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Science education: Biology, Study notes of Science education

Angeles University (AU)Science education

They're found in a variety of foods and beverages, including barley, tea, and wine, and are powerful antioxidants.

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GRPS, JKLB, MDSP, AAP
NUCLEIC ACID
● One of the biologically important macromolecule that is why they called it “BIOMOLECULE”
o Biomolecules are Carbohydrates, Lipids, Nucleic Acid, Protein
● Its function is to carry genetic material
TYPES OF NUCLEIC ACIDS
● Cells in an organism are extract replicas
o because it has capability to make new cells or know as replication process
o they copy the genetic code or material
● Cells have information on how to make new cells
● Molecules responsible got such information are nucleic acids
o Found in nucleus and are acidic in nature
● A nucleic acid is polymer in which the monomer units are nucleotides
o Monomer – basic structure or simplest
▪ monosaccharide is monomer of Carbohydrates
▪ fatty acid is monomer of Lipids
▪ nucleotides is monomer for Nucleic Acid
o Polymer – largest
▪ Ex: Carbohydrates and Lipids
▪ Carries the Genetic materials
TWO TYPES OF NUCLEIC ACIDS
● DNA (Deoxyribonucleic Acid)
o Found within cell nucleus
o Storage and transfer of genetic information during replication and transmission
o Passed from one cell to other during cell division
● RNA (Ribonucleic Acid)
o Occurs in all parts of cell
▪ As long as it has a ribosome, it has the ability for protein synthesis
▪ Most of the organelles are ribosome containing
o Primary function is to synthesize the proteins
NUCLEOTIDES: BUILDING BLOCKS OF NUCLEIC ACID
NUCLEIC ACIDS:
● Polymers in which repeating unit of nucleotide
o Nucleotide + Nucleotide = Nucleic Acid
o DNA Sequence & RNA Sequence
o there are several nucleotides present in Nucleic Acid
● A nucleotide has three components:
o Pentose Sugar:
▪ Monosaccharide with five carbons
o Phosphate Group (PO43-)
o Heterocyclic Base
PHARMACEUTICAL BIOCHEMISTRY
MIDTERM TOPIC 1 PART 1: NUCLEIC ACID
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GRPS, JKLB, MDSP, AAP

NUCLEIC ACID

● One of the biologically important macromolecule that is why they called it “BIOMOLECULE” o Biomolecules are Carbohydrates, Lipids, Nucleic Acid, Protein ● Its function is to carry genetic material TYPES OF NUCLEIC ACIDS ● Cells in an organism are extract replicas o because it has capability to make new cells or know as replication process o they copy the genetic code or material ● Cells have information on how to make new cells ● Molecules responsible got such information are nucleic acids o Found in nucleus and are acidic in nature ● A nucleic acid is polymer in which the monomer units are nucleotides o Monomer – basic structure or simplest ▪ monosaccharide is monomer of Carbohydrates ▪ fatty acid is monomer of Lipids ▪ nucleotides is monomer for Nucleic Acid o Polymer – largest ▪ Ex: Carbohydrates and Lipids ▪ Carries the Genetic materials TWO TYPES OF NUCLEIC ACIDS ● DNA (Deoxyribonucleic Acid) o Found within cell nucleus o Storage and transfer of genetic information during replication and transmission o Passed from one cell to other during cell division ● RNA (Ribonucleic Acid) o Occurs in all parts of cell ▪ As long as it has a ribosome, it has the ability for protein synthesis ▪ Most of the organelles are ribosome containing o Primary function is to synthesize the proteins NUCLEOTIDES: BUILDING BLOCKS OF NUCLEIC ACID NUCLEIC ACIDS: ● Polymers in which repeating unit of nucleotide o Nucleotide + Nucleotide = Nucleic Acid o DNA Sequence & RNA Sequence o there are several nucleotides present in Nucleic Acid ● A nucleotide has three components: o Pentose Sugar: ▪ Monosaccharide with five carbons o Phosphate Group (PO 43 - ) o Heterocyclic Base

