PROTEINS AND NUCLEIC ACIDS

PROTEIN FACTS:

Protein – comes from the Greek word “proteios” that means first or primary. Proteins usually used as a
catalyst, protector, storage, transporter. Proteins are also essential for cellular communication and
structural support. Proteins contain the same set of 20 amino acids that are linked to unbranched
polymers. Proteins are made up of one or more polypeptide that are coiled or folded into 3-dimentional
structure.

Catalyst – agents that helps in the speeding of chemical reactions.

Polymers- a chain of building blocks that are identical and connected by a covalent bond (chemical bond
that involves the sharing of electrons pairs between atoms).

Peptide bond- the bond in amino acid

Polypeptide – a long chain of amino acid bonds. This is formed through dehydration process

Amino Acid – an organic molecule that has an amino group and carboxyl group (O- OH covalent bond)

Enzymatic Proteins – these are proteins that acts as a catalyst to metabolism

Types of proteins and their functions:

Enzymatic Proteins – these are proteins that act as a catalyst to metabolism (ex: digestive enzymes
catalyse the hydrolysis of food molecules)

Storage Proteins – used for storage

Hormonal Proteins – coordination of an organism’s activities (ex: Pancreas produces insulin (protein).
Insulin helps deliver glucose to the tissues for the production of energy. This action helps in the blood
sugar concentration)

Contractile and Motor Protein – responsible for the movement ( ex: actin and myosin (protein) helps in
the contraction of muscles)

Defensive Proteins – defensive, parang ikaw, charot! This helps defend your body against diseases (ex:
Antibodies (protein) helps destroy viruses and bad bacteria)

Transport Proteins – the “jnt express” of proteins. They deliver molecules and substances to where they
belong (ex: Hemoglobin (protein) transports oxygen from the lungs to other parts of the body)

Receptor Proteins – response of the cell to chemical stimuli (ex: the membrane of the nerve cell has
receptor protein that detects signal from other nerve cells)

Structural Proteins – for support (sana all) (e.g keratin (protein) of hair and other skin appendages,
supports the smoothing down of cells from hair strands.
Shape of protein:

Globular protein – proteins that are shaped spherical

Fibrous protein – proteins shaped like long-fibers

Hydrophobic interaction – caused by exhaustion of non-polar substances by water molecules. When

non-polar amino acids are close together, van der waals interaction help hold them together.
Hydrophobic interaction is vital in tertiary structure.

Disulfide Bridges – a covalent bond that further reinforces the shape of a protein. Disulfide Bridges have
2 cysteine monomers that has a sulfhydryl group (-SH), are glued together by the folding of the protein.

Denaturation – process where protein or any weak linkages are separated (ex: hydrogen bonds)

NUCLEIC ACID FACTS:

Nucleic Acid – are polymers made up of nucleotides. DNA and RNA are the two types of nucleic acid.

DNA and RNA – enables living organism to reproduce

DNA – provides direction and directs RNA synthesis. Double helix

RNA - controls Protein synthesis. Single helix

Protein Synthesis – amino acids are arranged into proteins through RNA and DNA, enzymes.

Gene Expression – flow of genetic information from DNA to proteins.

mRNA- carries genetic instruction for building of proteins from nucleus to cytoplasm. Prokaryotic cells
lacks nuclei but still uses RNA to convey instructions from DNA to ribosomes.

Transfer RNA – bring amino acids to ribosomes during synthesis of a polypeptide. It usually 80
nucleotides long.

Ribosomes- sites of protein synthesis located between cytoplasm and the region between nucleus and
plasma membrane.

Polynucleotides – nucleic acid that exist as polymers. It consists of two nucleotides

Nucleotides- has a pentose (five-carbon sugar) nitrogenous base, 1-3 phosphate group

Nucleoside- nucleotides without phosphate groups

Nitrogenous bases : Pyrimidine and Purine

Pyrimidine – Cytosine (C) Thymine (T) Uracil (U)

Purine – Adenine (A) Guanine (G)

Sugar-phosphate-backbone – repeating pattern of sugar phosphate caused by bondings.

Deoxyribose – sugar in the DNA. Lacks oxygen atom on the second carbon ring

Ribose- the sugar in DNA

Phosphodiester Linkage – consists of phosphate group and used to link nucleotides

Antiparallel – 5’ to 3’, two sugar phosphate backbones

PROTEIN CONCEPTS:

What is the real function of proteins?

A human body contains tens of thousands of different proteins that have also different jobs in our body.
Each protein is different and is built with different structure intended for each function. Proteins are
very versatile and are diverse in terms of functions. Each protein has a unique three-dimensional shape.

Explain this image further:

This is a general formula of an amino acid. As you can see, an

amino acid wouldn’t be complete if an amino group and
carboxyl group is not present. Magbisaya Ko kay kapoyg
englis, if mo tan aw ka sa tunga ang amino acid kay naay
asymmetric carbon atom. Mao na sha kanang C na naka pink,
gitawag na siya og alpha carbon. So all in all, the amino acid
has 4 sets, an amino group, a carboxyl group, a hydrogen
atom and a side chain (R). Lahi lahi na siya per amino acid.
Sige basaha balik para kasabot ka.

