bio2010 final exam

Know the four major biological macromolecules

Lipids, carbohydrates, proteins, and nucleic acids.

Why do hydrogen bonds form between water atoms

water molecules are polar - oxygen atom has negative charge and hydrogen atoms have positive charges;
negative atoms attracted to positive atoms of other water molecules

which are polymers and which are not

All of them are polymers except lipids.

atomic number

the number of protons in the nucleus of an atom

Understand how polymers are built from monomers and how they are broken down

Polymers are built from monomers by combining monomers through dehydration reactions, and they are broken apart by hydrolysis.

The atomic nucleus

The small, dense region consisting of protons and neutrons at the center of an atom

dehydration reaction

A chemical reaction in which molecules combine by removing water from between the two molecules (H and OH groups come together to release a water and bind)

atomic mass

Number of protons and neutrons

Hydrolysis

Breaking down complex molecules by the chemical addition of water to a binding site, separating the monomers.

Lipids (the only non-polymer of the bunch)

Lipids are hydrophobic molecules made of fatty acids.

understand the structural differences between fatty acids and phospholipids

Fatty acids are completely hydrophobic while phospholipids have hydrophobic bodies and hydrophilic heads with the phosphates.

isotopes

Atoms of the same element that have different numbers of neutrons

appreciate how the structure of phospholipids is responsible for cellular membranes

The hydrophilic heads combined with they hydrophobic tails allow the phospholipids to create a bilayer that is semipermeable.

valence electrons

Electrons on the outermost energy level of an atom

Identify common carbohydrates from their structures

Sugars, often contain carbon, hydrogen, and oxygen.

know how monosaccharides combine to form polysaccharides

Dehydration reactions

identify some common polysaccharides made specifically of glucose monomers

Glycogen, amylose, etc.

Covalent bonds

Bond where two atoms are connected to each other by the sharing of two or more electrons

Understand the nature of cellular membranes: What are they made of?
What are the properties of the molecules of a membrane and how do they affect membrane and cellular function

Cellular membranes are made of a phospholipid bilayer, with some transport proteins distributed throughout the membrane. The phospholipid contains a hydrophilic head and a hydrophobic tail, and two of these phospholipids can line up with their heads facing outwards to create the bilayer.

which types of atoms form covalent bonds with each other

nonmetals

Know how different molecules can cross a cellular plasma membrane. What molecules can pass right through and why?

Small non-charged particles can pass through the membrane because they can fit in the gaps between the phospholipids and they do not have any charge that would cause any disruption while going through the membrane.

Know how different molecules can cross a cellular plasma membrane. What molecules can pass through with the help of membrane proteins but without the expenditure of energy and how does this happen?

Larger molecules can pass through the membrane through transport proteins when there is a larger concentration of these molecules outside of the cell. This occurs because of diffusion, and the cell is trying to reach equilibrium.

Know how different molecules can cross a cellular plasma membrane. What molecules require the expenditure of energy to cross the membrane and how does a cell achieve this?

If a molecule requires the cell to expend energy to make it cross through the membrane, it is likely going against the concentration gradient and takes the cell away from equilibrium. The cell achieves this by converting ATP to energy on the transport protein and this energy is used to transport the molecule through the membrane.

polar vs. non-polar covalent bonds

Non polar have the same electronegativity when polar have a slight more positive end and more negative end

Understand the impact that solutions of different tonicity have on cells. Be able to describe the direction of osmosis for a cell in different solutions

Isotonic: Same tonicity. There should be no change in the cell because the concentrations are equal.
Hypotonic: The concentration of the solute is greater inside of the cell than outside of the cell, the cell will swell and possibly burst.
Hypertonic: The concentration of the solute is lower inside of the cell than outside of the cell, the cell will shrivel.

single vs. double covalent bonds

The number of pairs of electrons shared between two atoms determines the type of the covalent bond formed between them (1\=single, 2\=double, etc.)

