Nucleic Acids and Respiration

Nucleic Acids and

Respiration

“From Gene to Protein

The energy for life”

Raluca Herascu and Wei Guo

HL-B8/B9

Summary of the Presentation

• Nucleic Acids

– Types and Structure

• DNA

• RNA

• Polynucleotides

– Role of DNA in Heredity

– Role of DNA and RNA in Protein Synthesis

– Types of DNA Profiling

• Respiration

– Aerobic Respiration

– Anaerobic Respiration

Nucleic Acids

• Natural polymers made up of nucleotides

• Two types: Deoxyribonucleic Acid and Ribonucleic Acid • Nucleotides are made up of three parts

– A phosphate group – A pentose sugar – A nitrogenous base • By convention, the carbons in sugar are denoted by a prime (‘)

to distinguish it from the carbons of the nitrogenous base and the phosphate group

- The phosphate group attached to the 5-prime carbon and a nitrogenous base is attached to the 1-carbon

A nucleotide

Deoxyribonucleic Acid (DNA)

• Uses of DNA:

– Storage of genetic information

– Allows living organisms to reproduce

– Coordinates, with RNA, the process of protein synthesis

• DNA is composed of:

– A phosphate group – Ribose (as the sugar)

– The organic nitrogenous bases: Adenine, Guanine, Thymine, and Cytosine

• Adenine and Guanine are purines

• Cytosine and Thymine are pyrimidines

• The phosphate and ribose in the DNA make up its backbone and are bonded together by covalent phosphodiester bonds • The sugar and nitrogenous bases are also bonded together by

Deoxyribonucleic Acid

• But, the nitrogenous bases of complementary strands are bonded by hydrogen bonds

– There are 2 bonds between thymine and adenine – There are 3 bonds between cytosine and guanine

• There are two strands in a DNA double helix, running in anti-parallel fashion

– Hydrogen bonds hold the strands together due to the side chains present

Formation of Polynucleotides

• Polynucleotides are formed when one or more

nucleotides are bonded together

– This is the principle of the elongation of a DNA strand

as well as its reproduction

• DNA elongation takes in the cell’s nucleosome

where the genetic information is found

– Nucleotide triphosphates (unbonded nucleotides with

three phosphate groups) are abundant in the cell’s

nucleolus

• They will be used as the new bases in the

growing chain

Formation of Polynucleotides

• The nucleotide triphosphate, with the help of the

enzyme polymerase, attach to the 3-prime carbon on

the DNA backbone. The energy for this reaction is

provided by the hydrolysis of the bonds between the

phosphate groups

• Nitrogenous bases are specific in their pairing

and one DNA strand determines the arrangement

of the complimentary strand

• This specificity allows for self-replication and

guides the production of RNA

Ribonucleic Acid (RNA)

• RNA consists of a very similar structure to DNA

except for these key differences:

– Uracil replaces thymine

– Ribose replaces deoxyribose

(pentose; lacks an oxygen on the

second carbon atom)

– RNA is single stranded

Comparative structures of uracil and thymine: thymine has an extra methyl group

Comparitive structures of ribose and pentose

Types of Ribonucleic Acid (RNA)

• There are three types of RNA molecules involved

in the processes that we are studying

– Messenger RNA (mRNA)

– Ribosomal RNA (rRNA)

– Transport RNA (tRNA)

Protein Synthesis- Background Information

• Chromosomes are basically a very long DNA

sequence which store genetic information

– there are 23 pairs of (different) chromosomes in

the human body

• A gene is a finite and discrete unit of heredity that is

coded by a sequence of nitrogenous bases

• Through a series of processes, the nitrogenous

bases will come to dictate a series of amino acids

– These amino acids will form a polypeptide which

will in turn form a protein :

GENE TO PROTEIN

• Proteins directly or indirectly determine the

observable characteristics of an individual

• These processes are known as

transcription and

translation

Transcription

• In this process, the DNA helix is unwinded (with

the help of the enzyme helicase) and a

complimentary strand of RNA is formed

– This RNA is known as mRNA

• The mRNA undergoes editing processes until a

specific sequence of bases is achieved

• The mRNA exits the cell’s nucleus and enters the

cell’s cytoplasm

Translation

• Once the mRNA exits the nucleus and enters the cell’s

cytoplasm, it is directed to the ribosome- also known as rRNA • Inside the ribosome, the base sequences on the mRNA will be

interpreted and correspond to specific amino acids

– Each triplet of base pairs are referred to as a codon while each codon corresponds to a specific amino acid

