Bio 251 - Exam 2

Front 1

Metabolism

Back 1

- how cells use and make energy

- similar in all living things

- FROM energy source TO usable forms of energy

Catabolic pathways break down complex molecules and release energy

Anabolic pathways build complex molecules and consume energy

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Exergonic reaction




Endergonic reaction

Back 2

-energy out, energy released

-energy in, energy requiring

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ATP, adenosine triphosophate

Back 3

- a cell's usable form of energy; "energy currency"

- made of ribose (sugar), adenine, and 3 phosphate groups

- when a phosphate group is removed, a large amount of energy is released

-- ATP is then used to power endergonic rxns such as synthesis of a protein or large polysaccharide cells try to capture energy released from exergonic reactions so that they can use it to make ATP

Front 4

Redox rxns

Back 4

Energy is released when electrons at higher energy are removed from one molecule and transferred to a different molecule to which they are bound more tightly (and thus have less energy)

Oxidized is a molecule which has lost electrons, reduced is a molecule which has gained electrons

Front 5

NAD+ (oxidized)

NADH (reduced)

nicotinamide adenine dinucleotide

Back 5

- electron acceptor and electron carrier

Front 6

Cell respiration

Back 6

the slow incremental breakdown of biological molecules necessary for ATP production

does not require oxygen for some organisms

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What is the primary source of energy used in cell respiration?

Back 7

Carbohydrates, most commonly glucose (6C)

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What are the three stages of cell respiration?

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-GLYCOLYSIS: a molecule of glucose is partially digested into two smaller molecules and some of the released energy is captured as NADH; some ATP is made

-KREBS CYCLE: the oxidation of these two moleculesis completed, and more energy-carrying molecules (such as NADH) are formed; some ATP is made

ELECTRON TRANSPORT: most ATP is made in this step; all of the energy carriers formed in the above stages are oxidized, molecules such as oxygen are reduced, and the released energy is used to produce ATP

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Glycolysis

Back 9

-common to prokaryotic and eukaryotic cells alike

-first steps: ENERGY REQUIRING (endergonic). ATP is hydrolyzed, provides energy for next step.

-glucose (6C) is cleaved into two 3C compounds. --both molecules are oxidized; NAD+ is reduced to NADH

-both molecules eventually become pyruvate; highly exergonic steps are coupled to the synthesis of ATP from ADP and phosphate

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Krebs Cycle

Back 10

-pyruvate was converted from 3C to 2C shortly before Krebs, where the third C was released as CO2, and a molecule of NAD+ is reduced to NADH

-2C compound joins a 4C compound to form a 6C compound

-6C compound is oxidized in a series of steps back to 4C, losing two Cs released as CO2 and two NAD+ reduced to NADH

-in one step, FAD is reduced to FADH2

-ATP is made in one step as well

-at the end, both pyruvates will have been completely oxidized

-most energy from glucose molecule is now present as NADH and FADH2

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Electron Transport

Back 11

- the first components of the chain oxidize NADH or FADH2

- electrons pass through the entire chain in redox reactions that end once they are passed to a final electron acceptor

-the final electron acceptor, now reduced by the electrons that have passed down the chain, is released as waste

-as electrons pass down chain, this supplies energy to pump protons (H+) across the membrane.

-the buildup of protons supplies energy for ATP synthesis via a proton gradient (higher concentration of protons on one side of the membrane vs the other)

-the protons flow back to the cytoplasm (prokaryotes) or mitochondrial matrix (eukaryotes) through ATP synthase, releasing energy and spinning the synthase, forming ATP in the process.

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Where do you find the ETC in prokaryotes?

In eukaryotes?

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- embedded in the plasma membrane

-inner mitochondrial membrane

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Oxygen as a final electron acceptor

Back 13

-oxygen accepts electrons released by NADH or FADH2 at the beginning of the electron transport chain, being reduced to H2O (water=waste product)

-aerobic respiration requires oxygen as a final electron acceptor

-anaerobic microorganisms rely on other final electron acceptors, such as sulfate (SO42-) and nitrate (NO3-); CO2 can be used as well, being reduced to methane

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Incomplete glucose oxidation

Back 14

... results in fermentation

Front 15

Fermentation

Back 15

With a final acceptor, NADH is oxidized in ETC, resulting in ATP synthesis.

