Monday, November 2, 2015

Rudimentary Preparation for The Bio. Mock Exam


!!! Mini summaries of the chapters 2,3,4,5 and answers to the book questions !!! I certainly have some mistakes, typos etc, hopefully not important.



Chapter Two 2 WATERRR 2

- The chemical behavior of an atom depends on the number of electrons in its outermost (highest) energy level.

- Atoms crave for completely filled outer levels.
- Electrons are lost, gained, or shared until this condition is reached

1. An atom of nitrogen has 7 protons and 7 neutrons.

- What is its atomic number? Seven
- What is its atomic mass? Fourteeen
- How many electrons does it have? Seven

2. How do the isotopes of a single element differ from each other?
- They have different number of neutrons.

3. The half-life of radium-226 is 1620 years.
- If a sample of material contains 16 milligrams of radium-226, how much will it contain in 1620 years? Half of the initial, so, 8mg.
- How much will it contain in 3240 years? Half of what we had in 1620 years, so 4mg.
- How long will it take for the sample to contain 1 milligram of radium-226? Another two times of halfing, so 6480 years in total.


4. What is the octet rule, and how does it affect the chemical behavior of atoms?
- Atoms of main-group elements tend to combine in such a way that each atom has eight electrons in its valence shell, giving it the same electronic configuration as a noble gas.

More than 95% of the weight of an organism consists of oxygen, hydrogen, carbon, and nitrogen, all of which form strong covalent bonds with one another.


5. What is the difference between an ionic bond and a covalent bond? Give an example of
each.
- In covalent bonds the atoms share one or more valence electrons forming a compound or even large molecules. Example: N2.
- In ionic bonds atoms have more or less electrons than protons so they stay close due to the positive-negative attraction but there's no electron sharing. Example: NaCl

The central oxygen atom in water attracts the electrons it shares with the two hydrogen atoms. This charge separation makes water a polar molecule.



6(a). What types of atoms participate in the formation of hydrogen bonds?

- A hydrogen bond is formed between the partial positive charge of a hydrogen atom in one molecule and the partial negative charge of another atom.
-That happens either in another molecule or even in a different portion of the same molecule (in the case of macromolecules).



How do hydrogen bonds contribute to water’s high specific heat?
- Hydrogen bonds give water molecules a strong attraction to each other.
- In order to evaporate water and to energize each water molecule from the liquid to gas state, you have to break the hydrogen bonds between the water molecules.
- Since a lot of heat and energy is needed to break hydrogen bonds, water has a relatively high specific heat.

7. What types of molecules are hydrophobic? What types are hydrophilic? Why do these two types of molecules behave differently in water?
- Non polar molecules are hydrophobic and non-soluble in water.
- Polar molecules are hydrphilic and water-soluble.

- Water is cohesive and adhesive.

- It has a great capacity for storing heat.
-Water is a good solvent for other polar molecules and bad for nonpolar molecules.

The H+ concentration in a solution is expressed by the pH scale.

- pH equals the negative logarithm of the H+ concentration.

8. What is the pH of a solution that has a hydrogen ion concentration of 10–3 mole/liter? Would such a solution be acidic or basic?
- It's just log10[H+] = 3. The solution is acidic since its PH< 7.



CHAPTER three3333eeee MACROMOLECULZ


1. What types of molecules are formed by dehydration reactions? What types of molecules are formed by hydrolysis?

- Dehydration reactions are condensation reactions and can build all kinds of macromolecules.
- When two subunit molecules fuse together, one of them loses an -OH group and the other an H atom.
- That's a dehydration synthesis and gives one larger molecule and a molecule of water.
- Dehydration reactions need energy to break the existing bonds.
- Dehydration synthesis is being catalyzed by enzymes.
- Hydrolysis breaks down macromolecules to simpler compound molecules.
- Hydrolysis releases energy.
- Every 'break' in the macromolecule needs one molecule of water to be shared by the constituent compounds.


2. How are amino acids linked to form proteins?

- Aminoacids or peptides are linked with the 'peptide bond' to form a polypeptide chain.
- The amino group —NH2 end of one amino acid joins to the carboxyl group —COOH end of another.
- The formed peptide chain cannot rotate freely around these bonds.

