Topic 1 - Chemistry of life: Water

Only 25 of the 90 natural elements (periodic table) are essential for life.  We call these biogenic elements.
They can be divided into two groups:  macroelements (need lots) and microelements (needed in small quantities)

O - O2, H2O
C - CO2, organic compounds (lipids, carbohydrates, proteins, nucleic acids, vitamins)
H - H2O, CH4
N - amino acids, proteins, nucleic acids

-the most important inorganic compound
70-95% of most organisms (98% in jellyfish, about 70% in humans)
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- from the molecular structure you can see that water is a dipolar molecule with electron sharing
-hydrogen bond:  attraction of opposite charges, weak bond, H end attracts O end of another H2O or an anion
-very important in holding large molecules together, eg. proteins, DNA, etc
1. Excellent solvent - H2O attracts ions and surrounds them, split ionic bond (dissociation) and prevents reassociation by creating hydrate shells (vizburok) around them, therefore they dissolve. eg. NaCl.  It also works for polar molecular substances eg. sucrose.  H2O can't dissolve apolar substances
2.Thermal properties: High thermal capacity (fajhő) - this is the amount of heat needed to raise the temperature of 1g by 1 degree Celsius.  Water has a high boiling point (liquid at ambient temperature and pressure)
3.  Surface tension (force that causes surface to contract to occupy the least possible area): Highest of any liquid except mercury, therefore water is pulled into spherical shapes and it creates a surface film, which supports insects, creates a habitat and causes capillarity (cohesion and adhesion) in plants' xylem.
4. Freezing properties: At temperatures LESS than 4C,  volume is high and density is low, therefore ice floats - this protects organisms that live in water.  At 4C water is densest and collects at the bottom.  Ice is a thermoinsulator.

Topic 2 - Chemistry of Life: Organic compounds

Organic compounds
-carbon based molecules, also called biomolecules

The role of carbon
Carbon has 4 electrons in its outer valence shell, therefore it can form very stable compounds by covalent bonding (a very strong type of bond).
The compounds formed can range from simple molecules to very large macromolecules.  They can be straight chains, branched chains or even rings, with single, double or triple bonds, therefore very diverse C skeletons.

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 Isomers increase diversity.  Isomers are compounds with the same atoms (chemical formula), but different 3D structures eg. glucose and fructose.

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How large compounds are formed 
Monomers are smaller organic compounds which form the basis for the larger compounds.  They are often bound together in repetitive chains, therefore they are called the subunits of the larger compounds.
The larger compounds are called polymers.

Starch and glycogen are polymers made of many glucose monomers.

Polymers are formed by condensation reactions.

Hydrolysis breaks down polymers into monomers.

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Topic 3 - Chemistry of Life: Carbohydrates (Szénhidrátok)

-most common organic compounds (biomolecules)
-are energy sources for cells - broken down by cellular respiration (needs O2)-17kJ/g, half as much as lipids, but breakdown is much faster
-can be mono-, di- and polyssacharides

a.  Monosaccharides
-sweet, H2O soluble, crystalizable
-general formula:  (CH2O)n
Triose sugars (n=3)
-these are all intermediate products (köztes termékek) in biochemical reactions
-most common: glyceraldehyde (oxidation product of glycerol)
Pentose sugars (n=5)
-biologically important: parts of nucleotides and nucleic acids, most common are deoxyribose and ribose

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Hexose sugars (n=6)
-most common monosaccharides, eg. alpha-glucose, beta-glucose (szölőcukor), fructose (gyümölcscukor) and galactose are all isomers of C6H12O6 and form the monomers of most di- and polysaccharides
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b.  Disaccharides
-2 monosaccharides combine by condensation to form a disaccharide
glucose + fructose = sucrose (table sugar) - remember this is the main form in which carbohydrates are transported in plants!
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2 alpha glucoses = maltose - common in germinating seeds, result of hydrolysis (break down) of starch
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glucose + galactose = lactose (tejcukor) - found in milk
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c.  Polysaccharides
- largest carbohydrates
- long chains of monsaccharides (hexose sugars)
- can be folded
- general formula: (C6H10O5)n
- broken down into monomers (by hydrolysis) if needed for energy
- insoluble in H2O because of size
- not sweet
- cannot crystalize

