2 - Molecular

DNA hydrogen bonds

Hydrogen bonds hold two polynucleotide chains of DNA together between complementary bases, 2 for A-T and 3 for

C-G, connected strands run in opposite directions and twist into double helix

DNA Replication (definition)

Semi-conservative process that uses a pre-existing strand as a template to synthesize new strands

DNA Replication enzymes

helicase, primase, DNA polymerase, ligase

Primers

short single-stranded nucleic acid used in the start of DNA synthesis, they guide DNA polymerase to the section of DNA that needs to be replicated

Complimentary base pairing

hydrogen bonding between nitrogenous bases; in DNA, thymine (T) pairs with adenine (A), and guanine (G) pairs with cytosine (C); in RNA, uracil (U) pairs with A, and G pairs with C

Helicase

An enzyme that breaks the hydrogen bonds between complementary base pairs, thus separating the polynucleotide strands, and unwinding the double helix by

DNA Polymerase

An enzyme that synthesizes new DNA strands from two parental template strands and free deoxynucleotide triphosphates, which then align opposite their complementary base partners, the enzyme then splits up the leftover phosphates and uses the released energy to link the nucleotide to the new strand

Transcription

synthesis of a complementary RNA strand from DNA, formed by RNA polymerase

Transcription process

1. RNA polymerase separates DNA strands and synthesizes a complementary RNA copy from a DNA strand

2. DNA strands are separated, ribonucleoside triphosphates align opposite their exposed complementary base partner

3. RNA polymerase removes additional phosphate groups and uses the gotten energy to covalently join the nucleotide to the sequence

4. RNA sequence has been synthesized, now it detaches from the DNA molecule and forms double helix

Gene

A sequence of DNA on a chromosome that transcribes into RNA, it codes for specific traits.

Where does transcription occur?

Transcription of DNA into RNA happens in the nucleus and then RNA is moved to the cytoplasm

antisense strand

strand of DNA that runs 3' to 5' that is transcribed, complementary to the sense strand, acts as a template strand

sense strand

strand of DNA that runs 5' to 3' that is not transcribed, identical to RNA sequence, contains the genetic code for a protein

mRNA

A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

RNA polymerase

Unwinds DNA and adds nitrogenous bases to a growing RNA chain

Codon

Triplet of DNA or mRNA nucleotide bases which correspond with specific amino acids or stop signals during protein synthesis

Genetic code

set of codons of mRNA, which code for corresponding amino acids for each codon combination with 64 codon possibilities and 4 possible bases, mRNA coding begins with a start codon AUG and ends with a STOP codon

Degeneracy

same codons code for the same amino acids

polymerase chain reaction (PCR)

A method of producing thousands of copies of DNA segment using the enzyme DNA polymerase

Insulin

A protein hormone synthesized in the pancreas that regulates blood sugar levels by facilitating the uptake of glucose into tissues

polymerase chain reaction (PCR)

A method of amplifying DNA quantities, it starts with denaturation where DNA is heated to 90 C to separate strands, then annealing where DNA is cooled to 55 C to allow primes annealing, and finally elongation where sample is heated to optimal temp. for a heat-tolerant polymerase to function in 75 C

tRNA

An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA

Amino acids

building blocks of proteins

Polypeptides

a polymer of amino acids joined together by peptide bonds.

Four classes of macromolecules

carbohydrates, lipids, proteins, nucleic acids

Catalysis

acceleration of a reaction rate by a molecule that will not be consumed by the reaction

Anabolism

synthesis of complex molecules from simpler molecules, forming macromolecules from monomers via condensation, it's involved in: reduction reactions, intake of energy for new bonds, gluconeogenesis, synthesis of complex mol.

Catabolism

breakdown of complex molecules into simpler molecules, creating monomers from polymers via hydrolysis, involved in: oxidation reactions, release of energy during bond breaking, glycolysis, breakdown of complex mol.

Hydrolysis

complex molecules are broken down by using water molecules to sever bonds

Condensation reaction

monomers form together via covalent bonding and creates a by-product of water

Monomer

molecules that join together to form polymers/macromol., monosaccharides, amino acids, nucleotides

Polymer

a large compound formed from multiple monomers, disaccharides, polysaccharides, dipeptides, polypeptides, polynucleotide chains

Urea

nitrogenous waste excreted in urine

Synthesis of urea (Falsifying vitalism)

Vitalism stated that urea could only be made in living organisms because it was an organic compound, and thus needed a "vital force"

In 1828, Friedrich Wohler synthesized urea artificially using silver isocyanate and ammonium chloride, the first time that an organic compound had been synthesized artificially

Vitalism

the belief that there's a vital life force needed to create organic compounds

Carbon importance?