– This is known as the genetic code and it is both universal and degenerate

• These amino acids will be brought to the ribosome by tRNA and the formation of a polypeptide will commence

• Once the specific protein is formed, the mRNA, rRNA, and tRNA will separate

• The polypeptide sequence will undergo further conformational changes in order to become a functioning protein

DNA Profiling

• All individuals have variations in their genetic information

• Certain sequences are repeated throughout a gene while the length of each sequence determines the individuality

• When a DNA sample is gathered as evidence, restriction enzymes are used to cut the sample into a specific coding sequence that matches the coding sequence that will be compared

• These sequences are known as microsatellites and there are certain splits that occur in each sample (regions where there are no codons) that are specific to each individual

Gel Electrophoresis

• The samples are placed into wells cast in a gel

• The gel is immersed in a conducting fluid and an electric field is applied • Sample will move across the gel a certain distance depending on its size • The bands obtained are then labeled with radioactive phosphorus

• X-ray film is used to detect radiation and a fingerprint is obtained

• This fingerprint is then used for comparison purposes such as paternity cases, criminal cases, and to map evolutionary traits of species

• There is a slight chance of error with this process as individual gene sections may match – because we are dealing with such a small region

Respiration

• Cellular respiration denotes the process by which nutrients are converted into useful energy in a cell

• There are two types of respiration

– Aerobic respiration (in the presence of oxygen) – Anaerobic respiration (in the absence of oxygen) Aerobic Respiration

- Glucose is converted into pyruvate with carbon dioxide

and water as byproducts

- Pyruvate is the anion of 2-oxoporpanoic acid

- Glucose undergoes oxidation while oxygen undergoes reduction

C₆H₁₂O₆ +6O₂ 6CO₂ + 6H₂0 Refer to page 297 in Course Companion

• This process that converts 1 mole of glucose into 2 moles of pyruvate is known as glycolysis

• Adenosine triphosphate (ATP) is formed here as well as in the subsequent Krebs cycle

– This is used for energy in the body

Respiration

• Anaerobic respiration

– Glucose is converted into pyruvate

– Pyruvate is then converted into

lactate

in humans

– Pyruvate is converted into

ethanol

with the byproduct

of

carbon dioxide

(the process of fermentation) by

yeast

• Glucose

undergoes

oxidation

while

oxygen

undergoes

reduction

C

H

O

 2 C

H

OH + 2CO

(fermentation)

• In anaerobic respiration, 1 mole of glucose is

converted into 2 moles of ATP, albeit ATP is

converted more quickly

The Role of Iron and Copper Ions

• Transition metals form cytochromes (essentially a protein linked with a metal compound) in the body

• They are an important component of electron transferring processes that occur during cellular respiration

• As a result, they take part in enzyme-catalyzed oxidation of organic molecules in the body

Oxidation C₆H₁₂O₆ + 6H₂0  6CO₂ + 24 H+ _{+ 24 e} -Fe 3+ _{+ e} -  Fe 2+ _{or Cu} 2+ _{+ e}-  Cu + Reduction O₂ + 4H+ _{+ 4e}-  2H 2O Fe 2+  Fe 3+ _{+ e- or Cu} +  Cu 2+ _{+ e}

-The Role of Iron and Copper Ions

• The Haem group in a hemoglobin molecule is made up of iron • Hemoglobin, the red blood cell molecule, carries oxygen

throughout the blood, and thus throughout the body

• Hemoglobin contains four large polypeptide groups and four iron (II) ions, each surrounded by a haem group

• Without the haem group, hemoglobin would not be able to carry any oxygen

• Similarly, haem is a prosthetic group, which means haem is essential for proteins to be able to carry out their functions • At high oxygen concentrations, oxygen forms co-ordinate

bonds and the haem group forms a ligand • At low concentrations, the reverse occurs

• Note that: CO₂ and CN- _{are poisonous for the body as they}

form stable complexes with iron in the haem group - thus haemglobin is prevented form carrying oxygen