3. Explain what is meant by the primary, secondary, tertiary, and quaternary structure of a protein.

- Proteins consist of long amino acid chains folded into complex shapes.
- Proteins' primary structure is just the sequence of the amino acids that comprise a protein chain. That's defined by the sequence of the gene that encodes the protein.
- The amino and carboxyl groups of the fused amino acids form hydrogen bonds along the chain.
- Those bonds in space create coil or sheets of the amino acid sequence chain .
- That folding of the amino acid chain is the protein's secondary structure.
- Coil-like secondary structure is called α-helix.
- Sheet like secondary structure is called β-pleated sheet.
- Tertiary structure is the final folded shape of one polypeptide chain.
- In tertiary structure the non polar side groups of the protein 'hide' inside and the polar ones face the outside.
- The initial sequence of amino acids determine the final structure of a protein.
- That means that if we unfold (denature) a polypeptide chain it's possible to spontaneously refold back into it's characteristic shape.
- A protein often consists of a few polypeptide chains connected with each other. That arrangement is its Quaternary Structure.
- When two or more polypeptide chains associate to form a functional protein, the individual chains are referred to as subunits of the protein.


- DNA is a two stranded linear polymer.
- DNA stores hereditary information in sequences of nucleotides.
- The two opposing DNA strands form a double helix.
- Cells translate nucleotide sequences on the DNA producing complementary single strands of RNA.
- That RNA is then transcribed to amino acids that form the eventual protein.

4. What are the three components of a nucleotide? How are nucleotides linked to form nucleic acids?

Each nucleotide is made of:
- One five-carbon sugar.
- One organic nitrogenous base
- One a phosphate group.
- Nucleotides link in chains to form nucleic acids.
- The nucleotides form phosphodiester bonds between the phosphate group of one and the sugar group of the next.
- The organic nitrogenous bases can be either purines (A,G) or pyrimidines (C,T ,U).

In DNA has thymine and RNA uracil.


- Adenine bonds with Thymine in DNA and Uracil in RNA with 2 hydrogen bonds. Α=Τ/A=U

- Guanine bonds with Cytosine with 3 hydrogen bonds.  G≡C

See the figures, they help a lot !!!


- Some types of lipιds are: waxes, mono/di/triglycerides, phospholipids, terpenes, steroids, and prostaglandins.

- The phospholipid molecule has a polar “head” at one end (the phosphate group) and two long, nonpolar “tails” at the other.

Phospholipids form bilayer membranes.

5. What are the two kinds of subunits that make up a fat molecule, and how are they arranged 
in the molecule?
- Fats consist of one glycerol molecule and 3 attatched fatty acids (one to each carbon of the glycerol backbone).
- Unlike phospholipids, fat molecules do not have a polar end. 
- Fats are also called triglycerides!
- Organisms store the energy for long periods in the many C—H bonds of fats.

- Carbohydrates store energy in their carbon-hydrogen (C—H) bonds.

- The most important carbohydrate is glucose, a six-carbon sugar.

- Excess energy resources can be stored in complex sugar polymers: starches (in plants) and glycogen (in animals and fungi).


8(a). What does it mean to say that glucose, fructose, and galactose are isomers?

Isomers have the identical chemical groups in different configurations.

Glucose, fructose, and galactose can be written as C6H12O6 but are different functionally.

8(b). Which two are structural isomers, and how do they differ from each other? Which two are stereoisomers, and how do they differ from each other?
- Glucose and fructose are structural isomers. That means that identical chemical groups bonded to different carbon atoms.
- Glucose and galactose are stereoisomers. They have identical chemical groups bonded to the same carbon atoms but in different orientations. (like your face mirrored)
- - -

Chapter FOUR 4 4 4 4 4 4


1. What characteristics of living things are necessary characteristics (possessed by all living things), and which are sufficient characteristics (possessed only by living things)?

Necessary:
- Cellular organization
- Sensitivity
- Growth
- Development
- Reproduction
- Regulation (Mechanisms that coordinate internal processes)
- Homeostasis (relatively constant internal conditions, different from their environment)
- Sufficient:
Heredity: A genetic system is the sufficient condition of life

2(a). What molecules are thought to have been present in the atmosphere of the early earth?

