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The foundations of biochemistry
Georgina Franco Escobar A01421342
César Antonio Solís Utrilla A01171050
Michael Pascual Palacios Z. A01201902
Carla Mondragón González A01204017
Lilian Andrea Espinosa España A01270835
Its aim is to explain biological forms in terms of chemical functions
biomolecules are carbon compounds with different functional groups.
Functional groups
Groups of atoms that give a molecule its characteristics for chemical reactions.
Functional groups are attached to the carbon backbone of a molecule.
Increase polarity and reactivity of organic molecule.
Allows for hydrogen bonds to form with water and other polar molecules
In amino acids, the amino groups bonds covalently to the carboxyl group of another amino acid.

Increase polarity and reactivity of organic molecule.
Biomolecules containg the carbonyl group tend to be volatile and soluble in water.
All sugar molecules have one carbonyl group
Amino acid chain
Contains a carbonyl and a hydroxyl group
Makes the molecules highly polar and reactive (due to the two oxygen atoms)
Often referred to as carboxylic acids because of their tendency to release hydrogen ions.
Ionized form (COO-)
Amino acids
Pyruvic acid
Increase polarity of organic molecule due to electronegativity of oxygen atom.
Allows for hydrogen bonds to form with water and other polar molecules.
Alcohols- Glycerol
The phosphate groups are highly acidic.
Exist almost exclusively in ionized state (release two hydrogen atoms).
Makes the molecule highly reactive due to presence of 4 oxygen atoms.
The transfer of a phosphate group releases energy (ATP).
The minimal difference in electronegativity between sulfur and hydrogen, it is nonpolar.
Not soluble in water.
This group helps to stabilize protein.
Amino acids
The aim is to describe the two steps process , transcription and translation by which the information in genes flows into proteins

Deoxyribonucleic acid, hereditary material in humans and almost all other organisms.
The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). 
Double helix permits to copy the information.

How do we sequence DNA?

How do we sequence DNA?

DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.
The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography.

Basic methods
Maxam-Gilbert sequencing
Chain-termination methods

Shotgun sequencing
Bridge PCR

Advanced methods and de novo sequencing

**The large quantities of data produced by DNA sequencing have also required development of new methods and programs for sequence analysis.

In all eucaryotic cells DNA never leaves the nucleus, instead the genetic code (the genes) is copied into RNA which then in turn is decoded (translated) into proteins in the cytoplasm.

The cytoplasm is a dangerous environment for the DNA and the daily transcription of genes to proteins would be very harmful to the DNA, which has to stay intact in order to maintain life.

To regulate the rate of protein synthesis. 

Ribonucleic acid, molecule made up of one or more nucleotides.

The structure of RNA is similar to DNA, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl (-OH) group that DNA does not.

What happens next?
Translation is the final step on the way from DNA to protein.
It is the synthesis of proteins directed by a mRNA template.
The information contained in the nucleotide sequence of the mRNA is read as three letter words (triplets), called codons. Each word stands for one amino acid.
During translation amino acids are linked together to form a polypeptide chain which will later be folded into a protein.

What's a protein?
Proteins are the building blocks and workers of our cells.

DNA's long sequence, composed of only four different letters, get converted into the 100,000 or so different kinds of protein molecules that perform the daily work in our body.

This is accomplished by the cell's protein-making factory and is called translation.

Two types of cell
Evolution of a cell
Many types of cell with different structure and function
Monomeric Units
Small units of atoms from different elements that interact with others
Supra molecular Complex
Give energy to the cell, obtain by the cellular respiration
Amino acids
-Give structure to the protein, determine it function.
-They have a base and acid part.
-Chiral Nature (except glycine)
-Join by a peptide bond
- Essential: obtain in our diet.
-Non essential: our body produce them.

