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UGH MCB
exam two X(
123
Biochemistry
Undergraduate 3
10/26/2014

Additional Biochemistry Flashcards

 


 

Cards

Term
anabolic reaction
Definition

a metabolic pathway

building up of biological molecules, produce complex molecules that cytoplasm is made of, consume energy in the form of ATP

Term
Catabolic reaction
Definition

release energy that is used to produce ATP

involved in breaking down of complex molecules to yield simple molecules that the cell can use as synthetic raw material

Term
enzymes
Definition

the catalyst of biochemical reactions (specific to substrate it acts on-lock and key model)

most are proteins

a typicla enzyme can make a reaction go 100 million times faster

impairment of just one can cause Xp

cannot make an unfavorable reaction occure-destabilizes chem bonds in substrates, promotes formation activated complex (state between substrates and products)

Term
active site of an enzyme
Definition

catalytic site

usually a pocket or cleft where substrates bind

functional groups on amino acids that surround the active site bind the substrate molecules-encourages of new chemical bonds leading to the formation of the product

Term
where are enzymes found?
Definition

in medium (outside cell): exoenzymes-secreted, help digest large molecules (starch) to release smaller molecules (sugar) the cell can absorb, some exoenzymes are toxins-disease causers

Embedded in cytoplasm membrane: involved in respiration, some pump ions across mmebrane, otherse pump nutrients in and waste out, or cause metabolic canges inside due to outside signals

in the cytoplasm of bacterial cell: over 1000 different enzymes, synthesize aa, protein, nucleoties, nucleic acids, sugars, etc, or break down nutirents to simple compounds producing ATP

Term
exoenzymes
Definition

Hydrolytic enzymes

lipase: digest fats

amylase: digest starch

gelatinase: digest protein

Term
enzyme catalyzed biochemical reaction steps
Definition

1) substrate binds enzyme at activation site

2) flex of enzyme produces strain/distortion of chem bonds found in substrate

3) substrate chem changed into product

4) product released

5) enzyme emerges unchanged ready to bind another molecule

Term
what is a poison
Definition
a type of enzyme inhibitor
Term
Hydrolase enzyme classification
Definition

hydrolysis (catabolic)

ex: lipase (break down lipid molecules)

lactose+H2O=Galactose+Glucose

Term
Isomerase enzyme classification
Definition

rearrangement of atoms within a molecule (catabolic or anabolic)

 

Ex: phosphoglucoisomerase-> converts glucose into fructose during glycolysis

Term
Ligase or polymerase enzyme classification
Definition

joining of 2+ chemicals (anabolic)

ex: acetyl-CoA synthesis (acetate+coenzyme A = acetyl CoA for kreb cycle)

Term
Lyase enzyme classification
Definition

splitting a chemicals into smaller parts without water (catabolic)

 

ex: fructose-> G3P and DHAP during glycolysis

Term
oxidoreductase enzyme classification
Definition

transfer of e- or H atoms from one molecule to another

 

ex: lactic acid dehydrogenase (lactic acid oxidized to form pyruvic acid during fermentation)

Term
Transferase enzyme classification
Definition

moving functional group to another

molecule (may be anabolic)

 

Ex: hexokinase (transfer phosphat form ATP to glucose in glycolysis first step)

Term
asparatate->methionine
Definition

6 steps


humans lake the enzyme to make methionine so must consume methionine in diet (also folic acid for women)

 

has feedback inhibition from formed products

Term
simple vs conjugated enzymes
Definition

simple: chain of aa

conjugated: proteins + added organic or inoganic moleucles that are closely associate with the protein

Term
apoenzyme
Definition
protein portion of a conjucated enzyme without any cofactors
Term
cofactor
Definition
small molecule that binds to an enzyme to help produce the catalytic activity (coenzyme if it is an organic molecule)
Term
things that can affect the activity of an enzyme
Definition
protein denaturation, temp, pH, substrate concentration, presence of competitive inhibitors, allosteric inhibitors/activators (bind to separate location on enzyme to change active site shape), feedback inhibition (in a series of bindings the original substrate produces a inhibitor for itself to bind to the original enzyme preventing further products from being formed)
Term
enzymes can and cannot
Definition

can make biochemical reactions progress faster by reducing activation energy barrier by stabilizing transition state

