BIOCHEM EARLY EARTH CONDITIONS, ORIGINS OF LIFE, DNA/VIRUSES, PROTEINS & ENZYMES (Flashcards)

A comprehensive set of flashcards covering early Earth conditions, origins of life theories, nucleic acids, recombinant DNA, viruses, and proteins/enzymes to help review for exams.

What were the major gases in Earth's early atmosphere and what environmental condition did this create for life?

Carbon dioxide (CO2), water vapor, methane (CH4), ammonia (NH3), hydrogen (H2), and hydrogen sulfide (H2S); no oxygen and no ozone (O3), leading to high UV radiation.

What were the major environmental factors marking Earth’s early state besides atmospheric composition?

Extremely volcanically/geologically active, frequent lightning, meteorite impacts, solar radiation, and radioactive decay.

What were the major biomolecule groups important for life and their building blocks?

Carbohydrates (monosaccharides), Proteins (amino acids), Lipids (fatty acids and glycerol), Nucleic Acids (nucleotides).

What is the building block and primary function of carbohydrates?

Monosaccharides; provide immediate energy and energy storage.

What is the building block and primary function of proteins?

Amino acids; build/repair tissues and act as enzymes to speed up reactions.

What is the building block and primary function of lipids?

Fatty acids and glycerol; store long-term energy and form cell membrane barriers.

What is the building block and primary function of nucleic acids?

Nucleotides; store and transmit genetic information and enable protein synthesis.

Which theory suggests life came from space via meteorites or comets?

Panspermia; proposed by Svante Arrhenius.

What is the Hydrothermal Vent Theory in brief?

Life began in deep-sea vents through chemosynthesis (H2S + CO2 + O2 → sugars + sulfur + water); iron-sulfur minerals provided a rich, protected environment; Dr. Günter Wächtershäuser proposed iron–sulfur world hypothesis.

Describe the RNA World Hypothesis and its proponent.

RNA came before DNA, storing genetic information and catalyzing reactions; coined by Dr. Walter Gilbert in 1986.

What is the Clay Hypothesis?

Clay minerals may have helped assemble organic molecules and served as templates for biomolecule formation; proposed by Dr. Alexander Graham Cairns-Smith.

What does Abiogenesis refer to?

Origin of life from non-living matter through gradual chemical evolution; spontaneous generation as a historically debated idea.

What important experiment did Francesco Redi perform and what did it show?

Redi’s experiment showed maggots on decaying meat came from fly eggs, not the meat itself, refuting spontaneous generation for larger organisms.

What are the Oparin–Haldane Theory and its key idea?

Life originated gradually from non-living matter through chemical evolution; primordial soup concept.

What was the Miller–Urey Experiment and its significance?

Laboratory simulation of early Earth conditions showing formation of amino acids from inorganic precursors; supported chemical evolution theories.

What is the difference between DNA and RNA in terms of sugar and structure?

DNA uses deoxyribose and is typically double-stranded; RNA uses ribose and is typically single-stranded.

What bases are purines, and which bases do they include?

Purines have two rings; Adenine (A) and Guanine (G).

What bases are pyrimidines, and which bases do they include?

Pyrimidines have one ring; Thymine (T), Cytosine (C), and Uracil (U in RNA).

What are complementary base pairs in DNA?

Adenine pairs with Thymine (A-T) and Guanine pairs with Cytosine (G-C).

What are complementary base pairs in RNA?

Adenine pairs with Uracil (A-U) and Guanine pairs with Cytosine (G-C).

What are the two types of sugars found in nucleic acids?

Deoxyribose in DNA; Ribose in RNA.

What are nucleotides?

Monomers of nucleic acids composed of a sugar, phosphate, and nitrogenous base.

Name the major scientists associated with DNA’s history mentioned in the notes.

Friedrich Miescher (nuclein/DNA), Alfred Hershey and Martha Chase (DNA carries genetic info, via viruses), James Watson and Francis Crick (double helix), Albrecht Kossel (coined the term DNA).

What is recombinant DNA and what is a closely related concept?

DNA molecules containing covalently linked segments from two or more sources; also called chimeric DNA.

What enzyme enables production of recombinant DNA by cutting DNA at specific sequences?

Restriction endonucleases (molecular scissors).

List the basic steps in recombinant DNA technology.

1) Isolate gene of interest; 2) Cut DNA with restriction enzymes; 3) Insert into a vector (e.g., plasmid); 4) Transform host organisms (usually bacteria); 5) Clone and express the gene to produce proteins.

What is a plasmid and its role in cloning?