TYPES of polysaccharides:
i.  Storage polysaccharides
-insoluble, therefore they won't diffuse out of cells and won't affect osmosis
STARCH: found in plants - made of 2 types of chains
-amylose: unbranched alpha-glucose, stains blue with iodine
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-amylopectin:  alpha-glucose chain with side branches, stains red-purple with iodine
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-the chains fold and pack together into starch grains (keményitőszemcse) - 20% amylose, 79% amylopectin, 1% fatty acids and phosphates
 GLYCOGEN: found in animals and fungi
- alpha-glucose is arranged like amylopectin (branched), but the chains are shorter and more branched.
-glycogen is found particularly in muscle and liver cells.
-human glycogen stores provide enough energy for a few hours.

ii.  Structural polysaccharides
- makes up 50% of the plant cell wall
- each molecule is a chain of approximately 10 000 beta-glucose, unbranched
- OH-groups form H-bonds with neighbouring chains to create a lattice
- about 2000 chains mass together to form microfibrils, which are visible under an electron microscope

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- the lattice is linked together by hemicellulose, which is a short polysaccharide
-cellulose is indigestible to animals (we consider it the "fiber" in our diet!)
-used to produce cotton, rayon, cellophane, celluloid and paper
- found in arthropod exoskeletons and fungal cell walls
- long chains of beta-glucose, but on each monomer the OH-group is substituted by a nitrogenous group (NHCOCH3)

Topic 4 - Chemistry of Life: Proteins

Proteins are large molecules.

They are not really soluble, rather they form colloids
- colloids are about 500nm, which is larger than particles in solution, but smaller than particles in suspension
- colloids exist in a "sol-gel state", whereby sometimes they appear to be liquid and at other times they are jelly-like (much of the material in cytoplasm is colloid)

Proteins contain: C, H, O and N, sometimes S and P

There are an almost limitless number of proteins, which vary between species and are often species-specific (fajlagosok).  They determine the characteristics of a species.

Types of Proteins
a.  Structural proteins - these form the organism. eg. hair, nails, feathers, etc.
b.  Physiological proteins - these carry out functions, examples include:
-enzymes (biocatalysts)
-carrier molecules (szállítómolekulák)
- pigments (eg. various colour molecules in skin and eyes, haemoglobin in red blood cells)
- hormones (chemical messengers)
- contractile material in muscles
- antibodies (disease protection)
** Proteins are rarely stored (only in seeds and eggs).  Proteins are only broken down for energy if a living organism is starving.

- a protein is a polymer.  Its monomers are called amino acids.

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- some amino acids are basic, others are neutral - this depends on the variable group
- some amino acids are polar and others are apolar - this depends on the variable group
-amino acids are soluble in water, where they form dipolar ions (zwitterion = ikerion), this means they have BOTH acid-base properties, so they have good buffering capacity.

Synthesis of polypeptides
- amino acids attach to each other by condensation to form covalent peptide bonds
2 amino acids condense to form a dipeptide, 3 form a tripeptide and many joined together form a polypeptide.

Formation of a dipeptide
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- if more than 100 amino acids attach together it is considered a protein
- polypeptides (and proteins) are broken down by hydrolysis
*both condensation and hydrolysis require enzymes to occur.

Primary structure: this is the number and sequence of the amino acids.
*Insulin was the first protein to have its primary structure determined by a researcher named Fred Sanger
Secondary structure: This type of structure is created by H-bonds forming between amino acid monomers
Alpha helix (eg. keratin - a major component of hair and skin)

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Beta-pleated sheet (eg. silk protein)

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-both structures can be found in a single protein.

Tertiary structure:  This is the secondary structure folded in 3-dimensional space.
-usually forms globular shapes
-bonded by S-bridges (requires the amino acid cysteine), ionic bonds, H-bonds and van der Waals forces

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Quaternary structure:  A protein has quaternary structure if it is formed of 2 or more subunits (polypeptides).  They are held together by various forces including hydrophobic interactions, H-bonds and ionic bonds.
eg. Haemoglobin

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Proteins can further be catagorized as simple or complex.  A simple protein contains only amino acids, complex proteins often include other elements, such as the iron containing haeme molecule found in haemoglobin (above).