DO NOT

change nature of reactants/products

change chemical potential energy of substances

change free energy of a reaction

make unfavorable reactions favorable

Term
ATP
Definition

adenosine triphasphate

bonds between phosphates unstable w high chem potential energy

energy released when ATP looses a phosphate (forms ADP)

Drives unfavorable biosynthetic reactions

cell stores energy by trapping energy from catabolic reaction and using it to attach a phosphate to ADP

cell uses for: substrate activation, power cellular motion and pump ions/other molecules across membrane

Term
substrate-level phosphorylation
Definition

1 of 2 ways cells make the most of ATP


-energy to form high energy phosph-anhydride bond comes from hydrolysis of higher energy bond


a phosphate group is being added to ADP to make ATP and cell must form a metolic intermediate that has very high energy bond joining the phosphate group to an organic coupound before SLP occurs

Term
proton-ATPase
Definition

the second way cells make the most of ATP

(H+-ATPase)

-uses potential energy of proton motive force. (chemoosmotic theory or oxidative phosphorylation)

requires there to be an intact membrane separating tow comparments of differing proton concentrations, can be established by using chemical reactions of respiration via e- transport chain (redox reactions pump H+ across resultin in electrical charge across membrane)

Term
redox reactions
Definition

=oxidation-reduction

reduction=gain of e- (becomes more -)

add 2 H or remove an O


(oxidation is the opposite)

add O or remove 2 H


chemoheterotrophic organisms use redox to make energy

Term
the electron donor
Definition
starts as a reduced compound that gets oxidized during the course of the reaction (also called reducing reagent)
Term
chemoheterotrophy
Definition

both enegy and C derived from organic compounds

aerobic, anaerobic respiration, and fermentation

Term
oxidation of glucose
Definition

achieved by 20 discrete steps allowing energy to be released slowly to be efficiently utilized by the cell

glycolysis, Kreb, and e- transport chain pathways

 

(difference between fire and the cell: fire released unctontrolled, high ignition temp and dry fuel, uses cellulose a polymer of glucose)

Term
respiration vs fermentation
Definition

Glycolysis branches off into either after producing   2 pyruvic acids


respiration: kreb cycle and e- transport chain

fermentation: pyruvic acid used for formation of products

 

Term
glycolysis
Definition

glucose (10 steps) 2 pyruvate (C3H4O3)

"partial oxidation" activated by attachment of two phosphates to form fructose-1,6-bisphosphate


2 ATP required to start

4 ATP produced substrate level phosphorylaation   (2 ATP net gain)

2 molecules NAD+ reduced to 2 NADH and 2 H+

Term
The Krebs cycle
Definition

Tricarboxylic acid cycle or citric acid cycle (pyruvate dehydrogenase reaction)

8 reactions resulting in oxidation of 2 pyruvate to 6 CO2

8 NAD+ reduced to NADH + H+

2 FAD reduced to FADH2

2 ATPs made by substrate level phosphorylation

 

Term
e- transport chain
Definition

oxidative phosphorylation= series of redox inolving membrane bound enzymes and e- carriers that result in


the reoxidation of NADH + H+ back to NAD+

reduction of O2 to H2O and the production of 34ATPs per glucose

yields Proton Motive Force sufficient to produce 3 ATPs per NADH oxidized at 2 ATPs per FADH2 oxidized


mitocondria in eukaryotes and cytoplamic membrane in bacteria

Term
steps to e- transport chain
Definition

NADH + H+ is oxidized to NAD+


electrons passed between carriers and protons pumped across the membrane


oxygen reduced to H2O, in aerobic respiration oygen is terminal e- acceptor. Protons flow through ATP synthase and generate ATP from ADP + Pi

Term
aerobic respiration
Definition

oxidation of glucose to CO2 and H2O

uses glycolysis, krebs cycle, e- transport chain and oxidative phosphorylation

yields 38 ATPs per glucose molecule

Term
proton motive force
Definition

created by e- transport chain

used for ATP synthesis

active uptake of nutrients

ion pumps

flagella rotation


sufficient to produce 3 ATPs per NADH oxidized and 2 ATPs per FADH2 oxidized

Term
Anaerobic respiration
Definition

NADH + H+ is still oxidized back to NAD+ using membrane bound e- transfer chain

Terminal e- acceptor not O but instead some oxidized mineral (if proper mineral present bacteria can use respiration to produce energy in absense of air)