Amino acid structure
-Conform by a nitrogen base with a n-glucosidyc bond with a sugar. And phosphate join to the sugar by a covalent bond.
-Interact to for DNA chain (histone, chromatin, chromosome)
- DNA : thymine, cytosine, adenine, guanine.
-RNA: Uracyle rather than thymine.
- Present
- Involve in many biological process as an enzyme.
- They transport and keep vital substances, give support and coordinate movement to the cell.
- More than 100000 different protein in our body
Form by monomeric units together, present in the organelles of a cell
Conform by carbohydrates
Present in the membrane vegetable cells
Conform the animal cellular membrane
Function as solvent and also to keep energy
Intermediate filaments
Present only in eucariote cells.
Keep the DNA in a organized way:

Micro tubules
Micro filaments
Made by proteins
Made by protein Actine
- Divide in cellular mitosis
Made by a protein name tubuline
DNA chain
Genetic section
Lysell, J., & Eidhagen, F. (n.d.). Rna-transcription. Retrieved from http://www.nobelprize.org/educational/medicine/dna/b/transcription/index.html
Twyman, R. (2003, January 8). Dna sequencing. Retrieved from http://genome.wellcome.ac.uk/doc_WTD021036.html
What is DNA?. (2014, September 1). Retrieved from http://ghr.nlm.nih.gov/handbook/basics/dna
What is RNA?. (n.d.). Retrieved from http://exploringorigins.org/rna.html
Chemical section
Biomolecules and cell structure. (n.d.). Retrieved from http://bioserv.fiu.edu/~walterm/Fund_Sp2004/lec2_biomolecule_cell/biomolecules.htm
Fromm, R. (1997). Introduction to sulfur functional groups. Retrieved from http://www.3rd1000.com/chem301/chem301x.htm
Functional groups and biomolecules. (n.d.). Retrieved from https://dls.dcccd.edu/biology1-3/functional-groups-and-biomolecules
Functional groups. (n.d.). Retrieved from http://www.as.utexas.edu/astronomy/education/spring07/scalo/secure/AbioFunctionalGrpsVollIRspect.pdf
Griffin, D. (n.d.). Structure and function of biomolecules. Retrieved from http://projectsharetexas.org/resource/structure-and-function-biomolecules
Pearson Education. (n.d.). Concept 6: The functional groups. Retrieved from http://www.phschool.com/science/biology_place/biocoach/biokit/function.html
Birth and death evolution

DNA replication
Histones regulate the packaging and unpackaging of different genome regions to respond specific cellular signals.
Histones are proteins that provide the physic support in which the metabolic processes, inherent to the genetic material, takes place.
It´s a gene duplication where the original gene continuous to do its function so the new gene is free to undergo faster mutations and can develop complementary functions. Natural selection is in charge of determining if the mutation is beneficial or not and to accept it or reject it. This process increments the number of genes in the genome as well as specialization and diversification.
Histones are clasified in 5 families:
H2A, H2B, H3, H4, which conform the central body of the nucleosome and H1 which are in charge of sealing the 2 DNA spins.
This molecular mechanism (packaging) helped the evolution of complex cells, because it has solved the accumulation of genetic material problem and it helped the regulation of DNA in precise and coordinate ways.
Evolutionary section
Romero, R. G., Ausió, J., Méndez, J., & López, J. M. (December 2011). El papel clave de las histonas.
Investigación y ciencia.
Wiley. (2014).
DNA replication.
Retrieved September 6th 2014, from: http://www.wiley.com/college/pratt/0471393878/instructor/animations/dna_replication/index.html
National Institute of Health. (September 01, 2014).
Genetics home reference
. Retrieved 06 September 2014, from: http://ghr. nlm.nih. gov/glossary=rna
Duve, C. d. (April 1996). The birth of the complex cell.
Scientific American.
DNA replication
Changes in the nucleotide sequence of DNA produce mutations. A mutation can lead to death or into a better equipped organism. This advantaged, that may be gained, can help survive the mutated specie. Survival and reproduction of the fittest individuals in a challenging or changing environment is called natural selection.
Endosymbiotic theory
The proteins responsible for DNA replication are: helicase, SSB protein, primase, slidig clamp, DNA polymarase, RNase H and DNA ligase.
DN replication is the process whereby an entire double-stranded DNA is copied to produce a second, identical DNA double helix.
Unwinds the the DNA double helix into two individual strands.
SSB protein
They coat the single-stranded DNA. This action prevents the DNA strands from reannealling to form double-stranded DNA.
Is a RNA-polymerase that synthesizes the short RNA primers needed to start the strand replication process.
DNA polymerase
Strings nucleotides together to form a DNA strand.
Sliding clamp
Holds the DNA polymerase onto the DNA strand during replication.
RNase H
Removes the RNA primers.
DNA ligase
Links short stretches of DNA together to form he continuous DNA strand.
Cellular section
Chang R. y Goldsby K. (2013) “Química” (11a edición, vol1.) México D.F. Mc Graw Hill.