Protein Stability and Denaturation
A protein will be stable (maintain its shape and function) if the environment it is in is appropriate.  The most common environmental factors that will cause a protein to denature (lose its shape and/or function) are temperature and pH levels.  Some proteins have a wide range of tolerance (can function at 4C and at 40C), while others have a very narrow range.  This is a protein-specific characteristic.  An example of protein denaturation is when we cook an egg.  The white of the egg is almost entirely made of the protein albumin.  At room temperature it is a clear liquid.  If we increase the temperature, the protein starts to denature (lose its shape and therefore function too) and it become solid and white.  Denaturation occurs because the bonds between the amino acids are broken.
Sometimes denaturation is permanent (like cooking an egg), other times it can be reversible.

Topic 5 - Chemistry of Life: Lipids

Lipids are insoluble in water because they are nonpolar.
BUT, they do dissolve in apolar solvents, like alcohols, ethers, etc.

Lipids include:
Fats and oils

A. Neutral fats and oils
- these have high energy content
-structure:  made of a backbone with adjoining fatty acid chains
the backbone is an alcohol, commonly glycerol,

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Fatty acids:  there is considerable variation in fatty acids, but basically they are hydrocarbon chains.  If all the bonds are single, then it is saturated, because it contains the maximum possible H's.  It will form a fat (solid).
The general formula is CH3(CH2)nCOOH.  
CH3 is the methyl group.
(CH2)n is the variable chain, for example if n=16, then it is a stearic acid chain (common in adipose tissue - zsírszövet).
COOH is the carboxyl group.
If the chain contains double bonds, then it is unsaturated.  It will form an oil (liquid).

Cells produce fats and oils by condensing (see lecture 1) a glycerol and 3 fatty acids.  These molecules are also called triglycerides.

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The fatty acid part forms long apolar "tails", which repel water, so are hydrophobic.

Function: energy storage - found in adipose (also called fat) tissue (animals) and storage parenchyma (oily plant seeds).  Yeild 38kJ/g, therefore they are very high in energy.
Additional functions:  heat insulation, mechanical protection, waterproofing, solvents for vitamins A,D,E and K.  

B.  Phospholipids
- structurally similar to above, BUT phosphoric acid (foszforsav) takes the place of 1 fatty acid.

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This change creates a hydrophilic "head" region of the molecule and the 2 fatty acid chains form a hydrophobic tail.

Hence, phospholipids are very important in the formation of plasma membranes of cells, where they form a phospholipid bilayer, with the hydrophobic tails pointing towards each other and the hydrophilic heads in contact with the surroundings.

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C.  Steroids
-insoluble in water
-the basic structure is a sterane skeleton to which various side groups attach.

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Some examples of steroids include:
Cholesterol (important for plasma membrane rigidity)

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Bile acids (important in lipid digestion)
Sex hormones (estrogen, testosterone) and other steroid hormones

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Phytosterols (in plants)

D.  Carotenoids
- have conjugated double bonds (the single and the double bonds alternate), which makes them coloured (pigments)
-pigments are longer chains, volatile oils are shorter chains

Examples include:
Vitamin A
Carotene (orange)

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Licopene (red)
Xanthophyll (yellow)

E.  Waxes
- formed by fatty acids and an alcohol that is larger than glycerol
- important for waterproofing in plants
- found on arthropod exoskeletons (waterproofing)
- wax for bee hives

Topic 6 - Chemistry of Life: Nucleic Compounds (nukleinvegyületek)

1st found in the cell nucleus, hence the name.
-contain C, H, O, N and P, sometimes S

-energy storage and transport (ATP)
-transport of molecular groups (coenyzme A, NADH, NADPH)
-genetic material, aka nucleic acids (DNA, RNA)

 Nucleotides - these are the monomers of all nucleic compounds
-3 parts:  1 pentose sugar, 1 nitrogenous organic base, 1 phosphoric acid
pentose sugar:  ribose forms RNA (ribonucleic acid), deoxyribose forms DNA (deoxyribonucleic acid)
nitrogen base:  2 types of bases exist - purines (double ring, a 6-sided ring and a 5-sided ring) and pyrimidines (6-sided ring).  There are 2 kinds of purines and 3 kinds of pyrimidines.
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phosphoric acid (H3PO4):  gives the nucleotides their acidic character

Nucleotides are formed by condensation reactions binding the pentose sugar, the phosphoric acid and the nitrogenous base.
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1.  Energy storing and transporting nucleotides
-energy is gained from food (eg. ice cream).  Through digestion it is broken down into its various parts, many of which are sugars, which can be broken down by hydrolysis to the simplest sugar - glucose.

