Bio 12U Exam Review

replication fork

the point of separation of the two parent DNA strands during replication

replication bubble

the separating of DNA in both directions during replication

DNA polymerase III

the enzyme responsible for synthesizing complementary strands of DNA during DNA replication. Also proofreads and corrects errors on the DNA strand.

RNA primer

a sequence of 10 to 60 RNA bases that is annealed to a region of single-stranded DNA for the purpose of initiating DNA replication

RNA primase

the enzyme that builds RNA primers

leading strand

the new strand of DNA that is synthesized continuously during DNA replication towards the replication fork

lagging strand

the new strand of DNA that is synthesized in short fragments, away from the replication fork, which are later joined together

okazaki fragments

short fragments of DNA that are a result of the synthesis of the lagging sttrand during DNA replication

DNA polymerase I

an enzyme that removes RNA primers and replaces them with the appropriate deoxyribonucleotides during DNA replication. Also proofreads the final strand.

DNA ligase

the enzyme that joins DNA fragments together by catalyzing the formation of a bond between the 3' hydroxyl group and the 5' phosphate group on the sugar-phosphate backbones

exonuclease

an enzyme that cuts out nucleotides at the end of a DNA strand

template

a single-stranded DNA sequence that acts as the guiding pattern for producing a complementary DNA strand

semiconservative

process of replication in which each DNA molecule is composed of one parent strand and one newly synthesized strand

DNA helicase

the enzyme that unwinds double-helical DNA by dusrupting hydrogen bonds

anneal

the pairing of complementary strands of DNA through hydrogen bonding

Single-strand binding protein

replication enzyme that prevents parent DNA strands from annealing to each other once they have been separated by helicase

DNA

(Deoxyribonucleic acid) Composed of long chains of individual units called nucleotides consisting of; deoxyribose, a phosphate group, and a nitrogenous base

nitrogenous bases

Form the rungs in DNA (Adenine, Guanine, Cytosine, Thymine) (Uracil replaces Thymine in RNA)

purines

Double ring structure (A & G)

pyrimidines

Single ring structure (T & C)

antiparallel

DNA strands oriented in opposite directions, such that the 5'-phosphate end of one strand is aligned with the 3'-hydroxyl of the other strand.

RNA

(Ribonucleic acid) sugar component is ribose, uracil instead of thymine as one of the bases, it is single stranded

Complementary Base Pairing

Pairing of the nitrogenous base of one strand of DNA with the nitrogenous base of another strand; adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C)

replication origin

specific sequence of DNA that acts as a starting point for replication

DNA polymerase II

repairs damage to DNA, including damage that occurs between replication events

telomeres

a repeating sequence of DNA at the end of a chromosome that protects coding regions from being lost during replication

cell senescence

period in a cell's lifespan when it loses the ability to divide and grow; often referred to as cell aging

Hayflick limit

total number of times that a normal cell can divide

telomerase

enzyme that adds new telomere sequences to the ends of chromosomes

nucleosome

unit of DNA storage, consisting of 8 histones with DNA strands wrapped around them.

solenoids

group of 6 nucleosomes

histones

positively charged proteins around which DNA is tightly coiled

Ion

Charged particle formed when an atom loses or gains electrons, so that the atom does not have an equal number of protons or electrons.

Electronegativity

Measure of the relative abilities of atoms to attract electrons.

Non-polar Covalent Bond

Chemical bond in which electrons are shared equally between two bonded atoms, such as carbohydrates and proteins.

Polar Covalent Bond

Chemical bond in which electrons are shared unequally between two bonded atoms with different electronegativities.

Polar Molecule

Molecule that has an unequal distribution of charge and net dipole, as a result of the polar bond within the molecule and the shape of the molecule.

Hydrogen Bonds

Weak attractions between polar molecules that contain hydrogen atoms bonded to the more electronegative atoms oxygen, nitrogen, or fluorine.

Hydrophillic

"water-loving"; describes molecules that interact with water.

Hydrophobic

"water-hating"; describes molecules that do not interact with water.

Organic

Term generally used to describe substances made up of carbon-based molecules, such as carbohydrates and proteins.

Inorganic

Term generally used to describe substances that do not cantain carbon, such as water and sodium chloride.

Macromolecules

Large molecules that are often made of distinct smaller units.

