Exam 2 - Part 1 Flashcards
what is the combination of all reactions in the cell?
metabolism
what is catabolism?
- fueling reactions
- energy conserving reactions
- provide ready source of reducing power (electrons)
- generate precursors for biosynthesis
- energy comes in, breaks it down, and is then used
anabolism
- the synthesis of complex organic molecules from simpler ones
- requires energy from fueling reactions
- taking starch, turning it into glucose, and eventually using it to make ATP
- energy from catabolism fuels this reaction
what is a fueling reaction?
- catabolism
- reaction in which you break down molecules and extract energy from them
what is the energy currency of the cell?
ATP
where does the energy fueling the cell come from?
building blocks
what are precursors?
building blocks, like amino acids or lipids
chemical work
synthesis of complex molecules
- build polymers
transport work
take up nutrients, eliminate waste, and maintenance of ion balances
- pass through the cell membrane
mechanical work
cell motility and movement of structures within cells
- moving molecules within a cell, chromosomes during meiosis
what type of reaction is anabolism?
redox reaction
- the source of energy is high reduced (more electrons and more energy)
- electrons are extracted from this molecule making it oxidized (losses electrons)
- example: NAD becomes NADH
thermodynamics
- a science that analyzes energy changes in a collection of matter called a system (like a cell)
- all other matter in the universe is called the surroundings
what is the first law of thermodynamics?
- energy can be neither created nor destroyed
- total energy in the universe remains constant
- however energy may be redistributed either within a system or between the system and its surroundings
what is the second law of thermodynamics?
physical and chemical processes proceed in such a way that the disorder of the universe increases to the maximum possible
entropy
amount of randomness (disorder) in a system
- related to the second law of thermodynamics
free energy
amount of energy at standard conditions of concentration, pressure, temperature, and pH
what is the role of ATP in metabolism?
exergonic breakdown of ATP is coupled with endergonic reactions to make them more favorable
the more negative G (free energy) is, what happens to energy?
the more energy there is available outside
- reaction can occur without outside energy
- endergonic
the more positive G (free energy) is, what happens to energy?
the reaction is not favorable and requires energy
- endergonic reaction
what kind of a reaction is ATP?
- ATP releases energy by releasing a high energy phosphate to become ADP
- endergonic reaction, it has excess energy to give
where does ATP come from?
- metabolic activity
- fermentation, respiration, photosynthesis
- extract from a source to make ATP, which turns into energy
Redox reactions
- involved in many metabolic processes
- electron carriers are often used to transfer electrons from an electron donor to an electron acceptor
- types: ATP to ADP, PEP (intermediate in glycolysis) to 1,3-biphosphate, glycerite
what happens when electrons are transferred from a donor to an acceptor?
- can result in energy release which can be conserved and used to form ATP
- the more electrons a molecule has, the more energy rich it is
oxidizing reaction
- one electron is donating
reducing reaction
one electron is accepting
an electron acceptor and donor are what?
a conjugate redox pair
what products are made from glucose?
glucose (C6H12O6) becomes CO2 and H2O
- makes 38 ATP
what is the standard reduction potential?
- equilibrium constant for an oxidation reduction reaction
- a measure of the tendency of the reducing agent to lose electrons
the more negative the standard reduction potential is
the better the electron donor
the more positive the standard reduction potential is
the better the electron acceptor
the greater the distance between the standard reduction potential, and the donor and acceptor
- the more negative G is
where are electron carriers in chemmoorganotrophs?
- located in plasma membranes of bacteria and archaea
- located in mitochondria membranes in eukaryotic cells
what are some examples of electron carriers?
NAD, NADP, FAAD, Coenzyme Q (CoQ), and cytochromes
what is the first electron carrier in the ETC?
NAD
- most negative standard electron potential
what is the last electron carrier in the ETC?
cytochromes
what is the difference between an electron carrier and an electron acceptor?