Carbon atoms are the basis of organic compounds because they have 4 valence, meaning they can form 4 covalent bonds

Organic compounds

Compounds that contain carbon

Carbohydrate (general)

polar compound made up of carbon, hydrogen, and oxygen atoms; main macromolecule used for energy (short-term energy), recognition, and for structure

Lipids (general)

non-polar compound made up of various components with either simple, complex or derived forms, lipids are components of cell membranes and cholesterol, function as long-term energy stores as fats and oils, or signaling molecules like steroids

Nucleic acids (general)

polar compound containing hydrogen, oxygen, nitrogen, carbon, and phosphorus, the genetic material of cells that predetermines inherited features, DNA functions as a code for protein assembly, RNA has a role in protein synthesis

Protein (general)

polarity varies based upon amino acid, but a macromolecule that contains carbon, hydrogen, oxygen, nitrogen, and sometimes sulphur, functions as enzymes, structural mol. and more

Monosaccharides

single sugar monomers which make up glucose, fructose, galactose, function as short-term energy and taste sweet

Disaccharides

sugar polymer made up of 2 monosaccharides, sucrose, lactose, maltose, functions as transport

Polysaccharides

sugar polymer made up of more than 2 monosaccharides, cellulose, glycogen, amylopectin, amylose, function as longer-term energy

Lipid classes

Lipids usually contain a fatty acid chain, and don't have a recurring monomer, but have 3 different classes: triglycerides, phospholipids, steroids

triglyceride structure

glycerol + 3 fatty acids

phospholipid structure

2 fatty acids, 1 glycerol, 1 phosphate group

steroid structure

4 ringed structures

fatty acid chain

building block of a lipid, consists of a carbon line chain with carbons around, except the end which is ―COOH (C double bonded to O, and single bonded to OH)

unsaturated fatty acid

A fatty acid possessing one or more double bonds between the carbons chain

Protein structure

proteins consist of amino acids/polypeptide chains; then have other structure levels

primary structure

how the amino acid chain folds depending on the chemical properties of variable groups

secondary structure

amino acid sequences fold into a spiral - alpha helice, or into pleated/creased sheets - beta-pleated sheets, this is due to the hydrogen bonding between carboxyl and amine groups

Tertiary structure

overall 3D structure of a polypeptide due to interactions of the variable groups of the amino acids

quaternary structure

If a protein consists of more than 1 polypeptide then a 4th level occurs, structure looks like multiple 3rd level structures

nucleotide structure

consist of 5 carbon sugar, phosphate group, nitrogenous base and form long polynucleotide chain

Peptide bond

bond between the carboxyl group of one amino and the amine group of another amino, COHN

glycosidic linkage

bond between two monosaccharides

ester linkage

a bond between a hydroxyl group and a carboxyl group

phosphodiester bond

a bond between pentose sugars and phosphates of adjacent nucleotides

Translation

process of protein synthesis by decoding mRNA message into a polypeptide chain

Translation process

1. Ribosomes bind to mRNA in the cytoplasm and move along the molecule in a 5' - 3' direction until reaching a start codon AUG.

2. Then anticodons on tRNA molecules align opposite appropriate codons according to complementary base pairing.

3. After aligning each tRNA molecules carries specific amino acids corresponding to genetic codes.

4. Ribosomes catalyze the formation of peptide bonds between aminos via condensation and ribosome moves along mRNA molecule making a polypeptide chain till reaching a STOP codon, polypeptide chain is released.

universality

genetic code is universal and the same amongst most organisms, because the same codons code for the same amino acids, this allows for transfer of genes between species for example insulin

insulin production

insulin protection genes are extracted from human cells, spliced into a plasmid vector for autonomous replication and expression and put into a bacteria cell which is allowed by universality of codons, those bacteria are taken and fermented, produced human insulin now which is taken

Decoding mRNA to DNA

mRNA is a complementary copy of a DNA gene, and can be deduced into a sequence. For mRNA to DNA conversion: C is replaced with G and vice versa, U with A, A with T

Decoding mRNA to Polypeptides

mRNA can be translated into codons and then into a polypeptide chain by organizing thecodon triplets, it starts with AUG, ends with STOP.