Thoroughly understand the concepts involved in co-transport and how those concepts apply to both cellular respiration and photosynthesis

Co-transport involves using the movement of an ion with its concentration gradient to move another molecule against its concentration gradient in one transport. After photosynthesis the sugars produced are carried out of the chlorophyll through a co-transport and are carried into other parts of the cell. During cellular respiration, the sugar is carried into the cell also by co-transport.

Ionic bonds

Formed when one or more electrons are transferred from one atom to another

Know the difference between anabolic and catabolic pathways and how that difference affects energy flow either into or out of the molecules involved

Anabolic pathways involve building larger molecules and requires energy in order to create the bonds. Catabolic pathways break down larger molecules and release energy from the molecules.

which types of atoms form ionic bonds with each other

nonmetal and a metal exchange electrons

Understand the relationship between free energy, spontaneous reactions and entropy

Free energy is the energy associated with a reaction that is capable of doing work. If the free work associated with a reaction is negative, then the reaction is spontaneous, which means it is not driven by an outside force. Entropy is a measurement of randomness or uncertainty. If a reaction is spontaneous, free energy and entropy decreases

Weak interactions

forces believed to cause the nuclei of some atoms to break apart

Know how a change in free energy drives a reaction and how that applies to the storage of potential energy

-During a spontaneous change, free energy decreases and the stability of a system increases (exergonic-energy released)
-Increase of free energy of system and promote instability (endergonic-energy required)
Exergonic reaction provide the energy for the endergonic one

Hydrogen bonds

Very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the electrostatic atom in another molecule

chemical equilibrium

a state of balance in which the rate of a forward reaction equals the rate of the reverse reaction and the concentrations of products and reactants remain unchanged

Understand the concept of coupling an exergonic reaction to an endergonic reaction in order to drive the endergonic reaction that otherwise would not take place

-A cell has to do chemical, transport, and mechanical work but in order to do that cells manage energy resources by energy coupling
-ATP powers cellular work by coupling exergonic reactions to endergonic reactions
-Coupled reactions:
Glutamic acid + ammonia \= glutamine (endergonic)
ATP\= ADP + P (exergonic)
-ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways

Understand the effect of an enzyme on the energy dynamics of a reaction

Enzymes lower activation energy for a specific reaction
-Enzymes catalyze reactions by lowering energy barriers
enzymes do not provide any energy
enzymes have no effect on delta g

importance of hydrogen bonds between water atoms

keeps water liquid over a wider range of temperature than is found for any other molecule its size

What does it mean for a molecule to be oxidized?

For a molecule to be oxidized, it means it lost an electron.

What does it mean for a molecule to be reduced?

If a molecule is reduced, it gained an electron.

Why are reduction and oxidation reactions always coupled with each other?

The two reactions are coupled together because a molecule cannot lose an electron if there is not another molecule that is able to pick up the electron.

What do redox reactions have to do with energy transfer, Cellular Respiration, and Oxygen

Cellular respiration makes use of redox by using electron carriers to carry the electrons and the energy of the bond that is gained from breaking apart the glucose, and that energy is used to create ATP. The oxygen used during cellular respiration goes from being neutral to containing a -2 charge because it is converted from O2 to CO2 and H2O during cellular respiration.

hydrogen bonds are responsible for changes in temperature

When heat is absorbed, hydrogen bonds are broken and water molecules can move freely

Be able to break down cellular respiration into four distinct parts

Glycolysis, oxidation of pyruvate, citric acid cycle, oxidative phosphorylation.

hydrogen bonds are responsible for the storage and release of heat energy

When the temperature of water decreases, the hydrogen bonds are formed and release a considerable amount of energy

Glycolysis

the breakdown of glucose by enzymes, releasing energy and pyruvic acid.

how hydrogen bonds are responsible for the nature of specific heat and calories

water has a high specific heat capacity, which is defined as the amount of heat needed to raise the temperature of one gram of a substance by one degree Celsius. The amount of heat needed to raise the temperature of 1 g water by 1 °C is has its own name, the calorie

Oxidation of Pyruvate

When pyruvate moves into the mitochondrion and becomes Acetyl CoA

the ability of polarized (hydrophilic) molecules to dissolve in water

As a result of water's polarity, each water molecule attracts other water molecules because of the opposite charges between them, forming hydrogen bonds. Water also attracts, or is attracted to, other polar molecules and ions, including many biomolecules, such as sugars, nucleic acids, and some amino acids

Citric Acid Cycle

Completes the breakdown of glucose by oxidizing a derivative of pyruvate (Acetyl CoA) to carbon dioxide.

inability of non-polar (hydrophobic) molecules to dissolve in water

these molecules separate from water rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution) ex:oils and fats

Oxidative Phosphorylation

The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.

