated counts, turbidity
a single, viable (living) bacterium will give rise to a single colony on an agar plate. usually necessary to dilute your bacterial sample so it is possible to count your colonies.
standard place count
each single, viable bacteria spread on the agar will divide to form a colony. plate different dilutions to obtain a plate with a countable number of colonies per plate. you would then multiply countable colonies by your dilution factor to figure out how many bacteria are in your initial sample.
serial dilutions
culture placed onto an etched glass slide and the microorganisms are manually counted using a microscope. culture can also be put into a machine that will automatically count cells.
direct microscopic count
the cloudy appearance of media when bacterial growth is present. the amount of light that passes through the culture can be measured using a spectrophotometer. degree of cloudiness, reflects the relative population size
turbidity
are these environmental factors affecting bacterial growth physical or nutritional: pH, temp, oxygen, moisture, hydrostatic pressure, osmotic pressure, radiation
physical factors
are these environmental factors affecting bacterial growth physical or nutritional: fastidious, carbon sources, nitrogen sources, sulfur and phosphorous, trace elements, vitamins
nutritional factors
organism must have a
certain environmental condition
obligate, Ex: obligate aerobe
organism can adjust to
and tolerate the environmental
condition, but it can also live in other conditions
facultative, Ex: facultative anaerobe
- the pH at which microorganism
grows best
optimum pH
Many MO produce acids (lactic acid, pyruvic acid)
that makes the area more acidic and slows
growth by acting on the cell membrane (without
environmental buffers)
Classification of bacteria according to their
tolerance of acidity or alkalinity
pH
pH (.1-5.4)
acidophiles
pH 5.4 - 8
neutrophiles (most disease causing MO)
pH 8-11.5
alkaliphiles
Preferred temperature is
determined by
when enzymes function best
Like temps around 15-20 C
Obligate (die at temps above 20C)
Facultative (grow best under 20C, but
can grow at higher temps as well)
psychrophiles
Like temps around 25-40 C
mesophiles
Like temps around 50-60 C
Obligate (cannot grow at temps lower
than 37C
Facultative (grows best at higher
temps)
thermophiles
are looking to become stable and will do so by stealing an e- from another
molecule damaging cell components
superoxide O2 and hydrogen peroxide H2O2
Most cells have developed enzymes that
neutralize these chemicals:
superoxide, dismutase, catalase
– utilizes oxygen and can detoxify it
aerobe
does not utilize oxygen (but can live with it around)
anaerobe
requires only a small
amount of oxygen
microaerophilic
grows best at higher CO2
concentration than normally present in the
atmosphere (like ~5-10%, only 0.04% in air)
capnophile
Pressure from
standing water
hydrostatic pressure
Bacteria able to
withstand high
pressure are
barophiles (they die at atmospheric pressure because their enzymes require the high pressure to maintain the correct conformation of their enzymes
Solutes in environment can affect
water content of bacteria
plasmolysis
lots of solute in environment
less solute in environment
turgidity
used as a curing agent to
prevent bacterial growth
salt
require moderate to
large amounts of salt for life – up
to 30%!
halophiles
do not require high
concentration of solute but can tolerate it when it occurs
osmotolerant
commensal member
benefits, other member neither harmed
nor benefited (+/0)
commensalism
parasite is dependent and
benefits; host is harmed (
parasitism
members cooperate to
produce a result that they could not
do alone
synergism
actions of one organism
affect the success or survival of others
in the same community (competition)
antagonism
result when organisms
attach to a substrate by some form of extracellular matrix that binds
them together in complex
organized layers
biofilms
what are the metabolic processes rules
cells need nutrients, require energy from light, energy is often stored in ATP, enzymes are needed for both catabolic and anabolic reactions, macromolecules are made, cells grow by assembling these macromolecules into cellular structures, cells divide in two once they have doubled in size.
sum of all the chemical processes carried out by living organisms
metabolism
synthesis of more complex molecules from simpler molecules. growth, reproduction, repair of damaged cellular structures. requires energy
anabolism
breaking down of complex molecules into simpler molecules. provides a source of energy used for movement, transport, and synthesis of complex molecules
catabolism
How is energy harvested/captured from the
breaking down of complex molecules?