Without a final acceptor, the cell regenerates NAD+ by oxidizeing NADH and reducing pyruvate; the reduced form of pyruvate being released as waste, or fermentation waste product

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The "safety net" (Fermentation)

Back 16

Although some cells can get by on the small amounts of ATP made in glycolysis, fermentation is how cells "get by" until a final elecetron acceptor becomes available again

Some cells can live off of fermentation indefinitely

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Examples of fermentation waste product

Back 17

Lactate; animal's muscle cells. pyruvate reduced to lactate

Ethyl alcohol: yeast cells. pyruvate reduced to ethyl alcohol, with a release of CO2

--> this fermentation allows for baking and brewing

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Pasteur & fermentation

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- found that yeast released alcohol as metabolic waste in the absence of oxygen

-discovered that if certain bacteria entered wine, they competed w/ yeasts for sugar, converting it into acetic acid (sour)

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Food items aided by fermentation

Back 19

Bread. anaerobic environment caused by dough. S. cerevisiae is used (fungus). ethanol evaporates as bread bakes.

Wine. grape juice (must)=sugar source. S. Cerevisiae

In foods, lactic acid produced as a waste product of fermentation contributes to low pH; protects from spoilage

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Chloroplasts and Mitochondria

Back 20

-involved in a cell's produtction and use of energy

-in chloroplasts, CO2 and H2O are converted into sugar, using the energy found in sunlight (PHOTOSYNTHESIS), found in cells in leaves and stems of plant, found in algae

-mitochondria only found in a few eukaryotic cells

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Structure of Chloroplasts and Mitochondria

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- double membrane (stroma in chloroplast, matrix in mitochondria)

-in chloroplasts, there are stacks of membranous vesicles within the stroma called thylakoids

-structure= resemble bacterial cells; own DNA; produce own proteins; evidence for ENDOSYMBIOSIS

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Cyanobacteria

Back 22

-photosynthetic; photosynthetic pigments

-contributed to abundance of oxygen in atmosphere, making aerobic life possible on Earth

-release oxygen in aquatic environments, remove nitrogen from atmosphere and convert it into a form usable by plants (nitrogen fixation)

Front 23

Autotrophs

Back 23

-self-feeders; make their own food; necessary resources to do so; green plants and many prokaryotes

-gain energy through either a metabollic pathway that uses light (photoautotrophy( or one that ignores it (chemoautotrophy)

Front 24

Photoautotrophs

Chemoautotrophs aka lithotrophy aka chemolithotrophy

Back 24

convert the energy in light to ATP; pigments that absorb photons; photolysis of H20 or H2s supplies electrons

use chemical energy in certain molecules to make ATP; extreme environments; rock eaters; electrons derived fromoxidized inorganic compounds/elements. Fe2+, H2, H2S, NH4+, NO2-

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Photosynthesis, used by Photoautotrophs

Back 25

the ability to create biological molecules out of carbon dioxide and hydrogen-containing compounds, using sunlight as an energy source; endergonic

-originated in Bacteria

-does not happen the same way for all photoautotrophs

-glucose is made; resources required are carbon, oxygen, and hydrogen (CO2 and H2O)

-two step process

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LIght dependent reactions

Back 26

-energy in sunlight is used to make ATP (solar to chemical energy)

-a molecule of NADP+ is reduced to NADPH, which serves as a source of hydrogen to make glucose

-NADPH is an electron carrier

-Photophosphorylation

-H2O or an inorganic compound (H2, H2S, S0) is the e- source

chlorophyll, form complexs, embedded into membranes (thylakoids in cyanobacteria, plasma membranes in prokaryotes, chlorophyll in eukaryotes)

light strikes chlorophyll complex-> high energy->electron transport chain->electrons pumped across membrane, ATP produced, NADP+ reduced to NADPH; light splits water, oxygen released,

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Calvin-Benson Cycle Reaction