Ralph A. Burns (2003) “Fundamentos de Química” (4ta edición, vol1.) México. Pearson Educación.

RNA or a similar molecule may have been the first gene and the first catalyst. It had random sequences which later were selectively replicated. Later on, primitive translation system was developed. Also, the RNA genomic material began to be copied into DNA and it
also started to translate into protein.
The Ribonucleic acid, is one of the two types of nucleic acids that found in all cells. RNA transmits genetic information from DNA to proteins produced by the cells.
It describes how a large host cell and ingested bacteria become dependent on one another for survival, resulting in a permanent relationship.
Cell wall.
Circular DNA attached to the membrane.
Present in stromatolites colonies.
Common ancestor loses the ability to create the cell wall.
Digestion through secretion of enzymes.
Fast growth.
Intern membrane contraction.
Development of cytoeskeleton.
Development of primitive organelles.
Membrane contraction surrounded circular DNA (nucleus precursor).
Enzymes compartments for intern digestion (organelles).
Cell started its phagocyte nature.
Apparition of peroxisomes to counteract the toxicity of environment (rich in oxygen) due to the autotrophic bacteria.
Bacteria ingestion: mitochondria precursor.
Bacteria ingestion: plasts precursor.
The aim is to describe the process how energy is extracted and channeled in living cell in quantitative and chemical terms.
Every living organism needs energy to do its natural process.

The unit of energy for cells is ATP.
Heterotrophic and Autotrophic organisms can transform organic compounds into energy.
It is a set of metabolism that occur in the cells of organisms (mitochondria, chloroplasts) to convert organic compounds into biochemical energy that can harness, and then release waste products.
Two types of respiration
In Glycolysis we are taking glucose (molecule 6 carbon) and break to form two molecules of Pyruvate (molecule 3 carbon) produces 2 ATP and NADH (high energy electrons).
Pyruvate Dehydrogenase Complex
Pyruvate diffuses into the mitochondria and then reaches Pyruvate Dehydrogenase, Complex, pyruvate es convertido acetyl CoA (2-carbon molecule).
Dispose of a coal as CO2
In the Krebs cycle will break even more the molecule of acetyl CoA discarding the last two carbons as CO2 and yielding 2 ATP, NADH and FADH2 (high energy electrons).
Acetyl CoA
Both NADH and FADH2 are sent to the third stage which is the chain of electron transport, where all these electrons will move you through a series of proteins, and the energy of these proteins is used to pump protons (hydrogen ions) out of the inner membrane (intermembrane space), which reach the ATP synthase which will be added to other protons and oxygen (electron acceptor) producing water and 32-34 ATP.
It takes place in the muscles when under stress and bacteria, no oxygen, no mitochondria.
The glucose enters glycolysis produces pyruvate, NADH and 2 ATP.
Then there is an additional CONVERSION of pyruvate to lactic acid because this is the acceptance of NADH to lactic acid.
At the end of this cycle being repeated each time producing more ATP and Acid Lactic.
The Acid Lactic is broken with the aid of oxygen.
What if there is no oxygen and continue with these electrons (NADH)?
It is another option for some breathing bacteria and works almost like lactic acid fermentation.
Divided even more pyruvate to form ethyl alcohol which accepts electrons from NADH the only difference is the production of CO2 .
Photosynthesis and Respiration
Photosynthesis is just the opposite of cellular respiration.
Physical section
Andersen, P. (04 de 04 de 2012). Cellular Respiration. Obtenido de https://www.youtube.com/watch?v=Gh2 P5CmCC0 M
Gil Nonato C. Santos, E. A. (2012). Biology Ii for High School. Philippine: RBS.

Chemical compounds exist in stereoisomers
Molecules with the same chemical bonds but different spatial arrangements
Interactions between biomolecules are stereo-specific
Geometric isomers
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