PMF generates ATP, can generate 36 ATP per glucose

Term
Fermentation
Definition

ATP generated by substrate level phosphorylation

terminal e- acceptors are organic compounds

anaerobic and no light required or oxidized minerals, inefficient, extracts only a fraction of potentail energy in the food molecules

2 ATPs per glucose, lactic acid and ethanol fermentation

Term
Lactic acid fermentation
Definition

glucose partially oxidized to pyruvate (glycolysis)...NADH oxidized back to NAD by reduction of pyruvate to lactic acid

yield 2 ATP per glucose


made by a variety of bacteria (some used in cheese and yogurt production and tooth decay)

Term
Ethanol fermentation
Definition

glucose->pyruvate via glycolysis

pyruvate decarboxylated to yield acetaldehyde. NADH oxidized back to NAD by reduction of acetaldehyde to ethanol

yield 2 ATPs per glucose


made by bacteria and fungi, especially yeasts

biproduct CO2

Term
Acetic Acid
Definition

made in mixed acid fermentation by many bacteria also by Acetobacter and Gluconobacter wich produces vinegar which is a two step process.

1) yeasts are used anaerobically to produce ethanol from sugar

2) Gluconobacter/Acetobacter used to aerbically partially oxidize ethanol to acetic acid

Term
Photoautotrophy
Definition

photosynthesis

energy from light, carbon from CO2

oxygenic (water) and anoxygenic (H2S)

generates ATP (convert CO2 to sugar) & NADPH (reducing agent)

Term
Calvin Cycle
Definition

photosynthesis-dark reaction

fixation of C both photoautotrophic and chemoautotrophic (sugar from CO2 requires ATP-energy and NADPH-reducing)

Term
Chemoautotrophy
Definition

require some reduced compound + some oxidized compund as starting material for redox

yields energy so ATP and NADPH can be made

Used to assimilate CO2

hydrogen sulfide oxidation (H2S is the reducing agent)

uses e- transport chain proton gradient

(deep ocean volcanic vent and tube worms)

Term
hydrogen oxidizing bacteria
Definition

fix CO2 using RuBisCo-type enzyme (calvin cycle)

either with or without O2

can use NO3-

Term
Replication
Definition

DNA to 2 DNA

(DNA reproduction)

Term
Transcription
Definition

mRNA

synthesis of RNA

(DNA=1RNA strand)

Term
Translation
Definition

(info in mRNA synthesizes a protein)

synthesis of a protein converts info in a nucleotide language into the aa language

Term
what is the enzyme that makes new DNA?
Definition
DNA polymerase III
Term
nucleotide groupings
Definition

G-C

T-A

Term
Primer
Definition
short piece of DNA or RNA that binds to template and has a free 3 prime end
Term
Enzymes used in DNA replication
Definition

Helicase-separates strands of old DNA

single-strand binding protein-keeps apart

Primase-makes short RNA primers

DNA polymeraseIII-adds nucleotides to end of primer

DNA polymerase I-removes primers (fill gap)

DNA ligase-joins DNA pieces

DNA gyrase-controls super twisting

DNA topoisomerase- same as above

Term
Transccription (RNA created)
Definition
mRNA is the same as the the sense strand but made from the antisense strand (1000-3000nucleotides long, transcription bubble is 20 base pairs long)
Term
mRNA
Definition

copy of info in a gene needed to direct synthesis of a protein (sequence of nucleotides making up codons that will code for aa that will link to make a protein)


single stranded

quickly degraded

Term
rRNA
Definition

structural part of ribosome

ribosome=complex enzyme that synthesizes protein


more stable than mRNA (covered in ribosomal proteins)

regions of double stranding (hairpin-like structures)