Back 27

-CO2 absorbed from environment, then reduced in a series of steps by NADPH to produce a sugar

- Requires e- from reduced coenzyme, NADPH

- Hydrolysis of ATP provides energy for this process

-carbon fixation- the incorporation of atmospheric CO2 into organic molecules

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Chemoautotrophs

Back 28

-use CO2 as a carbon source, like photoautotrophs, but instead of light they use reduced compounds such as ammonia, methane, or hydrogen sulfide as an energy source

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Heterotrophs

Back 29

-different feeders; must eat or absorb molecules; all animals and fungi, along with many microogranisms

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Photoheterotrophs

Chemoheterotrophs aka Heterotrophy aka Organoheterotrophy

Back 30

-produces energy through photolysis of organic compounds or via a light powered proton H+ pump; ex Rhodobacter & Rhodopseudomonas;

anoxic zones of waters, mud, sludge, and in organic-rich water habitats

-Yields energy & carbon for biomass solely from organic compounds; Glycolysis plus others Krebs / CAC Electron Transport Chain; Aerobic, Anaerobic, Facultative anaerobes

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Chemoheterotrophs

Back 31

-During catabolism, fuels are oxidized to release energy

-- Energy is released upon oxidation - Electrons are passed to a final acceptor - Energy of es is stored as ATP & reduced coenzymes - NADH or FADH

Front 32

What is considered to be the first metabolic pathway to evolve?

Back 32

Glycolysis

Evidence? it occurs in all cells, unlike photosynthesis or specific types of respiration

Front 33

DNA

Back 33

-made up of nucleotides (which is composed of a 5 carbon sugar deoxyribose, a phosphate group and a nitrogenous base)

-double helix

Front 34

Nitrogenous Bases

Back 34

Single ring Pyrimidines

Double ring Purines

-purine bonds only with a pyrimidine

A--T while G----C

Front 35

Pyrimidines

Back 35

Cytosine and Thymine

Front 36

Purines

Back 36

Adenine and Guanine

Front 37

Gene

Back 37

a sequence of DNA nucleotides that codes for a single protein or part of a protein

Front 38

RNA

Back 38

the nucleic acid that acts a a messenger, carrying DNAs genetic message to the actual site where amino acids are assembled into proteins

-single stranded

-uracil instead of thymine

Front 39

Watson and Crick

Back 39

developed a model for the DNA structure

Front 40

chromosomes

Back 40

in prokaryotic and eukaryotic cells, DNA is organized into these discrete units; consists of DNA and associated proteins; proteins provide a scaffolding around which the DNA coils, allowing it to be condensed many times

Front 41

DNA Replication

Back 41

-DNA double helix separates; each "parent" strand serves as a template for the sythesis of a new "daughter" strand

-DNA POLYMERASE is the enzyme which "reads" nucleotide sequences during separation and synthesizes the daughter strands accordingly

-(the base sequence on parent strand dictates the complementary sequence on the new daughter strand)

Front 42

DNA: Genes to Proteins

~Protein synthesis

Back 42

two basic steps:

Transcription

and Translation

Front 43

Genome

Back 43

the sum total of an organism's genes

Gene- considered the basic unit of heredity

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Gene expression

Back 44

the conversion of a gene's nucleotide sequence into a protein

Front 45

Transcription

Back 45

-the genetic information encoded in the nucleotides of a gene are transferred to RNA through complementary base pairing

-RNA polymerase recognizes the beginning of a gene, binds to this site, and unwinds the DNA sequence to be transcribed

-this base sequence is called a promoter (start signal)

once RNA binds to promoter, it unwinds DNA to expose nucleotide bases; complementary RNA nucleotides are added, forming a RNA chain until transcription reaches the termination sequence

-RNA is released and RNA polymerase detaches

Front 46

Translation

Back 46

-mRNA carries DNA's message to the site in the cell where amino acids are assembled into proteins