– At a cellular level large molecules such as
glucose are broken down via many small steps
so energy can be captured and little is lost or
wasted
* This energy capture is in the form of
electron transfer…energy is stored in the
chemical bonds of ATP, NADH, and FADH2
* This energy is released when these bonds
are broken
The energy required for all reactions
to begin (exergonic AND endergonic)
[initial push to get out of bed in the
morning – then go through rest of the
day]
activation energy (E a)
higher Ea means
slower reaction rate
Where does Activation energy
come from?
heat energy from surroundings. heat increases molecule motion, causing higher chance of collisions of reactants.
provide a surface (active site) to bring
molecules (substrate) in the correct orientation
for the reaction to occur to create the product
enzymes
Place on the enzyme where substrate(s) are brought
together to create product(s). very specific to its substrate molecules
enzyme active site
– transported extracellularly, where they
break down large food molecules or harmful chemicals
exoenzymes
retained intracellularly and function
there
endoenzymes (most enzymes are endoenzymes)
protein
component of enzyme
apoenzyme
nonprotein,
organic molecule
loosely bound to
enzyme, brings helpful
pieces for reaction
coenzyme
inorganic ion
– Improve the fit of the
substrate and enzyme
– Minerals
cofactor
how does a cell stop enzymes from always pumping out product?
inhibition
Depends entirely on concentration of inhibitor in relation to concentration of substrate
* Reversible inhibition if inhibitor falls out of active site normal substrate can easily fit in
* Most inhibition is irreversible as the Enzyme is destroyed
competitive inhibition
Reversible, noncompetitive
* Seen in many metabolic pathways to avoid making
product the cell already has enough of so resources
can be shifted elsewhere to make a product the cell
feedback inhibition
- A build up of product on one side will
push the reaction towards the
substrates and vice versa - Using up the product in a subsequent
reaction will drive the reaction towards
product
concentration
– Binds to enzymes that repair breaks in
peptidoglycan cell wall during cell growth
cell lysis
penicillin
– Disrupt an enzyme necessary for folic acid
synthesis (an important coenzyme for many
other enzymes)
– Without it, enzyme activity is halted and
growth is disrupted
– Humans are not affected by sulfa drugs
because we do not synthesize folic acid, rather
we must get it via diet
sulfa drugs
Metabolic “battery”
* Hydrolysis = breaking ATP ADP
* ATP utilization and replenishment is a constant cycle in active
cells
* ATP generation is the goal of metabolism!
Adenosine Triphosphate: ATP
ATP can be formed by three different
mechanisms:
substrate level phosphorylation, oxidative phosphorylation, photophosphorylation
Which mechanism of formation of ATP: – transfer of phosphate group from a phosphorylated compound (substrate) directly to ADP
substrate level phosphorylation
Which mechanism of formation of ATP: – series of redox
reactions occurring during respiratory pathway
generates about 90% of cell’s ATP
oxidative phosphorylation
Which mechanism of formation of ATP: – ATP is formed utilizing the
energy of sunlight and redox reactions
photophosphorylation
- Coenzyme, electron carrying molecule
- Carries e- to be used in fermentation or in
the electron transport chain (“electron
taxi”) - NAD (oxidized form without an e-) is in
limited supply and must be available for
glycolysis to proceed
NAD +/ NADH
Second coenzyme and electron carrying
molecule (FADH2 Flavin adenine
dinucleotide) is used in the electron
transport chain
– FAD+ is oxidized form ; FADH2 is reduced form
(accepts 2 e- and 2 H)
FAD +/ FADH2
the loss or removal of electrons
corresponding to loss of energy
oxidation
gain of electrons corresponds
to gain of energy
reduction
what is it called when a reduction oxidation reaction happens together.
a REDOX reaction
a chain of chemical reactions
mediated by protein enzymes
– Anabolic builds up
– Catabolic breaks down
– The product of one set of chemical reactions is the
substrate for the next
metabolic pathway
Occurs in Cytoplasm of cells
* 10 step process mediated by enzymes to break down glucose (6 Carbon Sugar) into two molecules of pyruvate
* Used by autotrophic and heterotrophic organisms
– Autotrophs make their own glucose via
photosynthesis and then break it down while
heterotrophs get it from an outside source and then break it down.
* Does not require Oxygen but can happen in its presence (anaerobic process)
glycolysis
what happens during glycolysis?
A 6C-molecule (glucose) is broken down into two 3Cmolecules (pyruvate)
* ATP energy is used to start the reaction via substrate
level phosphorylation
* Transfer of 2 e- to the coenzyme NAD to produce
NADH
* Energy is captured in ATP
A phosphate group is transferred to
each end of the glucose molecule for
two reasons:
– Increases the energy of glucose to start
glycolysis (overcomes activation energy)
– This modification is a way of keeping
glucose from leaking back out of the cell
via glucose transporters
* Typically there is more glucose inside a cell
than outside (Remember diffusion?)