Term
tRNA
Definition

brings correct aa into ribosome and positions it in place so the protein strand can grow

clover leaf structure (formed by hairpin formation)

one loop contains the anticodon-segment that complements specific codon in mRNA (64 total)

specific aa on acceptor arm

D-loop/TyC loop bind specific charging enzymes that attach the aa

Term
Start codon
Definition
AUG
Term
Stop codons
Definition

UAA, UAG, UGA

the 3 nonsense codons

(all the rest are sense codons - 61)

Term
Genetic code
Definition

universal

triplet code

64 codons

unambiguous (CUU is always Leucine)

degenerate (6 codons specify Leucine)

not punctuated

Term
+ strand RNA viruses
Definition
identical to viral mRNA
Term
- sense viral RNA
Definition
complementary to mRNA and must be copied by RNA-dependent RNA polymerase to make a + sense strand
Term
retrovirus
Definition
retrovirus RNA is copied by reverse transcriptase to make DNA copy of RNA genetic materail
Term
mutation
Definition

stable change, permanent and rare

passed on (inherited)

produces genotypic change

some cause phenotypic change

result of DNA base pairing error in replication

Term
substitution mutation
Definition
one nucleotide replaced by another
Term
deletion mutation
Definition
1+ nucleotides left out
Term
Insertion mutation
Definition
1+ extra nucleotides are added
Term
3 codon changes
Definition

missense mutation: encode diff aa, inactivate the enzyme

nonsense mutation: encodes early stop codon, eliminates enzyme

neutral mutation: minor, no effect to enzyme (change encodes same aa)

Term
transformation bacteria DNA transfer
Definition

uptake of naked DNA


DNA released from donor strain by lysis of dead cell, recipient strain take up the DNA

competent most efficient when size is small

if you shock the  recipient it is more likely to take up DNA

Term
conjugation mode of DNA transfer
Definition

direct cell to cell contact

narrow cytoplasmic bridge, donor cell stays alive, donation of one copy to recipient, use of plasmid F-pilus and sex pilus

F+ strain -copy of F plasmid in cytoplasm (e-coli)

HFT strain-F factor integrated in chromosome

Term
Transduction mode of DNA transfer
Definition

DNA from donor incorporated into a defective virus partical (transducing phage particle) that attaches recipient and injects DNA

Death of donor strain

DNA from donor must integrate into the genome of the recipient

Term
how foreign DNA survives in recipient
Definition

1) autonomous replicon, copied within the host cell and passed to future generations

2) integrates into host chromosome by homologous recombination, crossing-over, must be similar

3) integrates into host chromosome by transposition

Term
operon
Definition

bacterial genes organized into physically linked coordinately expressed groups

regulate gene expression

Term
lac operon
Definition

lactose


if lactose then small amount of allolactose

if no lactose the lac repressor protein binds the operon and blocks transcription,

when lactose is present allolactose binds receptor and inactivates it

Term
trp operon
Definition

aa tryptophan synthesis

 

high tryptophan in cytoplasm represses trp operon.

trp repressor protein is inactive in the absense of tryptophan

Term
restriction enzyme
Definition
recognize specific sequence of DNA and make a break in backbone (often produces sticky ends)
Term
bacteriocidal agent
Definition
a physical or chemical treatment that will kill bacteria
Term
bacteriostatic agent
Definition

prevent the growth of bacteria but wont kill

protect the product but not kill the product

add salt instead of incineration to meat

example is refrigeration

Term
factors affecting efficiency of bacteriocidal treatment
Definition

species of microorganism

material protecting

biological factors (age of cells, size of population)

environmental (storage temp, pH, water activity, presence of organic matter)

Term
killing microorganisms with radiation (UV light)
Definition

used in aquarioums and on instrument/lab bench surfaces

causes damage to DNA that increase the frequency of potentially fatal mutations

Term
killing microorganisms with radiation (ionizing radiation)
Definition

gamma ray or x-ray

used on food(strawberries, beef, poultry)

less effect on tast vs heat

Term
antiseptic
Definition
used on human skin
Term
disinfectant
Definition

used on inanimate objects

selective toxicity

good solubility in H2O

stable at room temp

toxicity at room temp

capacity to penetrate

non-corrosive

non-staining

non offensive (smell)