-ribosomes: a growing protein where amino acids are linked together

-ribosome attaches to the end of an mRNA and "reads" it, one codon at a time

-at each codon, the appropriate amino acid is trought into position by tRNA (transfer)

each tRNA has an anticodon complementary to the codon on mRNA

Front 47

codons

Back 47

mRNA sequence of bases in groups of three that specify a particular amino acid

Front 48

Protein production in prokaryotes

Back 48

-in eukaryotes, transcription occurs in the nucleus; since there is no nuclear membrane in prokaryotes, the two processes of transcription and translation are not separate but rather overlapping --> faster protein production

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regulated genes

constitutive genes

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genes that are turned on and off as condition warrants

nonregulated genes

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operons

Back 50

groups of genes the products of which are all involved in the same process, even though each one codes for its own protein; either all are "ON" (activated) or "OFF" (repressed)
-not found in eukaryotes

Front 51

Why use operons?

Back 51

The main advantage of
operons is that a single switch
can either turn on or off a
cluster of functionally related genes

Save time & energy

Make a lot of protein quickly

Front 52

Regulatory Gene

Back 52

- Encodes regulatory protein that binds to the
operator
- Always expressed; constitutive
- Not necessarily near the operon it controls

-bind to the operator region
Blocks RNAP
Prevents transcription of the operon

Inducer molecule
Binds to repressor & prevents binding to operator
Allows transcription to occur

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genotype cell

phenotype

Back 53

the specific genetic makeup of an individual for a particular trait

the physical expresssion of that genotype

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asexual reproduction

Back 54

a type of reproduction where a single parent gives rise to two identical daughter cells, each receiving the same genetic information

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sexual reproduction

Back 55

reproduction involving the mixing of DNA from two parent organisms to create offspring with a novel combination of genetic information

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gametes

Back 56

specialized sex cells

for some organisms:

females, they are EGGS

males, they are SPERM

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recombination

Back 57

the ability to generate new combinations of genetic material

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alleles

Back 58

alternative forms of the same gene

Front 59

Transformation

Back 59

-Griffith, S. pneumaoniae, mice

-DNA released by dead bacteria is taken up by a living bacterium and incorporated into its chromosome

Front 60

Transduction

Back 60

when a bacteriophage (bacterial virus) shuttles bacterial genes between donor and recipient cells; may result in the altering of genotype and phenotype of recipient bacteria

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Conjugation

Back 61

in addition to the main bacterial chromosome, some cells have an additional circular loop of DNA called a plasmid. conjugation is when bacteria with plasmids transfer the plasmids to other cells; in conjugation unlike tranformation and transduction, recipient cells must come into physical contact with donor cells; conjugating cells must be of opposite types

Front 62

Why is genetic recombination in prokaryotes significant for humans?

Back 62

resistance to antibiotics;

exchange of dangerous genes

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mutations

Back 63

damage to or mistakes in DNA base sequences; changes in genetic material; some are immediately repaired

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neutral mutation

missense mutations

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no change to production of protein

mutations which change the amino acid sequence of a protein; harmful or beneficial

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nonsense mutation

frameshift mutation

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a readable codon is converted to a stop codon

an extra base is either inserted into or deleted from new daughter DNA by DNA polymerase during replication

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mutation factors

Back 66

spontaneous mutations: random errors

mutagens: agents which increase the frequence of mutations; such as chemicals or radiation

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intercalating agents

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chemical mutagens which cause problems by inserting themselves at a replication fork during DNA synthesis

Front 68

free radicals

Back 68

highly reactive compounds that latch onto and damage other molecules including DNA

-formed from the bond-breaking from radiation; leftover atoms and molecules form free radicals

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thymine dimer

Back 69

two thymines covalently linked together; distorts the shape of DNA molecule

-cause: uv light breaks H bonds between thymine and adenine nucleotides; if two thymines are adjacent to each other on the same dna strand, then they bond

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proofreading

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self-checking capacity present in all cells completed by DNA polymerase; repairs mistakes

mismatch repair

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DNA mismatch repair enzymes

Back 71

a molecule of DNA polymerase replaces the removed bases

repair dimers

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mutations and evolution

Back 72

there would be no evolution if there weren't mutations;

if mutations never occurred, all members of a species would have the same genes and the same alleles of those genes