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Bio 173
EXAM II
83
Biology
Undergraduate 3
10/29/2011

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Term
reduction
Definition

when an atom or molecule gains an electron

 

NAD+ e- --> NADH

Term
oxidation
Definition

when an atom or molecule loses an electron

 

NADH --> NAD+ + e-

Term
glucose equation
Definition
C6H12O2 + 6O2 --> 6CO2 + 6H2O + energy
Term
3 pathways of energy formation
Definition

1) glycolysis

2) Kreb's Cycle (Cirtric Acid Cycle)

3) oxidative phosphorylation

Term
energy investment phase of glycolysis
Definition
glucose + 1 ATP --> phosphorylated glucose (reorganized molecule) + 1 ATP --> 2 3-carbon molecules (pyruvate)
Term
explain feedback inhibition in glycolysis
Definition
phosphofructokinase has two binding sites for ATP (ATP regulatory site and active site).  ATP binds to active site to start glycolysis, once enough ATP is produced, it binds to regulatory site- dramatically slows reaction rate
Term
energy pay off phase of glycolysis
Definition

2 NAD+ are reduced to NADH

4 ADP are physphorylated to ATP

pyruvate is formed (2 per 1 glucose)

Term
substrate level phosphorylation
Definition

production of ATP by transfer of a phosphate group from intermediate substrate directly to ADP.  An enzyme catalyzed phosphorylation reaction.

 

occurs during glycolysis and Kreb's cycle

Term
net gain from glycoysis
Definition

energy investment: -2 ATP

energy payoff: +4 ATP and +2 NADH

 

= 2 ATP, 2 NADH and 2 pyruvate

Term
cellular respiration
Definition

pyruvate converted to acetyl CoA with assistance from coenzyme A (CoA)

releases CO2

 

1 molecule of NADH is generated/ pyruvate

Term
pyruvate conversion and citric acid cycle reaction
Definition
2pyruvate + 8NAD+ + 2FAD + 2ADP + 2Pi --> 6CO2 + 8(NADH + H+) + 2FADH2 + 2ATP
Term
purpose and location of citric acid cycle
Definition

extracts energy from pyruvate

occurs in mitochondrial matri (euks)

cytosol (proks)

8 total steps

Term
net gain of citric acid cycle
Definition

2 CO2

3 NADH

1 ATP

1 FADH2

(x2 for 2 cycles per 1 glucose)

order: CO2 & NADH, CO2 & NADH, ATP, FADH2, NADH

 

 

 

 

Term
electron transport chain definition
Definition

uses energy in NADH and FADH2's electrons to generate ATP via oxudataive phosphorylation

1) NADH & FADH2 donates 2 electrons

2) electrons transferred along chain

3) O2 final electron acceptor

Term

electron transport chain

complex I

Definition

1) NADH is oxidized to NAD+

2) energy released from rxn pumps protons into lumen

3) Q transfers e- to complex III

Term

electron transport chain 

complex II

Definition

1) FADH2 is oxidized to FAD

2) energy released used to pump H+ into lumen

3) Q transfers e- to complex III

Term

electron transport chain 

complex III

Definition

Q delivers e- and H+

electronegativity increases at each complex

Term

electron transport chain

complex IV

Definition

1) cytochrome C transports e- from complex III to complex IV

2) more H+ are pumped into lumen

3) O2 accepts e- to form water

4) creates H+ gradient

Term
chemiosmosis
Definition
production of ATP via proton gradient
Term
ATP synthase
Definition
enzyme on membrane used to poduce ATP from H+ flow
Term
oxidataive phosphorylation
Definition

1) proton gradient drives "motor"

2) H+ flow from high to low concentration through ATP synthase

3) 26 ATP synthesized per glucose

Term
fermentaion
Definition

regenerates NAD+ from NADH and allows glycolysis to continue making ATP in the absence of O2

 

 (2 NADH -> 2 NAD+)

2 pyruvate -----> by-product

Term
catabolic pathways
Definition
the breakdown of proteins, carbs, fats for cellular respiration
Term
anabolic pathways
Definition

the synthesis of proteins, carbs, fats.