Term
solvent
Definition
denature protein and disrupt cytoplasmic membrane structure
Term
oxidizing agent
Definition
oxidation of organic compounds
Term
Heavy metals
Definition
inhibition of enzymes
Term
soaps and detergents
Definition

denature protein and disrupt cytoplasmci membrane structure but are weak and mostly just act to help clean a surface

detergent-synthetic derivative of fatty acid (more soluble in H2O-less likely to leave soap scum)

surfactants (reduce surface tension of H2O and increase solubility of oily particles)

soap-salt of fatty acid

Term
aldehydes
Definition
react with proteins and from cross-links that inactivate the enzyme and may cause the protein to precipitate
Term
Gaseous sterilants
Definition
strong alkylating agents taht damage DNA and proteins
Term
Acids and Bases
Definition
usefulness limited by corrosive activity
Term
Hypertonic solution
Definition
allows water out of cell
Term
Hypotonic solution
Definition
allows water into cell
Term
characteristics of idea antimicrobial drugs
Definition

selective toxicity

microbicidal

soluble in H2O

potent

stable

unlikely for microbial resistance to develop

complements host's defenses

not inactivated by other metabolites

does not casue allergies

does not increase host susceptibiltiy to further infection

Term
poisons do what
Definition

inhibit enzymes one way or another

(antibiiotics kill those important only to the bacteria)

inhibit:

peptidoglycan (cell wall)

translation by 70s ribosomes (protein synthesis)

folic acid biosynthesis

RNA polymerase or DNA polymerase

disrupt cell membrane

Term
Penicillins
Definition

binding protein is a bacterial enzyme that forms the peptide bond that cross-links one aa side chain in peptidoglycan to another peptide chains


Penicillin the drug acts a competitive inhibitor of this enzyme

Term
Cephalosporins
Definition

(beta lactam drugs)

competitive inhibitors of penicillin binding proteins

Term
sulfa drugs
Definition

inhibit folic acid synthesis

structural analog of PABA and competetive inhibitor of enzyme that converts PABA to dihydrofolate

Term
Aminoglycosides
Definition
bind 30s subunit of 70s ribosome and cause mRNA to be misread...causes the incorporation of incorrect aa into growing protein chain
Term
Tetracyclines
Definition
block binding of tRNA to ribosome-mRNA complex
Term
chloramphenicol
Definition
antibiotic blocks formation of peptide bonds between aa of growing protein chain
Term
Macrolides
Definition
stop movement of ribosome down mRNA
Term
Quinolones
Definition
antibiotic that inhibit bacterial gyrase, involed in controlling amout of supertwisting of DNA (ie this blocks replication)
Term
Polymyxin
Definition
detergent-like antibiotic that disrupts bacterial cell membrane
Term
Nucleotide analogs
Definition
Block DNA replication and cause mutations
Term
antibiotic resistance in bacteria
Definition

1) produce an enzyme that degrades/modifies the antibiotic. genes often located on plasmids (transferable)

2) alter pore protein may slow diffusion of drug into cell

3) gene for drug receptor mutated so receptor no longer binds antibiotic

4) resistant cell alter metabolism so can by-pass inhibited step

5) resistant cell aquire a gene for active transport protein that pumps antibiotic out of cell using ATP (can be found on plasmid/transposon)

Term
minimum inhibitory concentration
Definition

lowest concentration of anitbiiotic to inhibit a pathogen

low MIC indicates potent drug

Kirby-Bauer test-used to predict effectivness of antibiotics in treatment of patient

Term
Therapeutic index (TI)
Definition

toxic dose/effective dose

the higher the result the safer the drug

low indicates smaller margin of error as try to give enough to kill the infectious microorganism but not enough to hurt host

Term
anti fungal, antihelminthic, antiprotozoan drugs
Definition

are eukaryotic organisms so have 80s ribosomes not 70s so antibiotics inhibiting 70s wont work...

they also dont have cell walls of peptidoglycan so penicillins and cephalosporins wont work either


(most drugs that will work have toxic side effects and low therapeutic index)