- an electron carrier has a temporary hold on the e-
- an electron acceptor will permanently accept the e-
electron transport chain
- electron carriers are organized into the ETC
- first electron carrier has the most negative standard electron potential
- in mitochondria/chloroplast in euks
- plasma membrane in pros
- they are membrane bound
- some only deal with e- others can pump out protons as well
- FADH enters further into the system
what do enzymes do?
- carry out reactions at physiological conditions
- enzymes speed up the rate of a reaction to reach equilibrium quicker
- enzymatic activity: when a protein becomes quaternary it is functional
how can enzymes act as protein catalysts?
- high specificity for the reaction catalyzed and the molecules acted on
- increases the rate of a reaction without being permanently altered
substrates
reacting molecules
products
substances formed by reaction
what are enzymes made of?
some can be made of solely one of more polypeptides
others can have nonprotein components
apoenzyme
protein component of an enzyme
cofactor
nonprotein component of an enzyme
- prosthetic group: firmly attached
- coenzyme: loosely attached, can act as carriers/shuttles
holoenzyme
apoenzyme and a cofactor
activation energy
- energy required to form transition state complex
- enzyme speeds up reaction by lowering the standard potential energy
what impacts enzyme activity?
- substrate concentration
- pH
- temperature
denaturation
loss of enzyme’s structure and activity when temperature and pH rise too much above the optima
competitive inhibitor
- directly competes with binding of substrate to active site
- control activity of the enzyme by substrate level
- more substrate can be added to overcome the inhibitor
noncompetitive inhibitor
- binds enzyme at site other than active site
- changes enzyme’s shape so that it becomes less active
examples of competitve inhibitor
PABA (substrate) is used to make nucleic acids in bacteria, if sulfa drug is added (inhibitor) it can inhibit PABA and prevent bacteria from replicating
regulation of metabolism
- important for conservation of energy and materials
- maintenance for metabolic balance despite changes in the environment
what are the three major mechanisms for metabolism?
- metabolic channeling
- regulation of the synthesis of a particular enzyme (transcriptional and translational)
- direct stimulation of inhibition of the activity of critical enzyme (post-translational)
metabolic channeling
- differential localization of enzymes and metabolites
- compartmentation (differential distribution of enzymes and metabolite among separate cell structures or organelles)
- can generate marked variations in metabolite concentrations
what are two important reversible control measures in post-translational regulation of enzyme activity?
- allosteric and covalent regulation
allosteric
add a molecule to a protein and change its function
covalent
permanent change to a protein, changes the shape
feedback inhibition
- also called end-product inhibition
- inhibition of one or more critical enzymes in a pathway regulates entire pathway
aerobic respiration
final electron acceptor is oxygen
- takes an energy source and electron source and goes through the central pathway of metabolism (glycolysis and krebs) applies to anaerobic too
- exogenous reaction because the source must come from the outside, applies to anaerobic
anaerobic respiration
- final electron acceptor is different exogenous acceptor such as NO3-, SO4 2-, CO2, Fe 3+, or SeO4 2-
- in respiration, as electrons pass through the electron transport chain to the final electron acceptor, a proton motive force is generated to synthesize ATP
fermentation
- uses an endogenous electron acceptor - usually an intermediate of the pathway used to oxidize the organic energy source
- does not involve the use of an ETC or PMF, by product is the e- acceptor
- ATP synthesized by only a substrate level phosphorylation
- only goes through glycolysis
- absence of oxygen
- minimal ATP made - 2
- pyruvate makes lactic acid or alcohol
- both prokaryotes and eukaryotes can ferment
what are amphibolic pathways?