Discus the structure and function of proteins:

As you know, protein have a three-dimensional shape, this affects the jobs of proteins. The simplest
level is the sequence of amino acids. So that leads us to the next question,

What is the significance of the sequence of the amino acid to the function and structure of protein?

The sequence of the amino acid will decide what three-dimensional structure a protein should have,
considering the normal cellular conditions. Remember that a functional protein is not just a polypeptide
chain. It has a more twisted and coiled polypeptides.
Aside from the protein’s structure, what else determines its job?

The function of proteins really depends on how well the protein can recognize and bind to other
molecules. Take for example, the proteins ability to match shapes from molecules. Endorphin molecules
are a molecule produced by the body. Morphine molecules are a manufactured drug. These molecules
fit as a receptor proteins, resulting to relieving body pain.

Understanding the Primary, Secondary, Tertiary and Quaternary Structure of Protein:

Primary structure contains the sequence of amino acid. The primary structure of a protein is inherited
by genetic information. The role of the primary structure is that it dictate the secondary and the tertiary
structure, this is because of the R side chain present in the amino acid along with the polypeptide.

Secondary structure is made through the repeatedly coiled and folded polypeptide chain. Within the
backbone (no the amino acid one), ang oxygen atoms kay naay partially negative charged particles, unya
ang hydrogen atoms nga gi attach sa nitrogren naa say partial positive charge, so with these charged
atom present, makahimo ta og hydrogen bond. If kaisa lang ni sha mahitabo, normally ang kanang
hydrogen bond kay weak jud nan a linkage, but tungod kay gi balik2 shag buhat og in ana, makasupport
na sila og shape sa part sa protein.

Tertiary structure deals with the overall shape of the polypeptide. This result to the interaction of the R
side group na naa sa amino acid. Example ani kay ang “hydrophobic interaction”. Scroll up ka na naman
mads naa sa facts lakaw didto karun dayun oo nanugo ko

Quaternary structure is the overall protein structure that handles the aggregation of theses polypeptide
subunits.

How sensitive is the formation of the protein?

Even the slightest change of the formation of protein has a big impact on the human body. For instance,
the sickle cell disease. The sickle cell disease is a blood disorder that is inherited. What triggers or what
happened to the structure of protein that resulted to this? The sickle cell disease happen when valine
(amino acid) is substituted with glutamic acid (normal one) at the sixth amino acid in the primary
structure og haemoglobin.

What determines the protein structure?

We know now that the answer to this is the amino acid sequence present in the primary structure,
right? If nasayop kag guess, balik og basa dai kay nalimtan nana nimo, wa ko ga type2 dire para di ka
makasabot. However, the protein structure also depends of the physical and chemical conditions.
Factors to consider are, pH (Philippines yarn?) salt concentration, temperature. If one of these is altered
the chemical bonds and interactions in the protein maybe destroyed, resulting to the protein losing its
native shape. This is called denaturation. Most proteins are denatured if drastically transferred to a
nonpolar solvent from an aqueous environment. Proteins in the blood can also denature with very high
body temperature.
Is the misfolding of the polypeptides that bad?

Yes, this is actually supported by many researchers. Diseases like Cystic Fibrosis, Alzheimer’s,
Parkinson’s and mad cow disease are commonly associated with the misfolding of proteins.

NUCLEIC ACID CONCEPTS:

The roles of DNA:

DNA is the genetic material that organisms inherit from parents. Each chromosome has a DNA molecule.
DNA carries hundreds of genes. During cell division, the DNA molecules are copied and passed from
thousands of cells.

What is the role of the RNA in the gene expression?

The mRNA, is a given gene along a DNA molecule that interacts with the cell’s protein-synthesizing
machinery to direct production of a polypeptide that folds into a part of a protein.

What is the simplest flow of a genetic information?

Simple rana siya dzai. DNA – RNA – PROTEIN.

What is the 5’ to 3’?

The ends of a polymer should be different to complete the building of the nucleotide. One end has to be
5’ carbon and the other has to have 3’ carbon. We can say that a polynucleotide has a built-in
directionality along its sugar phosphate backbone, from 5’ to 3’ like a one way street.

Explain the base pairing of nucleic acid:

During the base pairing, the double helixes are always compatible with each other. AT GC. Adenine is
paired with Thymine, Guanine is paired with Cytosine. With this happenings, we can allow the DNA to
generate 2 identical copies of the DNA molecule during the pre-cell division. When the cell divides, the
copies are distributed to daughter cells, making the daughter cells genetically identical to the parent.
However, in RNA, Adenine pairs with Uracil, since the Thymine is not present in RNA.

HAPPY TUONING!