- Carbon dioxide (CO2) and nitrogen gas (N2),water vapor (H2O), Cyanide hydrogengas (H2) and compounds like hydrogen sulfide (H2S), ammonia (NH3), and methane (CH4).

2(b). Which molecule that was notably absent then is now a major component of the atmosphere?

- Oxyen bitches. Fresh, hefty, oxidizing O2.

3(a). What evidence supports the argument that RNA evolved first on the early earth?

- The “RNA world” argument bases on discovered ribozymes, RNA molecules that can behave as
enzymes, catalyzing their own assembly.
- So RNA is 2 in 1. Can pass on inherited information AND act like an enzyme! SO MUCH WIN.

3(b). What evidence supports the argument that proteins evolved first?

- The “protein-first” group argues that without enzymes (which are proteins), nothing could
replicate at all, heritable or not.
- Nucleotides, are too complex to form spontaneously again and again.
- Simple proteins are easier to synthesize from abiotic components than nucleotides.

4. What are coacervates, and what characteristics do they have in common with organisms? Are they alive? Why or why not?

- Coacervates are bilipid layer bubbles that can contain amino acids.
- They can divide if pinched in two, like bacteria and do facilitate some acid-base reactions.
- We can't say they are alive because they can't multiply autonomously in a hereditary way.


5. What were the earliest known organisms like, and when did they appear? What present-day organisms do they resemble?

- The earliest known organisms are prokaryotes (single celled with no nuclei).
- They have no external appendages, and probably no internal structure.
- They look like today's bacteria although some ancient forms
cannot be matched exactly.
- They appeared 3.5 million years ago according to microfossils


6. When did the first eukaryotes appear? By what mechanism are they thought to have evolved from the earlier prokaryotes?

- Eukaryotes appeared about 1.5 billion years ago.
- Their internal membrane system (endoplasmic reticulum) and the nuclear envelope may have evolved from infoldings of the plasma membrane of prokaryotic cells.
- Mitochondria and Chloroplasts may origin from bacteria that have entered other, larger bacteria.

- Instead of destroying one another they adapted to a lovely symbiosis and lived happily ever after.
- Organelles such as mitochondria, chloroplasts, and centrioles contain their own DNA, remarkably similar to bacterial DNA.

7. What sorts of organisms are contained in each of the six kingdoms of life recognized by biologists?

The Six Kingdoms:
- Plants

- Animals
- Protists
- Fungi
- Archaebacteria
- Eubacteria.

!!! Chapter Five daCELLL


The cell is the smallest unit of life.

- All living things are made of cells.
- Cell outer and inner membranes are made of phospholipid and proteins.
- The nuclear region contains the genetic material.
- Cytoplasm is the volume inside the cell but outside the nucleus.

1. What are the three principles of Asimov's the cell theory?


1) All organisms consist of one or more cells.
2) The cell is the basic unit of structure for all organisms.
3) All cells arise only from preixisting cells.


2. How does the surface area-to-volume ratio of cells limit the size that cells can attain?
- The larger a cell is, the longer it takes for substances to move from the plasma membrane to the center of the cell.
- As a cell’s size increases, its volume increases much more than its surface area.
If two spherical cells differ by 10 cm in diameter, the larger cell will have 100 times, the surface area, but 1000 times, the volume of the smaller cell

- Bacteria have prokaryotic cell structure.
- Prokaryotes do not have membrane-bounded organelles within their cells. 
- Bacterial DNA is a circular molecule.

3. How are prokaryotes different from eukaryotes in terms of their cell walls, interior organization, and flagella?
- Most bacteria have a strong cell wall composed of peptidoglycan. 
- No eukaryotes possess similar cell walls.
- Some bacteria use a flagellum to move & often feed.
- Flagella are long, threadlike protein fibers.
- The internal of bacteria is extremely simple, with macromolecules just swimming inside them.
- Eycariotes' interior is organized in complex structures and compartments.
- Organelles are membrane-bounded structures in the cell's cytoplasm.
- Complex biochemical processes can proceed simultaneously and independently in different organelles. 
- Many organelles and even the nucleus are parts of a complex endomembrane system.
- Plant cells often have a huge central vacuole.
- Both plant and animal cells contain vesicles.
- Vesicles are small sacs that store and transport different materials.
- Eycariotes have a nucleus (or more, or none few times).