Term
Antiviral
Definition

harder b/c inside cell

must inhibit certain enzyme found only in that virus

Term
primary spoilage
Definition
occurs in the field and is usually casue by insect infestations or moldy products
Term
secondary spoilage
Definition

occurs in th food processing plant or later

botulism in improperly canned food

Term
what are some herbs that naturally inhibit the growth of bacteria?
Definition
garlic, cloves, cinnamon, and oregano
Term
what are the components of milk
Definition

protein (C & N source also casein, immunoglobulins)

carbohydrates (lactose)

lipids (butterfat)

vitamins (B, A, (D added))

minerals (calcium)

trace elements

water

pH 7

isontonic salt concentration

Term
Pasteurization
Definition

form of heat treatment

does not kill all the microorganisms in the product like sterilization would

temps below 100celcius used

(Milk: 63 c for 30 min or 72 c for 15 seconds)

used for beer, wine, juice before fermentation step

(juice is pasteruized then incoulated with starter culture to insure consistent production of good wine)

started in 1900s to kill TB in milk

Term
different types of milk pasturization
Definition

Low temp holding: heated to 62.8 for 30 min

high temp: heated to 70 for 15 sec (flash pasteurization)

ultra high temp: 149 for a few seconds, well above boiling...no refrigeration of product till it is opened...loss of nutrients and taste and is more expensive than otheer techniques

Term
common tests for raw or pasteuried milk
Definition

standard plate count

breed smear

methylene blue test

phosphatase test

Term
how does milk spoil?
Definition

acid production: oxidize lactose to produce acid, sour, done to make yogurt and cheese

...

gas production: clostriduim, e coli, yeasts, stormy fermentation: produce acid and CO2 or H2 causing casein to precipitate and produce curds that float from the gas in them or explode

...

Ropy fermentation: produce capsular polysaccharides and grow inlong chains, stringy curds

Term
Milk can spoil how!?
Definition

progein digestion: degrade aa from casein to produce bitter taste, putrifaction, these bacteria are often thermoduric

...

Lipoltic: break down lipids in butter fat, rancid

...

alcoholic fermentation: yeast convert lactose to ethyl alcohol and CO2

...

Sweet curdlers: excrete enzyme rennit, curd form at neutral pH, bittering milk

Term
beer productin
Definition

sugar from barely converted to ethanol by yeast fermentation

Malting: barley moistened to germinate, seed enzymes begin breaking down starch into simple sugars, then grind into powder or malt

Mashing: malt+grains mix with H2O dissolving sugars. ENzymes from seeds still convert amylose to maltose (sugary liquid=wort)

spen grain, remove wart, hops added to wart and boiled

wort cooled yeast added, incubated with air bubbles allowing yeat to grow, then air shut off and anaerobic fermentation occurs

aged at low temp

Term
general steps in sewage treatment
Definition

primary: remove coarse solids

secondary: digestion of solid and dissovle nutrients by aerobic microorganisms

chem disinfection: kill pathogenic bacterial and solids

want to reduce BOD: measure of amount of oxygen used up by aerobic bacterail in water in a 5 day period

imhoff tank: anaerobic, bacteria/archaea bread down organic matter producing CO2 and methane, methane is burnt off for fuel)

Term
coiforms
Definition

indicator organism

small gram- that ferment lactose, non-spore forming and produce acid/gas in 24 hours

always present in large intestine/fecal material

present in large numbers thatn pathogenic bacterial in contaminated water

generally survive in water longer than pathogenic bacteria

easy to cultivate

Term
enterococci
Definition

fecal strptococci

small gram+ cocci found in the intestine

Term
microorganisms in biogeochemical cycles
Definition

help conversion of an element from one form to another by living organisms and non-biological chem reactions in the the environment (typically invovle redox)

sulfur cycle

nitrogen cylce

carbon cycle

Term
fecal oral cycle pathogenic bacteria
Definition

salmonella typhi

shigella dysenteriae/ e. coli

vibrio cholerae

campylobacter jejuni

helicobacter pylori

Term
fecal oral cylce pathogenic viruses
Definition

polio

hep A

rotoviruses (diarrhea)

Term
fecal oral cylce pathogenic protozoa
Definition

giardia lamblia (dysentery)

entamoeba histolytica (dysentery)

balantidium coli (dysentery)

crtptosporidium parvum (dysentery)

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