Molarity

the number of moles of solute per liter of solution

In an acidic solution

the number of H+ is greater than the number of OH-.
(pH less than 7)

Electron Transport Chain

A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.

Chemiosmosis

A process for synthesizing ATP using the energy of an electrochemical gradient and the ATP synthase enzyme.

A basic solution has...

a low H+ concentration, less than that of pure water
(pH greater than 7)

For each part of cellular respiration know the molecule(s) needed to begin the pathway, the molecule(s) produced at the end of the pathway, the important products derived from the pathway, and the location of each pathway in the cell

Glycolysis: Put in glucose, get pyruvate.
Oxiation of Pyruvate: Put in Pyruvate, get Acetyl CoA
Citric Acid Cycle: Put in Acetyl CoA, get CO2
Oxidative Phosphorylation: Put in e-, get ATP

logarithmic scale of pH

pH of 4 is ten times more acidic than pH of 5 and 100 times more acidic than pH of 6

Be able to follow potential energy as it is passed from a glucose molecule to ATP molecules

Glucose -\> NADH + FADH2 -\> Electron Transport Chain -\> Proton Motive Force -\> ATP

basic properties of the carbon atom

ability to bond with oxygen, hydrogen, nitrogen, phosphorus and sulfur. Carbon biochemical compounds are essential to all life on the planet. Because of its bonding ability, carbon can form single, double, or triple covalent bonds with other atoms

the number of unpaired valence electrons determines

The number of covalent bonds an atom tends to form

Be able to follow electrons as they are passed from glucose molecules eventually to oxygen

Glucose -\> NADH and FADH2 -\> Electron Transport Chain -\> Proton Motive Force -\> O2

Know where and how glucose and oxygen are consumed and where and how carbon dioxide and water are produced

Glucose is consumed in glycolysis and broken down into Pyruvate. Oxygen is consumed during the oxidative phosphorylation stage. Carbon dioxide is produced at the end of the citric acid cycle, and water is produced at the end of the oxidative phosphorylation.

hydrocarbons

Compounds composed of only carbon and hydrogen

Understand how photosynthesis and cellular respiration are related to each other

Photosynthesis produces the glucose that is used in cellular respiration to produce ATP.

Why hydrocarbons are hydrophobic

there is an equal sharing of electron between the Carbon atoms and the Hydrogen atoms (non-polar), thus, there is no charge separation in the molecule and it cannot form hydrogen bonds with water

Be able to describe the two major parts of photosynthesis

The light process, which occurs in the thylakoids, splits water molecules, releases O2, reduces NADP+ to NADPH, and generates ATP using photophosphorylation. The Calvin Cycle, which produces in the stroma, forms sugar from CO2 using ATP and NADPH.

what makes two molecules isomers of each other

has the same number of atoms of each element, but has a different arrangement of the atoms

The light reactions

The first of two major stages in photosynthesis (preceding the Calvin cycle). These reactions, which occur on the thylakoid membranes of the chloroplast or on membranes of certain prokaryotes, convert solar energy to the chemical energy of ATP and NADPH, releasing oxygen in the process.

Structural Isomers

differ in the covalent arrangements of their atoms

Calvin Cycle

reactions of photosynthesis in which energy from ATP and NADPH is used to build high-energy compounds such as sugars

cis-trans isomers (double bonds)

have the same covalent bonds but differ in spatial arrangements

Know where water and carbon dioxide are consumed and where oxygen, ATP, NADPH and glucose are produced

Carbon dioxide is consumed in the beginning of the Calvin cycle, while water is consumed in the light reactions. Oxygen, ATP, and NADPH are all produced in the light reactions, while glucose is produced at the end of the Calvin Cycle.