- function both as catabolic and anabolic pathways
- important ones: embden-meyerhof, pentose, and TCA cycle
pentose phosphate pathway
an amphibolic pathway that can operates aerobically/anaerobically oxidation steps produce NADPH, which is needed for biosynthesis
- provides precursors for making nucleic acids for biosynthesis
- not really used for ATP
microbial fermentations
- oxidation of NADH produced by glycolysis
- pyruvate or derivative used as endogenous electron acceptor
- substrate only partially oxidized
- oxygen not needed
- oxidative phosphorylation does not occur
TCA cycle
- citric/krebs
- a key source of carbon skeletons for use in biosynthesis
- after pyruvate is produced
- amphibolic
- 2 carbons enter from acetyl CoA
- 2 carbons come off as CO2
- synthetic process
- broken down to extract energy
- ATP made from GTP
for each acetyl-CoA molecule oxidized, the TCA cycle generates:
- two molecules of CO2
- 3 molecules of NADH
- one FADH
- one GTP
what is the chemiosmotic hypothesis?
- most widly used hypothesis to explain oxidative phosphotylation
- ETC organized so protons move outward from the mitochondrial matrix as electrons are transported down the chain
- protonexpulsion during electron transport results in the formation of a concentration gradient of protons and a charge gradient
- the combined chemical and electrical potential difference make up the proton motive force (PMF)
oxidative phosphorylation
- process by which ATP is synthesized as the result of electron transport driven by oxidation of a chemical energy source
- only 2 ATP molecules synthesize directly from oxidation of glucose to CO2
- most ATP made when NADH and FADH2 are oxidized in ETC
electron transport chain
- series of electron carriers that operate together to transfer electrons from NADH and FADH2 to a terminal electron acceptor
- electrons flow from carriers with more negative standard potential to carriers with positive standard potential
- as electrons transferred energy released
- in eukaryotes the ETC carriers are within the inner mitochonidrial membrane
what is the importance of the proton motive force?
- PMF drives ATP synthesis
- diffusion of protons back across the membrane (down gradient) drives formation of ATP
- ATP synthase: enzyme that uses PMF down gradient to catalyze ATP synthesis
- can also be used in flagella movement or to transport molecules across the membrane
what is the theoretical maximum tield of ATP during aerobic respiration?
38 ATP molecules
anaerobic respiration
- uses electron carriers other than O2
- generally yields less energy less energy because E0 of electron acceptor is less positive than E0 of O2
chemolithotrophy
- electron released from energy source which is an inorganic molecule transferred to terminal electron acceptor by ETC make ATP via oxidative phosphorylation
- have ecological importance
- several bacteria and archaea oxidize hydrogen
- they are metabolically flexible; use inorganics for energy or use organics for carbon
what are the three major groups of chemolithotrophs?
- hydrogen sulfide (H2S)
- sulfur (S)
- thiosulfate (SO2O3 2-)
- nitrifying bacteria oxidize ammonia to nitrate
dissimilatory nitrate reduction
- use of nitrate as terminal electron acceptor
- the anaerobic reduction of nitrate makes it unavailable to cell for assimilation or uptake
denitrification
- reduction of nitrate to nitrogen gas
- in soil, causes loss of soil fertility
nitryfing bacteria
- oxidize ammonia to nitrate
sulfur-oxidizing bacteria
ATP can be synthesized by both oxidative phosphorylation and substrate level phosphorylation
photosynthesis
energy from light trapped and converted to chemical energy
light reaction
- photosynthesis
- light energy is trapped and converted to chemical energy
dark reaction
- photosynthesis
- energy produced in the light reactions is used to reduce CO2 and synthesize cell constituents
oxygenic photosynthesis occurs in which organisms?
- eukaryotes
- cyanobacteria
anoxygenic photosynthesis occurs in which organisms?
- all other bacteria besides cyanobacteria
light reaction in anoxygenic photosynthesis
- H2O not used as an electron source, therefore O2 is not produced
- only one photosystem involved
- uses different pigments and mechanisms to generate reducing power
- carried out by phototrophic green bacteria, phototrophic purple bacteria, and heliobacteria
bacteriohodopsin-based phototrophy
- some archaea use a type of photography that involved bacteriorhodopsin a membrane protein which functions as alight driven proton pump
- a proton motive force is generated
- an ETC is not involved
what are the components of anabolism?