Nucleotide structure

phosphate group - circle attached to C5, nitrogenous base - rectangle attached to C1, central 5 carbon sugar - pentagon

RNA

a single strand ribonucleic acid that transfers genetic information from nucleus to cytoplasm for decoding, 3 types: mRNA, tRNA, rRNA.

RNA nitrogenous bases

Adenine, Uracil, Guanine, Cytosine

mRNA

messenger RNA is a "transcript" of the section of DNA that codes for a specific polypeptide

tRNA

transfer RNA carries amino acids to the ribosomes to make polypeptides

rRNA

ribosomal RNA component ribosomes and responsible for ribosomal catalytic activity

DNA

a double stranded deoxyribonucleic acid that stores genetic information for cells

DNA nitrogenous bases

Adenine, Thymine, Cytosine, Guanine

DNA structure

the phosphate group of a nucleotide is attached to 5 carbon sugar of another nucleotide at the 3rd hydroxyl group, creating a phosphodiester bond between 2 nucleotides

Crick and Watson

discovered the double helix structure of DNA, their model consisted of: antiparallel double strands that make a double helix, complementary base pairs in DNA strands, and exposed edges of bases for replication proteins and transcriptions proteins

cell respiration

production of ATP through the controlled release of energy from organic compounds, divided into 2 types - anaerobic and aerobic

anaerobic respiration

Cell respiration that does not require oxygen producing 2 ATP via breakdown of glucose in the cytosol by glycolysis

anaerobic respiration process and products

breakdown of glucose into 2 pyruvate mol, NADH hydrogen carries, and 2 ATP. It can continue without oxygen, but won't make ATP. It restores NAD+ for glycolysis, then continues to make ATP

anaerobic respiration in animals

In animals pyruvate is converted into lactate

anaerobic respiration in plants

In plants and yeast pyruvate is converted into ethanol and CO2

Glycolysis

the breakdown of glucose by enzymes, releasing ATP and pyruvate.

aerobic respiration

Cell respiration that requires oxygen producing 34 or 36 ATP via breakdown of glucose by glycolysis in the mitochondria and cytoplasm

aerobic respiration process

breakdown of glucose into CO2, water and ATP. Aerobic respiration begins with anaerobic glycolysis, but consists of the link reaction, Krebs cycle and electron transport chain.

Fermentation

anaerobic breakdown of carbohydrates to produce either ethanol and CO2 from yeast, or to produce lactic acid through fermenting bacterial cultures (cheese)

Respirometer

device that determines respiration rate by measuring oxygen and CO2 exchange

Respiration

production of energy by taking in oxygen and releasing CO2

respirometry process

-organism in a sealed contained

-CO2 production is measured with data logger or pH change in water

-Alkali is included to absorb CO2, oxygen consumption measured as change in pressure

How does anaerobic respiration maximize lactate production in human using muscle contractions?

Muscle contractions need a lot of ATP, when energy demand is exceeded oxygen can be supplied aerobically to break glucose into ATP. This produces lactate which leads to muscle fatigue, once exercise is done oxygen is back and lactate is made back into pyruvate.

Photosynthesis

process of synthesizing carbon compounds from CO2, water and sunlight in chlorophyll, reverse cell respiration

Chlorophyll

a photosynthetic green pigment responsible for light absorption needed for photosynthesis, absorbs light and releases electrons to make ATP

chlorophyll structure

Chlorin ring with a magnesium centre (reacts with light) and a hydrocarbon tail.

Chlorophyll properties

Absorption: Chlorophyll absorbs blue and red.

Reflection: Chlorophyll reflects green.

electromagnetic spectrum

a range of all possible frequencies and wavelengths of electromagnetic radiation, red is 700nm longest, and purple is 400nm shortest.

chlorophyll a and chlorophyll b

a reflects blue-green, b reflects blue-red

action spectrum

A graph that shows the overall rate of photosynthesis at different wavelengths of light

absorption spectrum

The range of a pigment's ability to absorb various wavelengths of light.

photolysis

the breakdown of substances in presence of light, the substance decomposes and forms products

stoma/stomata

small opening on leaf skin that allows carbon dioxide, water, and oxygen to diffuse into and out of the leaf

light-dependent reactions

The 1st step of photosynthesis where sunlight produces ATP and NADPH:

chlorophyll inside plants absorbs light and makes ATP, water also absorbs light which is then split via photolysis and creates oxygen, hydrogen, and NADPH, oxygen is released from the stomata, hydrogen, ATP and NADPH is used in the 2nd step