Glucose is used in cellular respiration (info on that to come) and energy is released from glucose and used to make new molecules for temporary storage - ATP

ATP (adenosine triphosphate) is the most important molecule in biology (no, I am not exaggerating!).  It is the general, universal energy source (which means that all living organisms can use it!)

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-to release energy, a phosphate breaks off to produce ADP (adenosine diphosphate)
-if another one breaks off, we get AMP (much rarer)
-ATP can be transported to any part of the cell and used for energy-demanding reactions

ADP + P + energy = ATP (to form ATP a condensation reaction occurs, to break down ATP a hydrolysis reaction occurs)

2. Transporting nucleotide-like molecules
-often coenzymes (molecules that help enzymes to complete reactions)
Coenzyme A (CoA)
-it is a nucleotide derivative (try to see the similarities with the nucleotide above!)
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-it takes part in cellular respiration
-its job is to carry acetyl groups that are created during the breakdown of glucose
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Nicotinamide adenine dinucleotide (NAD+)
-it takes part in cellular respiration (break-down reaction)
-it carries 2 hydrogens that are dissociated into protons and electrons
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Nicotinamide adenine dinucleotide phosphate (NADP+)
-it takes part in photosynthesis and other "building up" reactions.
-it also carries 2 dissociated hydrogens

3. Nucleic acids (genetic material)
- polymers of thousands of nucleotide monomers form polynucleotide chains by condensation
-the structure consists of a constant pentose-phosphate backbone to which variable nitrogenous bases are attached.
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DNA (deoxyribonucleic acid)
-its unique double helix structure was suggested in 1953 by Watson and Crick
-only 4 bases are used: G (guanine),C (cytosine), A (adenine) and T (thymine), but not U (uracil)!
-the two chains are linked together by H-bonds that form between the nitrogenous bases
-the chains run in opposite directions (this is called anti-parallel) and they are complementary (kiegészitő) to each other.  This means that G always pairs with C, and A always pairs with T.
-DNA is found in the cell's nucleus and it defines cell activity by controlling protein synthesis and defining genetic information
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RNA (ribonucleic acid)
-usually a single-stranded polynucleotide
-its bases are G, C, A and U (not T!)
-it can fold in on itself (to form short double stranded sections)
3 types:
a. ribosomal RNA (rRNA)/riboszomális RNS
-produced by information in DNA, it is large and complex
-it forms part of the ribosome (this is the organelle that synthesizes/makes proteins, it is formed of proteins and rRNA), so it has a structural role
-all organisms have very similar rRNA (this indicates that it appeared in the living world a very, very, very long time ago)
Computerized image of rRNA, without the surrounding protein
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b. transfer RNA (tRNA)/szallító RNS
-it is a small molecule
-it is found in the cell's cytoplasm
-it carries amion acids to the site of protein synthesis (to the ribosome)
-there are at least 20 types of tRNA - 1 for each amino acid
-each one binds to a specific amino acid at the acceptor stem
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c. messenger RNA (mRNA)/hírvivő RNS
-it is a long single-stranded molecule (often 1000's of nucleotides long)
-it is produced in the nucleus and is a mirror copy of 1 strand of the DNA helix
-it enters the cytoplasm, associates with ribosomes, and acts as the template (minta) for protein synthesis
-it is easily and quickly broken down, once it has brought the information about which protein to synthesize to the ribosome
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Topic 7: Overview of the Eukaryotic Cell

Generalized animal cell:

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Generalized plant cell:

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Cellular organelles:
1.  Cytoplasm:  the matrix in which all cell organelles and inclusions (insoluble waste or storage products) are found.  Made up of the cytosol and cytoskeleton.
-cytosol:  90% water, site of many biochemical reactions
-cytoskeleton:  made up of microtubules and microfilaments (string-like proteins).  Important in supporting the cell, giving its shape and some cell movements (like the pseudopods in amoebas!), as well as moving organelles within the cell and cell division.  The microtubules form parts of the cilia and flagella.