- energy from catabolism is used for biosynthetic pathways
- using a carbon source and inorganic molecules, organisms synthesis new organelles and cells
- antibiotics inhibit anabolic pathways
- great deal of energy
- metabolism is carefully regulated
turnover
continual degradation and resynthesize of cellular constituents by nongrowing cells
what do polysaccharides use for catabolism?
- sugars
- glycogen
- starch
- PHB
what do proteins use for catabolism?
- amino acids
- deamination
what do lipids use for catabolism?
- triglycerides
- beta oxidation
transcription
yields a ribonucleic acid (RNA) copy of specific genes
translation
uses information in messenger RNA (mRNA) to synthesize a polypeptide
what is the nucleic acid structure?
- polymer of nucleotides
- contains the bases adenine, guanine, cytosine, and thymine
- sugar is deoxyribose
- molecule is usually double stranded
what is the base pairing order?
- A and T go together and are bonded by 2 hydrogen bonds
- G and C are bonded together by 3 hydrogen bonds
what is the RNA structure?
- polymer of nucleotides
- contains bases adenine, guanine, cytosine, and uracil
- sugar is ribose
- most RNA are single stranded
- three main different types: mRNA, tRNA, rRNA
how is DNA configured in most archaea and bacteria?
- supercoiled
- DS
- circular
how is bacteria organized?
with the chromatin like protein
what is the configuration of DNA in eukaryotes?
- DNA is highly organized
- chromatin is associated with small basic proteins called histones
what is the combination of DNA and proteins?
nucelosome
what DNA organization is archaea most similar to?
eukaryotes
DNA replication
- complex process involving numerous proteins which help ensure accuracy
- the 2 strands separate each serving as a template for synthesis of a complementary strand
- synthesis is semiconservative, each daughter cell obtains one old and one new strand
DNA replication in bacteria
bidirectional from a single origin replication
- archaea have more than one origin
lagging strand
synthesized in short fragments call Okazaki fragments
- a new primer is needed for the synthesis of each okazaki fragments
proofreading
- carried out by DNA polymerase 3
- removal of mismatched base from 3’ end of growing strand by exonuclease activity of enzyme
- this activity is not 100% efficient
termination of replication
- replication stops when replisome reaches termination site on DNA
- topoisomerases temporarily break the DNA molecules so the strands can separate
what is a gene?
- the basic unit of genetic information
- defined as the nucleic acid sequence that codes for a polypeptide, tRNA or rRNA
- linear sequence of nucleotides with a fixed start point and end point
- codons are found in RNA and code for single amino acids
reading frame
organization of codons such that they can be read to give rise to a gene product
template strand
- directs RNA synthesis
- is read in the 3’ to 5’ direction
promoter
- located at the start of the gene
- is the recognition/binding site for RNA polymerase
- functions to orient polymerase
leader sequence
transcribed into mRNA but is not translated into amino acids
- shine delgarno sequence
- begins with AUG
what are oxidation reactions?
- source of energy is highly reduced
- the more electrons, the more energy
- this source is used to extract electrons
- glucose is highly oxidized because it is a major source of electrons
what are reduction reactions?
- from the energy made in an oxidation reaction
- another molecule will pick up the electrons from the molecule that was oxidized
- for example, NAD becomes NADH
what can reactions be?