Enantiomers (asymmetric carbons)

isomers that are mirror images of each other

Understand the relationship between the light reactions of photosynthesis and oxidative phosphorylation in cellular respiration

The light reactions of photosynthesis and the oxidative phosphorylation of cellular respiration produce ATP, and use the transport of electrons to create a proton-motive force which drives ATP synthase.

Hydroxyl group

-O-H ; adds polarity; It is present in Alcohols and Carboxylic Acid molecules

Helicase

is a molecule that separates the two strands of DNA during replication.

single strand binding proteins

bind to the separated DNA strands to keep them separated.

Topoisomerase

works down the DNA double-helix, untwisting and un-kinking the strand.

primase

attaches to a starting area and begins the RNA primer.

DNA polymerase III

In charge of synthesizing nucleotides onto the leading end in the classic 5' to 3' direction.

DNA polymerase I

works to put on the lagging strand and replaces the RNA primer sequences.

Ligase

connects the different fragments.

What is an Okazaki fragment and how are they eventually joined together to form a continuous DNA strand?

it is a strand of the lagging DNA that is short because it ran into the back end of an RNA sequence. They are joined together once the RNA is replaced with DNA and the two are joined by ligase.

Carbonyl group

-C\=O ; adds polarity; the carbon can serve as a reaction site for many reactions. It is present in Aldehydes, Ketones, Esters, Anhydrides, and Carboxylic Acids

Understand the differences between the replication of circular and linear chromosomes-What do telomeres do for Eukaryotic chromosomes and why are they necessary

Linear chromosomes replicate the normal way, with leading and lagging strands just going down the two strands, but in circular chromosomes the strand splits into a parent and daughter strand, where the two continue in the replication bubble until they reach the edge of the circle, then the two strands separate into their own two circles.
Telomeres are the edges of chromosomes that act as a cap, so when DNA replicates it does not lose the chromosomes at the edge of the strand.

Carboxyl group

-COOH ; consisting of a carbonyl group bound to a hydroxyl group; It is the main functional group in organic acids, meaning it increases in H+ so it is acidic

How does transcription differ in prokaryotic and eukaryotic cells?

In eukaryotes the mRNA must be processed before it can begin translation, and it is done in the nucleus.

Amino group

H-N-H ; decreases H+ so acts as a base

What is a promoter and what does it do for transcription

The promoter is the DNA sequence where RNA polymerase attaches, and it begins the process of transcription by allowing RNA polymerase to bind to it.

Thiol/Sulfhydryl group

-SH ; The amino acid cysteine contains a thiol group. adds polarity; 2 of these groups together forms covalent bonds between hydrogens called a disulfide bridge

How does RNA polymerase work

RNA polymerase attaches to the promoter region of DNA, begins to unwind the DNA helix, and attaches RNA bases corresponding to the DNA bases, and it slides along until it reaches the terminator sequence, where it detaches and releases the mRNA strand.

Phosphate group

PO4- ; adds polarity, has 2 full negative charges and releases energy

Methyl group

-CH3 ; non-polar, non reactive, only one ti reduce interactions with water

initiation

Transcription factors begin to bind to the promoter sequence, then RNA polymerase II binds around the transcription factors and the promoter sequence.

Elongation

The RNA polymerase II moves along the DNA strand, adding on RNA nucleotides to the 3' end of the growing RNA molecule, unwinding the double helix at about 10 to 20 bases at a time.

termination

RNA polymerase continues to make the new RNA strand until it reaches a terminator sequence, where RNA polymerase releases from the DNA and the RNA strand continues on.

Understand how Eukaryotic RNA transcripts are modified and for what purpose

The 5' end receives a modified 5' G-cap, the 3' end receives a poly-A tail, and spliceosomes go along the RNA strand and remove introns and bind exons together.

Aldehyde group

the second compound containing the carbonyl group (C\=O), one of the two groups attached to the carbonyl carbon is an alkyl group, while the other is a hydrogen atom