2.  Nucleus:  control center of most cellular activities.  It is surrounded by the nuclear envelope, which contains pores though which materials (proteins and RNA) can pass.  The nucleoplasm is found within the envelope, it is similar to the cytoplasm.  The nucleolus is the dark patch in the nucleus where ribosomal RNA is formed.  Chromatin (DNA and associated proteins) is found around the nucleolus.

3.  Endoplasmic reticulum (ER):  It is a series of interconnected, flattened sacs, tubes and channels formed by the phospholipid bilayer.  There are 2 types:  rough ER and smooth ER.  Rough ER appears bumpy because it is covered with ribosomes.  Its function is to isolate, store and transport proteins produced by the ribosomes.  The smooth ER produces and stores lipids.

4.  Golgi apparatus:  also made of phospholipid bilayers (or membranes), it functions to modify, sort and package macromolecules (like proteins and lipids)  for cell secretion (exocytosis) or use within the cell.  Imagine it is like a post office; it packages and labels items and sends them to different parts of the cell.

5.  Ribosomes:  make proteins from amino acids.  They can be found attached to the ER or floating freely in the cytoplasm.  They are made of rRNA and protein.

In the following picture, the connection between the various cell parts can be observed.  Information about how to build a protein comes from the nucleus as mRNA.  It attaches to the ribosome, which "reads" the mRNA and builds a protein from amino acids.  The protein is released into the rough ER, then it is packaged in a vesicle (this is a little membrane-bound bubble) and transported to the Golgi apparatus, where it may be modified, packaged into a new vesicle and then transported to the cell surface and released (exocytosis).

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6.  Mitochondria:  small membrane-bound organelles in the cytoplasm.  They are considered the "powerhouse" of the cell as this is where the reactions occur that create ATP (cellular respiration) that provide the cell with energy.

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7.  Chloroplasts:  Found only in plants and plant-like protists.  They are the site of photosynthesis and contain the green pigment, chlorophyll (along with other, less visible pigments!)

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8. Lysosomes and peroxisomes:  Special vacuoles, which are designed to digest things (such as worn-out or excess cell parts, food particles, invading viruses or bacteria, etc) with digestive enzymes.  They contain different digestive enzymes, therefore digest different things.  Lysosomes are formed from the Golgi apparatus, whereas peroxisomes are formed from the ER.

9.  Cell wall:  It is found in plant, algal and fungal cells.  It is completely permeable, but it contains cellulose (plants and algae) or chitin (fungus), which protects and supports the cell.

10.  Cell membrane:  It is a phospholipid bilayer.  It is both elastic and rigid and helps give the cell its shape.  It is selectively permeable, thus helps control transport of substances and homeostasis.  It is permeable to gases and water, but many substances can only pass through it with the help of proteins, such as channels, protein pumps and receptor proteins.  

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The Endosymbiotic Theory
-  proposed by Lynn Margulis at the end of the 1960s, it was initially ridiculed, but is now well-accepted.
-   suggests that certain prokaryotic cells engulfed (endocytosed) other cells, but instead of being digested, these cells continued to live and each provided the other with some benefits (symbiosis).
-  mitchondria:  an anaerobic bacteria engulfed a smaller aerobic bacteria.  Mutual advantages?  The aerobic bacteria provided the larger, anaerobic bacteria with the ability to survive in areas with oxygen, while the larger bacteria ingested food and provided protection to the smaller aerobic one.
-  chloroplast:  a photosynthetic bacteria was engulfed by a larger anerobic bacteria.  Advantages?  I am sure you can figure these out for yourselves!!
-  evidence:  These organelles are surrounded by a double lipid bilayer (their own, plus the one of the cell that engulfed them!).  These organelles also have their own DNA and divide independently of the cells that they are found in.

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