- cyclic, linear
- every reaction has an enzyme to catalyze it
post-translational activity
- protein is made and a group is added
- allosteric and covalent
- can change function or shape
- can be reversible
energy sources
- chemical = organic or inorganic molecule
- photo = light source, photosynthetic
carbon sources
- auto = fixes CO2 from the air
- hetero = break down of organic molecules
electron sources
- organo = organic molecules
- litho = inorganic molecules
substrate level phosphorylation
- compound of a high energy molecule is used to make another high energy compound
- the phosphorous combined with ADP to make ATP comes from the break of PEP, used in PTS in group translocation
central pathway of metabolism
- glycolysis (6 carbons)
- pyruvate (3 carbons)
- acetyl CoA, helps pyruvate enter the krebs (2 carbons)
- krebs, 2 cycles, all carbon is gone
- large molecule is broken down, purpose is to oxidized highly reduced polymers
Embden-Meyerhof pathway
- glycolysis
- at the end of glycolysis, 2 ATP is made
- has substrate level phosphorylation to make ADP into ATP
- amphibolic
Enter-Doudoff pathway
- makes only 1 ATP
- glucose to pyruvate
- also makes NADH to NADPH
- not amphibolic
primary producers
- uses CO2 from organic or inorganic sources to make electrons
phototrophy
chemical energy from glucose
what cycle do polysaccharides use?
glycolysis
what cycle do nucleic acids use?
glycolysis
what cycle do proteins use?
glycolysis and krebs
what cycle do fatty acids use?
glycolysis
what cycle do lipids use?
CoA
what is the flow of genetic information?
- central dogma: DNA is copied by RNA, RNA is used for protein synthesis
- replication yields two copies
- tRNA brings amino acids to make protein
what molecules are linked together in DNA and how many hydrogen bonds are there?
- G and C, 3 hydrogen bonds
- A and T, 2 hydrogen bonds
purine
G and A
pyridine
C and T
major grooves
used to grab and unwind the DNA
what are domains?
- a region on DNA that proteins use to interact wit DNA
- zinc finger and leucine zipper
- identify proteins capable of binding with DNA
- examples of these proteins are repressors, inducers, DNA and RNA synthesizers
GC content
- hard to break the bond
- there are more GC than AT
mRNA
codon for amino acids
tRNA
bring amino acids to ribosomes
- contain anticodon
rRNA
ribosomal, interaction between ribosome and mRNA
DNA replication
- every cell gets a copy, going to a daughter cell
- DNA is supercoiled and needs to be released
- the ORI opens the DNA
- DNA replication goes in the 5’ - 3’ direction, but can be synthesized the other way, just more steps involved
directional with 2 replication forks
DNA polymerase
- synthesizes the DNA
- has to start with a primer (made of RNA) for DNA pol to bind
- 5’ - 3’ direction is continuous
lagging strand
- DNA that is synthesized in the 3’ -5’ direction
- has to be added in pieces and synthesized with a new primer every time
- has Okazaki fragments
replisome
- complex that opens DNA
- places the primer
- replicates DNA
Shine-Delgarno sequence
- where the ribosome recognizes and binds to rRNA
- codon always starts with TAC
RNA polymerase
- sigma factor recognizes the promoter
- binds to the -10 or -35 region to open DNA
what is the process of transcription?
- sigma factor binds to DNA, flags down RNA pol. the sigma factor recognizes a promoter, which is where RNA pol can bind and open the DNA
- elongation occurs
- termination occurs intrinsically or rho dependent
- in prokaryotes, one mRNA can make multiple genes and make different polypeptides
transcription in eukaryotes
- similar process, expect there must be removal of introns
- has to move out of the nucleus and into the cytoplasm
- post-transcriptional = a guanine cap and poly A tail is added before moving into the cytoplasm
genetic code
- 3 base pairs makes one amino acid
- 64 possibilities = 61 code for amino acids, but 3 are stop codons
- AUG is always first
- UGA, UAA, and UAG are stop codons
- 1 amino acid can have multiple codons
translation in bacteria
- no post-transcriptional modification
- as the RNA is made, ribosomes can jump onto the strand and make proteins.
- multiple ribosomes can be replicating at the same time, making many polypeptides at a time, this is why bacteria grows so fast
- transcription and translation are coupled in prokaryotes