Monomers

Small repeating units that join together to make up polymers.

Polymers

Large molecules made of many repeating smaller molecules called monomers.

Cohesion

The sticking together of particles of the same substance

Adhesion

The sticking together of particles of different substances

What are the four main types of biological macromolecules

Proteins (PRO), Carbohydrates (CHO), lipid, and nucleic acid.

What type of bond links together smaller molecules to make macromolecules?

Covalent Bond.

What are the five properties of water?

Surface tension/cohesion, adhesion, solvent, solid water floats, and heat capacity.

What is the significance of surface tension/cohesion?

Cohesion is significant in the movement in water, if the water was not bonded together it would not flow. Also, cohesion and adhesion together make it possible to defy gravity.

What is the significance of adhesion?

Adhesion is significant because it allows water to move against gravity, especially in the xylem of plants.

Why is it significant that water is a universal solvent?

It is significant that water is a solvent because it is capable of breaking down ionic bonds as well as hydrogen bonds.

What is the significance of solid water floating?

Solid water floating keeps the water level stable. Water is the only substance that is denser in the liquid state than the solid state.

What is the significance of heat capacity?

Water holds heat well which helps to moderate temperatures.

-O-H

Hydroxyl
Polar, found in carbohydrates, lipids, proteins, and nucleic acids.

O
||
- C -

Carbonal
Found in Carbohydrates and Nucleic acids

O
/
-C
\
OH

Carboxyl
Found in proteins and lipids

O
||
O-P-O
|
O

Phosphate
-Found in nucleic acids

-S-H

Sulfhydryl
Found in proteins

H
/
-N
\
H

Amino Group
Found in proteins and nucleic acids

Metabolism

Name for chemical reactions in a cell

what are the products of glycolysis for ONE molecule of glucose?

2 net ATP
2 NADH
H2O
2 pyruvate

What are the reactants of glycolysis for ONE molecule of glucose?

2 ATP
4 ADP
2 NAD+
glucose
2 inorganic phosphates

What are the products of pyruvate oxidation for one molecule of glucose?

2 NADH
2 Acetyl-CoA
2 CO2

What are the products of the KREBS cycle for one molecule of glucose?

2 ATP
6 NADH
2 FADH2
CO2

What are the major structures (peripheral/integral proteins) involved in the the ETC?

In order:
NADH dehydrogenase
ubiquinone
cytochrome b-c complex
cytochrome C
cytochrome oxidase
ATP synthase

How is ATP produced in the cristae (Inner mitochondrial membrane)?

- the electrons from NADH and FADH2 are pumped through complexes, the energy released pumps H+ ions to the intermembrane space
- creates H+ ion gradient and increases proton motor force
- H+ ions move along [ ] gradient through ATP synthase complex into the matrix, creating ATP

The electrons in the ETC are accepted by _____, and form _____

Oxygen, water

Why is the actual # of ATP produced much lower than 36 or 38?

- Some protons leak through membrane without passing through ATP synthase complex
- ATP used to transport pyruvate from cytoplasm to mitochondria
- Some E used to transport ATP out of mito. for use in cytoplasm

Healthy diet consists of more than just glucose. If you ate something that contained protein (such as Alanine, glutamate), and fats, how would they be used for energy?

-Alanine: converted directed to pyruvate, glutamate can be converted to intermediates in Krebs.
- glycerol: converted to G3P for glycolysis
- fatty acids: transported to mitochondria where carbon atoms are removed in pairs creating Acetyl-CoA

What is the significance of phosphofructokinase?

Feedback control point: when enough ATP is produced, excess ATP binds to allosteric binding site on phosphofructokinase to inhibit enzyme.
- ADP activates this enzyme

Besides ATP, what other molecule can inhibit production of phosphofructokinase?

Citrate

What inhibits the conversion of pyruvate to Acetyl-CoA?

Excess NADH.

Explain the process of lactate fermentation.

Glycolysis produces NADH and pyruvate molecules that react with NADH to produce lactate. NAD+ is oxidized, allowing glycolysis to continue.

Explain the process of ethanol fermentation

Glycolysis produces NADH and pyruvate molecules, which get converted to Acetaldehyde. It reacts with NADH to produce ethanol. NAD+ is reoxidized. CO2 is produced.