4(a) What is the endoplasmic reticulum? What is its function?

- The endoplasmic reticulum (ER) is an extensive system of folded membranes that divides the interior of eukaryotic cells into compartments and channels.

4(b)How does rough ER differ from smooth ER?
- The rough ER synthesizes proteins.
- The smooth ER organizes the synthesis of lipids and other biosynthetic activities.

5(a). What is the function of the Golgi apparatus?

- The Golgi apparatus is the delivery system of the eukaryotic cell.
- It collects, packages, modifies, and distributes molecules (e.g lysosomes) that are synthesized at one location within the cell and used at another.

5(b)How do the substances released by the Golgi apparatus make their way to other locations in the cell?

- The Golgi apparatus puts the substances for transfer in (secretory) vesicles. Then the vesicles
travel to the receiving end in the cell or even are exported outside the cell.


6. What types of eukaryotic cells contain mitochondria? What function do mitochondria perform?

- Mitochondria can be found in all types of living eukaryotic cells.
- Mitochondria are the energy factories of the cells. They produce adenosine triphosphate (ATP) using energy stored in food.
- Fat cells and muscle cells have many mitochondria because they process a lot of enery.
- Various fibrous proteins make the cytoskeleton.
- The cytoskeleton provides structural support and other functions.
- Many eukaryotic cells possess flagella or cilia.
- Flagella and cilia are built in a 9 + 2 arrangement of microtubules.



7. What unique metabolic activity occurs in chloroplasts?
- Photosynthesis! 
- Chloroplasts allow cells to 'manufacture' their own food. 

8. What cellular functions do centrioles participate in?

- Centrioles are barrel-shaped organelles found in the cells of animals and most protists.
- Centrioles come in pairs 'inside' a centrosome.
- Centrioles help to assemble microtubules.
- Microtubules are long, hollow protein cylinders.
- Microtubules influence cell shape, move the chromosomes in cell division, and provide the functional internal structure of flagella and cilia.

9. What kinds of cytoskeleton fibers are stable and which are changeable?
- Eukaryotic cells may contain three types of cytoskeletal
fibers:
1. Actin filaments. Actin filaments are made of two twisted strands of actin (a fibrous protein).
Actin filaments are all over the cytoplasm but mostly below the plasma membrane in bundles known as stress fibers. The stress fibers can contract.
2. Microtubules. Microtubules are composed of 13 side-by-side stacks of tubulin (protein). They are continually polymerizing and depolymerizing, changing after few minutes or seconds.
3. Intermediate filaments. Intermediate filaments are composed of overlapping tetramers of protein. They form a ropelike structure of tremendous mechanical strength to the cell.


10. How do cilia compare with eukaryotic flagella?
- In eykariotes the structure of cilia is similar to that of flagella, but cilia are usually shorter. 
- A cell surface can have way more cilia than flagella.
- Cilia are short cellular projections that are often organized in rows.


11(a). What is the endosymbiont theory?

- The theory of endosymbiosis explains how some of today’s eukaryotic organelles evolved.
- Prokaryotes entered and lived inside other species of prokaryotes, creating the first eykariotes.
- The inside prokaryotes helped the host cells'metabolic activity.
- Mitochondria and chloroplasts are believed to have originated as bacteria.

11(b).What is the evidence supporting this theory?
- Both mitochondria and chloroplasts are surrounded by two membranes.
- Mitochondria are about the same size as most bacteria.
- The cristae formed by their inner membranes resemble the folded membranes in various groups of bacteria. 
- Mitochondrial ribosomes are similar to bacterial ribosomes in size and structure.
- Both mitochondria and chloroplasts contain circular molecules of DNA similar to bacterial ones.
- Finally, mitochondria divide by simple fission, splitting in two just as bacterial cells do.

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