PHARMACEUTICAL BIOCHEMISTRY

MIDTERM TOPIC 1 PART 1 : NUCLEIC ACID

GRPS, JKLB, MDSP, AAP

PENTOSE SUGAR

● Ribose is present in RNA ● 2 - deoxyribose is present in DNA ● Structural difference: o a—OH group present on carbon 2 in ribose ▪ Hydroxyl groups are attached in carbon 2 o a—-H atom in 2-deoxyribose ▪ Hydrogen is attached in carbon 2 ● RNA and DNA differ in the identity of the sugar unit in their nucleotides. NITROGEN-CONTAINING HETEROCYCLIC BASES ● There are a total five bases (four of them in most of DNA and RNAs) ● Three pyrimidine derivatives (CUT) – thymine (T), cytosine (C), and uracil (U) ● Two purine derivatives (AG) – adenine (A) and guanine (G) o Adenine (A), guanine (G), and cytosine (C) are found in both DNA and RNA. ▪ Mnemonics : CAG (Cat Ate Glue) – both DNA & RNA o Uracil (U) found only in RNA o Thymine (T) found only in DNA. 3 pyri derivatives (CUT) – Cytosine, Uracil, Thymine 2 puri derivatives (AG) – Adenine, Guanine DNA & RNA (CAG) – Cytosine, Adenine, Guanine DNA (U) – Uracil RNA (T) - Thymine PHOSPHATE ● Third component of a nucleotide, is derived from phosphoric acid (H 3 PO 4 ) ● Under cellular pH conditions, the phosphoric acid is fully dissociated to give a hydrogen phosphate ion (HPO 4 2 - ) COMPLEMENTARITY OF BASES ● NOTE: BE FAMILIARIZE OMCAKES!! ● The different bases in the nucleotides which make up DNA and RNA are: o Adenine o Guanine o Cytosine o Thymine (DNA only) o Uracil (RNA only) ● Chemical structure only allows bases to bind with specific other bases due to chemical structure

GRPS, JKLB, MDSP, AAP

BASE SUGAR NUCLEOTIDE NAME NUCLEOTIDE

ABBREVIATION

DNA NUCLEOTIDES

Adenine Guanine Cytosine Thymine Deoxyribose Deoxyribose Deoxyribose Deoxyribose Deoxy ade nosine 5’ – monophosphate Deoxy gua nosine 5’ – monophosphate Deoxy cy tidine 5’ – monophosphate Deoxy thy midine 5’ – monophosphate dAMP dGMP dCMP dTMP RNA NUCLEOTIDES Adenine Guanine Cytosine Uracil Ribose Ribose Ribose Ribose adenosine 5’ – monophosphate guanosine 5’ – monophosphate cytidine 5’ – monophosphate thymidine 5’ – monophosphate

AMP

GMP

CMP

TMP

Example DNA: o Base (adenine) + phosphate + deoxyribose o In abbreviation they have the letter “d”, for DNA.  Always fifth carbon - since this place where the phosphate is being attached. o DNA – deoxy o RNA - ribose  Example RNA: Base (adenine) + phosphate + ribose PRIMARY NUCLEIC ACID STRUCTURE SUGAR ● Phosphate groups are referred to as nucleic acid backbone ● Found in all nucleic acids ● Sugars are different in DNA and RNA o Backbone - sugar phosphate group o Sugar phosphate group - nucleic acid backbone o Backbone - standard, no changes, the changes are only the attachment (heterocyclic). ▪ Phosphate - no changes ▪ Sugar - standard ▪ Deoxyribose - DNA ▪ Ribose - RNA ▪ Heterocyclic - changes occur

PBIO221 (LECTURE):

PHARMACEUTICAL BIOCHEMISTRY

Midterm Topic 1 : Nucleotides PRIMARY STRUCTURE

  • A ribonucleic acid (RNA) is a nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil o Uracil is exclusive to RNA ▪ Once you see it, it is an indication that the structure is RNA ▪ Smaller
  • A deoxyribonucleic acid (DNA) is a nucleotide polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine o Thymine ▪ Indication of DNA the presence of thymine. ▪ Larger
  • Structure - Sequence of nucleotides in DNA or RNA o 4 available in DNA or 4 available in RNA o For the structure at the right side: to determine whether it is DNA or RNA
  • Presence of thymine or the uracil o Can also check by the pentose sugar ▪ Carbon 2 - has hydrogen only
    • Sequence has pentose sugar
    • The color blue in the picture - deoxyribose
    • All the pictures has 3 hydroxyl group
    • 5 end has free phosphate group
    • Pictures: o DNA sequence - thymine is present
    • Primary structure is due to changes in the bases o 4 available bases o 1 attachment only (can change)
    • Phosphodiester bond at 3’ and 5’ position
    • 5’ end has free phosphate and 3’ end has a free OH group
    • Sequence of bases read from 5’ to 3 o Sequence 5 to 3 - the connection is at carbon number 5 and carbon number 3 in the next sugar o Carbon number 5 of the first sugar - phosphate attached o Phosphate will attached in carbon number 3 in the next sugar o 3rd sugar - in the carbon number 5 phosphate, the attached number 3 will appear o Attachment of the phosphate - called as 3’, 5’ phospodiesterlinkage ▪ The attachment is in the carbon 3 and 5 or of each of the sugar.