used as storage

Term
photosynthesis
Definition

the conversion of light energy to chemical energy stored in the bonds of carbohydrates

occur in chroloplasts or plasma membrane/ cytosol

Term
parts of a chloroplast
Definition

stroma- vacant area within chloroplast

granum- stack of thylakoids

thylakoids- vesicle-like structures

lumen- inside of thylakoid

thylakoid membrane- contains pigment molecule that absorbs light energy and transfers that energy into electrons

Term
photosynthesis reaction
Definition
6CO2 + 6H2O + light --> C6H12O6 + 6O2
Term
fluorescence
Definition
electron drops back down to lower energy level; heat and fluorescence are emitted
Term
resonance
Definition
energy in electron is transferred to nearby pigment
Term
reduction/oxidation
Definition
electron is transferred to a new compound
Term
photosystem II
Definition

1) photons of light excite e-s from chlorophylls of P680 rxn center

2)excited e-s are passed to pheophytin (e- acceptor)

3) pheophytin transfer e- to PQ

4) e- flow down ETC to cytochrome complex. PQ carries e-s from PS II along with protons

6) H+released into thylakoid lumen

7)high [H+] causes flow through ATP synthase


Term
photosystem I
Definition

1) e-s excited @ P700 rxn center or from PC (from PSII)

2) flow down ETC to ferredoxin

3) ferredoxin donates e- to for rxn: NADP+ --> NADPH

Term
cyclic e- flow
Definition

produces ATP

 

1) PQ -->(ETC to make ATP) cystochrome complex --> PC --> P700 (excited e-) --> (ETC) ferredoxin

--> PQ

Term
3 types of ATP production
Definition

substrate-level phosphorylation

oxidative phosphorylation

photophosphorylation

Term
3 parts of the Calvin Cycle of Photosynthesis
Definition

1) carbon fixation

2) reduction

3) regeneration of CO2 Acceptor

Term
carbon fixation
Definition

addition of CO2 to 5-carbon sugar by Rubisco and ribulose biphosphate (RuBP)

forms 2 molecules of 3-phosphoglycerate (G3P)

1st step in calvin cycle

Term
reduction of G3P
Definition

addition of e-s to generate 2, 3-carbon sugars

use 6 ATP and 6 NADPH

1 G3P sent as output

Term
regeneration phase of calvin cycle
Definition

the rest of G3P keeps the cycle going by serving as substrate for 3rd phase in cycle

regenerate RuBP with addition of 3 ATP

Term
gene
Definition

portion of DNA that encodes a protein (RNA) product

unit of inheritance that determines traits or characteristics

Term
genome
Definition
entire library of genetic intructions
Term
DNA
Definition

deoxyribonucleic acid

substance of genes and directs its own replication

Term
The Chromosomal Theory of Inheritance
Definition

genetic material is located in chromosomes

chromosomes contain only DNA and protein

Term
Friedrich Miescher
Definition
discovered nucleic acid
Term
3 reasons of evidence that DNA is the genetic material
Definition

1) transformation of Strepoccocus

2) DNA component of T2 virus injected into host cell

3) DNA content doubles prior to cell division (and is halved by mitosis)

Term
Griffith's experiment
Definition

no hypothesis

injected mice with different strains of streptococcus

R strain (non pathogenic) S strain (pathogenic)

conc: R strain is benign, S strain is virulent, heat killed S strain, R strain transformed to S strain when added to heated S strain

Term

Avery, McCarthy, Maclead Experiment

 

What is the Transforming Factor?

Definition

removed either protein, RNA, or DNA from 1 of three cultures

observed which culture was transformed

conc: DNA is the transforming factor

Term
transformation
Definition
incorporation of external DNA into genome
Term
virus
Definition
particle made of protein and nucleic acid that uses cells to replicate
Term
phage (bacteriophage)
Definition
virus that infects bacteria
Term
Hershey & Chase Experiment
Definition

viral genes DNA or protein?

viruses either had radioactive P (DNA) or S (protein)

DNA in centrifuged pellet, protein in supernant

conc: viral genes consist of DNA, viral coats are proteins

Term
x-ray crystallography
Definition
method used to mathematically solve 3D structure of macromolecules
Term
Watson and Crick
Definition
solved the DNA structure
Term
purine-pyrimidone bonds
Definition