After glycolysis further metabolism
of pyruvate in the absence of oxygen
– No ATP but fermentation results in the removal of
e- from NADH freeing the NAD molecule to be
used again in glycolysis (recycle!)
* Many different pathways (Ex:
Homolactic acid fermentation and
alcoholic fermentation)
fermentation
Used by animals, fungi,
and some bacteria
Red blood cells, bacteria in
yogurt, muscle cells that
have run out of oxygen to
use. use to make cheese, yogurt, and buttermilk, pepperoni, pickles, sourdough, bread. Only 2 ATPs are produced.
lactic acid fermentation
Used by bacteria and yeast
* Again, only 2 ATPs are produced
* Pyruvate is reduced to make ethanol and releases CO2
* Process is used to make bread, beer, and wine
alcoholic fermentation
– Uses 2 ATP, yields 4 ATP (2 net ATP) and 2NADH
– In the presence of Oxygen the NADH will carry
the e- to the electron transport chain
– In the absence the NADH will be recycled to
NAD to replenish the supply and keep the
glycolysis wheel turning
glycolysis
– Does not yield any ATP but important for
recycling NADH (and the byproducts that are
released!)
fermentation
Where do the products of
glycolysis go?
- In the presence of oxygen, the Carbon
molecules go to the Doorway step to
prepare them for the Kreb’s Cycle. - The NADH goes to the Electron Transport
Chain.
Occurs in cytoplasm of prokaryotes and
mitochondria matrix in eukaryotes
pyruvate transformation
- In cytoplasm of prokaryotes, or mitochondria matrix of
eukaryotes - Further metabolizes glucose following glycolysis
- The Citric Acid Cycle (CAC), A.K.A. Kreb’s Cycle, A.K.A. TCA
cycle
Krebs cycle
which step in the krebs cycle: converts pyruvate to Acetyl-CoA
doorway/preparation step
which step in the krebs cycle: Acetyl groups are oxidized to carbon dioxide in 8 steps
oxidation of carbon
which step in the Krebs cycle: Hydrogen atoms are removed and their e- are
transferred to coenzymes NAD+ and FAD+ NADH
and FADH2
transfer of e- to coenzymes
which step in the krebs cycle: Addition of a phosphate (GDP + P = GTP) occurs
directly via a reaction of the Kreb’s cycle
* GTP is easily transferred to ATP so we can count
GTP as a gain of ATP
substrate level phosphorylation
the process leading
to the transfer of electrons from
substrate to final electron acceptor. Series of oxidation and reduction reactions
* Transfers e- from a level of higher energy to one of lower energy (cascade)
* Accepts e- from an e- donor and passes them to an e- acceptor
* Conserves energy from the e- transfer for ATP synthesis
Electron Transport Chain
How does the ETC make ATP
chemiosmosis- conversion of ADP + P to ATP via ATP synthase (an enzyme).
classified as an enzyme, a
motor, and an ion channel
* Protons enter at the intermembrane
space and cause the pump to spin which
causes ADP to be phosphorylated into ATP
* The ETC and ATP synthase are responsible
for 90% of aerobic ATP production
ATP synthase
what goes in for ETC
– 10 pairs of e- from NADH
– 2 pairs from FADH2
– 6 O2 (Aerobic respiration)
what goes out for ETC
– 34 ATP
– 6 H2O
where do metabolic reactions take place for glycolysis
prokaryote: cytoplasm, eukaryote: cytoplasm
where do the metabolic reactions for doorway to krebs cycle take place
prokaryote: cytoplasm, eukaryote: matrix mitochondria
where does the metabolic reaction for krebs cycle take place
prokaryote: cytoplasm, eukaryote: matrix mitochondria
where do the metabolic reaction for ETC take place
prokaryote: plasma membrane, eukaryote: inner membrane mitochondria
– Broken down by
beta oxidation (4
step process)
– Product is acetylCoA which then
feeds into Kreb’s
cycle
fat
Hydrolyzed into
amino acids
– Products vary and
can enter
glycolysis,
fermentation, or
the Kreb’s cycle
proteins
Relationship where two organisms live in close proximity, one benefits while the other may benefit, be harmed, or not be affected at all
symbiotic
completely assembled, functional enzyme
holoenzyme
changes shape of enzyme so it cannot bind to substrate
allosteric inhibitor