THE DNA DOUBLE HELIX

  • Nucleic acids have secondary and tertiary structure
  • The secondary structure involves two polynucleotide chains coiled around each other in a helical fashion
  • The polynucleotides run antiparallel (opposite directions) to each other, i.e., 5’ - 3’ and 3’ - 5’ Because it is their terminal end.
  • The bases are located at the center and hydrogen bonded (A=T and GΞC)
  • Base composition: %A = %T and %C = %G) o Example: Human DNA contains 30% adenine, 30% thymine, 20% guanine and 20% cytosine. · DNA Sequence o the sequence of bases on one polynucleotide is Complementary to the other polynucleotide
  • Complementary bases o are pairs of bases in a nucleic acid structure that can hydrogen-bond to each other.
  • Complementary DNA strands o are strands of DNA in a double helix with base pairing such that each base is located opposite its complementary base. o THAT IT IS WHY THEY BECOME DOUBLE HELIX : They are opposite, they link, via hydrogen bonding.
  • Examples: o List of bases in sequential order in the direction from the 5 end to 3' end of the segment: 5'-A-A- G-C-T-A-G-C-T-T-A-C-T-3' o Complementary strand of this sequence will be: 3-T-T-C-G-A-T-C-G-A-A-T-G-A- 5 BASE PAIRING
  • One small and one large base can fit inside the DNA strands: o Hydrogen bonding is stronger with A-T and G-C o A-T and G-C are called complementary bases PRACTICE EXERCISE
  • Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below: 5’ A-A-T-G-C-A-G-C-T 3’
  • ANSWER: 3’T-T-A-C-G-T-C-G-A 5’ REPLICATION OF DNA MOLECULES Replication
  • Process by which DNA molecules produce exact duplicates of themselves.
  • Old strands act as templates for the synthesis of new strands o They duplicate and we’ll have replication. DNA polymerase
  • Checks the correct base pairing and catalyzes the formation of phosphodiester linkages
  • The newly synthesized DNA has one new DNA strand and old DNA strand
  • DNA polymerase enzyme can only function in the 5 - to-3' direction o This cannot be catalyzed in 3-to-5 direction.
  • Therefore, one strand ( top; leading strand ) grows continuously in the direction of unwinding
  • The lagging strand grows in segments (Okazaki fragments) in the opposite direction
  • The segments are latter connected by DNA ligase
  • DNA replication usually occurs at multiple sites within a molecule (origin of replication)
  • DNA replication is bidirectional from these sites (replication forks) o They are different in directions. One is continuously unwinding, while the other one is in an opposite direction in segments.
  • Multiple-site replication enables rapid DNA synthesis

Chromosomes

  • Upon DNA replication the large DNA molecules interacts with histone proteins to fold long DNA molecules.
  • The histone–DNA complexes are called chromosomes: o A chromosome is about 15% by mass DNA and 85% by mass protein. o Cells of different kinds of organisms have different numbers of chromosomes. o Example: Number of chromosomes in a human cell 46, a mosquito 6, a frog 26, a dog 78, and a turkey 82
  • Chromosomes occur in matched (homologous) pairs. o Example: The 46 chromosomes of a human cell constitute 23 homologous pairs ▪ 23 from the mother and 23 for the father: 46 OVERVIEW OF PROTEIN SYNTHESIS
  • Protein synthesis is directly under the direction of DNA
  • Proteins are responsible for the formation of skin, hair, enzymes, hormones, and so on
  • Protein synthesis can be divided into two phases. o Transcription ▪ A process by which DNA directs the synthesis of mRNA molecules

o Translation

▪ process in which mRNA is deciphered to synthesize a protein molecule

RIBONUCLEIC ACIDS

DIFFERENCES BETWEEN RNA AND DNA MOLECULES

  • The sugar unit in the backbone of RNA is ribose ; it is deoxyribose in DNA.
  • The base thymine found in DNA is replaced by uracil in RNA
  • RNA is a single-stranded molecule; DNA is double- stranded (double helix)
  • RNA molecules are much smaller than DNA molecules, ranging from 75 nucleotides to a few thousand nucleotides. TYPES OF RNA MOLECULES Heterogeneous nuclear RNA (hnRNA)
  • Formed directly by DNA transcription.
  • Post-transcription processing converts the hnRNA to mRNA Messenger RNA (mRNA)
  • Carries instructions for protein synthesis (genetic information) from DNA o The molecular mass of mRNA varies with the length of the protein Small nuclear RNA
  • Facilitates the conversion of hnRNA to mRNA. o Contains from 100 to 200 nucleotides

POST-TRANSCRIPTION PROCESSING: FORMATION OF mRNA

  • Involves conversion of hnRNA to mRNA
  • Splicing o Excision of introns and joining of exons o Exon – a gene segment that codes for genetic information o Intron – a DNA segments that interrupt a genetic message

✓ The splicing process is driven by snRNA

  • Alternative splicing o A process by which several different protein variants are produced from a single gene o The process involves excision of one or more exons