A-T = 2 hydrogen bonds

G-C = 3 hydrogen bonds

Term
central dogma
Definition

long anticipated hypothesis that info in cells flows in one direction: DNA -> RNA -> proteins

yet there are exceptions

Term
Meselson-Stahl Experiment
Definition

semi-conservative vs. conservative vs. dispersive

(1 new, 1 old strand vs. 1 new double helix, 1 old vs. mixtures of new and old)

Term
helicase
Definition
catalyzes breaking of hydrogen bonds between base pairs and open double helix in transcription
Term
single-stranded DNA-binding proteins
Definition
stabilize single-stranded DNA in transcription
Term
topoisomerase
Definition
breaks and rejoins double helix to relieve twisting forces caused by opening of double helix during transcription
Term
primase
Definition
catalyzes snthesis of RNA primer on okazaki fragments on leading and lagging strands
Term
DNA polymerase III
Definition
extends okasaki fragment (5' -> 3') on leading and lagging strands
Term
sliding clamp
Definition
hold DNA polymerase in place during strand extension in transcription
Term
DNA polymerase I
Definition
removes RNA primer and replaces it with DNA on lagging strand
Term
DNA ligase
Definition
catalyzes the joining of okazaki fragments into continuous strand on lagging strand during transcription
Term
synthesis of leading strand
Definition

1) DNA is opened, unwound, and primed

2) starts at 3' end of template

3) DNA polymerase III synthesizes 5' -> 3' of new strand

Term
synthesis of lagging strand
Definition

1) primase synthesies RNA primer

2)DNA poymerase III synthesizes okazaki fragment

3) primase and DNA polymerase III synthesize another okazaki fragment

4) DNA polymerase I removes primer and extends

5) DNA ligase closes gap with phosphodiester bonds

Term
circular DNA termination
Definition
DNA ligase joins ends together
Term
linear DNA termination
Definition

telomerase replication:

1) extends unreplicated end twice

2) primase, DNA polymerase and ligase synthesize lagging strand to restore length

Term
chromatin packing
Definition

1) nucleosomes- DNA wrapped around histone proteins

2) higher levels- coiling, loops

3) further packing produces metaphase chromosomes

Term
why does RNA have uracil?
Definition
cytosine degrades into uracil and if uracil were in DNA, the cell wouldn't know which uracil bases to repair
Term
three stages of transcription in euks
Definition

1) initation

2) elongation

3) termination

Term
initiation of transcription in euks
Definition

transcription factors racognize and bind to DNA @ promotor

RNA polymerase binds, unwinds, and synthesizes

Term
elongation of transcription in euks
Definition

only one DNA template is used for base-pairing (3' end) 5' -> 3' end of new RNA strand

A pairs with U

Term
termination of transcription in euks
Definition

RNa polymerase stops adding rNTPs and RNA chain is released

occurs at specific site for each gene

Term
transcription in proks
Definition

RNA polymerase binds to sigma which guides to specific locations to start transcription (promotors)

RNA polymerase synthesizes new strand

termination triggered by hairpin loop

Term
RNA processing (only in Euks)
Definition

add 5' phosphate cap and 3' AAA tail

remove introns

Term
splicing
Definition

snRNPs- small nuclear ribonucleproteins bind at exon-intron boundry

RNA breaks at A

intron is cut in primary transcript (spliceosome)

exons ends bond covalently

Term
tRNA
Definition

short RNAs with intramolecular base pairing

anticodon base pairs with condon on mRNA

one end is attached to specific amino acid

Term
aminoacyl tRNA synthetase
Definition
active site binds tRNA with amino acid via ATP -> AMP
Term
wobble hypothesis
Definition

Crick- the anticodon of tRNAs can bind successfully to a codon whose 3rd position requires a nonstandard base pairing

 

tRNA can base pair with >1 type of codon

Term
ribosome structure
Definition

60% RNA, 40% protein

1 mRNA binding site, 3 tRNA binding sites (E,P,A)

lg subunit

small subunit

Term
initiation of translation
Definition

sm subunit binds to 5' end of mRNA

initiator amionacyl tRNA binds to start codon

lg subunit of ribosome binds

Term
elongation of translation
Definition

incoming tRNA, new tRNA to A site, antibind with codon, old tRNA to P site

translocation- ribosome moves down mRNA

E site exits

Term
termination of translation
Definition

when ribisome encounters a stop codon in A site

polypeptide is cleaved from A site

subunits dissociate

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