What is the photosynthesis equation?

6CO2 + 6 H20 + energy --> C6H12O6 + 6O2

_____ 'funnels' light energy to the reaction centre, and is made up of ______.

antenna complex, accessory pigments

Explain the path of electrons starting from photons of light absorbed, to Photosystem II

- photons of light is absorbed by pigment molecule
- antenna complex funnels light energy to the unique chlorophyll a molecules in the reaction centre P680 of photo system II

1NADH yields how many ATP? What about from glycolysis?

3 ATP, otherwise only 2 ATP from glycolysis

1 FADH2 yields how many ATP?

2 ATP

Each time an H+ ion moves in through the ATP synthase from the intermembrane space to the matrix, __________ decreases.

Proton motor force. this is the energy stored in the electrochemical gradient

In the light dependent rxns, ___________ pumps H+ ions into the _________.

b6-f complex, thylakoid space

What happens when light energy is absorbed by photosystem I?

- light E is transferred to rxn centre P700, where e- get excited
- the e- are accepted by e- acceptors, and used by the enzyme NADP reductase to form NADPH.
- NADPH is later used for the light independant rxns.

What is photophosphorylation?

- ATP synthesis using light energy of photos and chemiosmosis

What is non-cyclic phosphorylation?

e- are transferred one direction, from photosystem II to NADP+ to NADPH. (1:1 ratio of ATP and NADPH)

What is cyclic phosphorylation and why is it needed?

- e- from the photosystem I are passed to e- acceptor
- passed back to b6-f complex then back to photosystem I
- same e- is used, yielding only ATP, no NADPH or oxygen
- needed bc more ATP needed for light independant rxn

What are the major structures involved in the light dependant rxns?

In order:
P680 rxn centre
plastoquinone
B6-f complex
plastocyanin
P700 rxn centre
ferredoxin
NADP reductase

Where does carbon get fixed?

in the stroma

Light is required for the light dependent reactions because
A) it is the source for electrons
B) it splits the water molecule
C) it energizes electrons in the reaction center
D) it splits ATP molecules which generates the energy necessary to power the light independent reactions
E) none of the above

C)

In the electron transport chain, H+ ions are pumped through various complexes across the membrane from _____ to _____.

matrix to intermembrane space (IN TO OUT)

In the light dependant rxns, H+ ions are pumped through the B6-f complex from _____ to _____.

stroma to thylakoid space

What is the significance of the nature of the bundle sheath cells for C4 plants?

Bundle sheath are impermeable to CO2, so CO2 is concentrated in these cells making it more efficient

How does the adaptation of C4 plants work?

- In the outer mesophyll cells, CO2 is fixed by adding PEP, creating oxaloacetate.
- This gets converted to malate, which is transported into the bundle sheath cells, which has a high [ ] of Co2
- malate is then decarboxylated (meaning CO2 is RELEASED), resulting in pyruvate which is transported back to mesophyll cells and converted to PEP
- bundle sheath are impermeable to CO2 thus makes calvin cycle more efficient.

What is the name of the first stage of the Calvin Cycle and what happens here?

Carbon Fixation:
- CO2 is bonded with a 5C compound RuBP catalyzed by the enzyme rubisco
- forms PGA (3C)

What is the name of the 2nd stage of the Calvin Cycle, and what happens?

Reduction:
- PGA is converted to higher E state, activated by ATP and reduced by NADPH
- forms G3P, and some G3P leave cycle to form glucose (if G3P levels are high, starch is made)
- others move on to replenish RuBP

What is the name of the 3rd stage of the Calvin Cycle and what happens?

Regeneration:
- Most G3P are used to regenerate RuBP
- requires ATP

How many times must the Calvin cycle be completed to synthesize ONE glucose molecule? What are the reactants needed?

6 times,

6CO2
18 ATP
12 NADPH

Name the compounds involved with the Calvin Cycle.

- 6 CO2 reacts with RuBP. This rxn is catalyzed by rubisco
- forms 12 PGA
- 12 ATP and 12 NADPH required to convert to 12 G3P
- 2 G3P used to make glucose, 10 G3P continue on in cycle
- 6 ATP required to convert into 6 molecules of RuBP

What is the full name for RuBP?

Ribulose 1,5-bisphosphate