A small circular DNA molecule used as a cloning vector; can carry genes such as antibiotic resistance.

How do viruses differ from bacteria, fungi, and protozoa?

Viruses are acellular, have no metabolism, and require a host for replication; bacteria are prokaryotic and self-replicate; fungi and protozoa are eukaryotic.

What are the main components of a virus’s structure?

Genetic material (DNA or RNA, single or double-stranded), a capsid (protein shell), and sometimes an envelope derived from a host membrane; may contain viral enzymes like reverse transcriptase.

Where do DNA viruses replicate and which enzyme do they rely on?

In the host cell nucleus using host DNA polymerase.

Where do RNA viruses replicate and which enzyme do they use?

In the cytoplasm using viral RNA polymerase.

What is a retrovirus?

A virus that reverse-transcribes its RNA into DNA and integrates it into the host genome (e.g., HIV).

Outline the basic viral life cycle stages.

Attachment, Entry, Replication, Assembly, Release.

What is the difference between the Lytic cycle and the Lysogenic cycle?

Lytic: rapid replication leading to host cell lysis; Lysogenic: viral DNA integrates into the host genome and can replicate silently (latency).

What is the role of vaccines in viral infections?

Introduce weakened/inactivated virus or components to stimulate adaptive immunity (antibodies and memory cells); contributed to eradicating smallpox and reducing polio; examples include MMR, Influenza, and COVID-19 vaccines.

What are amino acids and how many are standard in proteins?

Amino acids are the building blocks of proteins; there are 20 standard amino acids.

What distinguishes essential from non-essential amino acids?

Essential amino acids cannot be synthesized by the body and must be obtained from diet; non-essential amino acids can be made by the body.

How are amino acid side chains classified?

Nonpolar (hydrophobic), Polar uncharged (hydrophilic), Polar charged (basic – hydrophilic cations; acidic – hydrophilic anions).

Name examples of nonpolar amino acids.

Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Methionine (M), Proline (P), Tryptophan (W), Phenylalanine (F) (group GAVWLIMP).

Name examples of polar uncharged amino acids.

Serine (S), Threonine (T), Cysteine (C), Asparagine (N), Glutamine (Q), Tyrosine (Y) (group STCNQY).

Name examples of basic amino acids.

Lysine (K), Arginine (R), Histidine (H).

Name examples of acidic amino acids.

Aspartic acid (D), Glutamic acid (E).

What is glycine’s significance among amino acids?

Glycine is the simplest amino acid.

What is a peptide bond and how is it formed?

A bond between amino acids formed by dehydration synthesis; links the carboxyl group of one amino acid to the amino group of the next.

What are N-terminus and C-terminus in a protein?

N-terminus is the start of the polypeptide (free amino group); C-terminus is the end (free carboxyl group).

What are the four levels of protein structure?

Primary, Secondary (beta sheets and alpha helices), Tertiary (3D folding), Quaternary (assembly of multiple tertiary units).

What does denaturation do to a protein?

Causes loss of folded structure and native conformation, often disrupting function.

Name common protein functions and examples.

Antibodies, Enzymes (DNA/RNA polymerase), Hormones (growth-related), Motor proteins (actin/myosin), Receptors, Transport proteins (hemoglobin), Structural proteins (collagen, keratin), Storage proteins (egg albumin, milk casein).

What is an enzyme and what makes them unique?

A protein (or RNA) that acts as a highly specific catalyst, enabling biological reactions to occur under mild conditions.

Where is the enzyme active site and what is its role?

The active site is the region of the enzyme with a specific shape and functional groups where substrate molecules bind to undergo a reaction.

What is activation energy and how do enzymes affect it?

Activation energy is the energy barrier to start a reaction; enzymes lower this barrier to accelerate the reaction.

Name the first digit (EC class) of enzyme classification and its reaction type.

Oxidoreductases – oxidation/reduction.

List digestive enzymes and their primary substrates/products.

Amylase (mouth) breaks starch to maltose; Sucrase (small intestine) breaks sucrose to glucose+fructose; Maltase (small intestine) breaks maltose to glucose; Lactase (small intestine) breaks lactose to glucose+galactose; Pepsin (stomach) digests proteins to peptides; Trypsin (small intestine) continues protein digestion; Lipase (small intestine) breaks fats to fatty acids and glycerol.

What are enzyme tests and name a few common examples?

Blood tests that measure enzyme levels to assess organ damage or disease; examples include ALT (liver), CK-MB (heart), Troponin (heart injury), Amylase (pancreas), Lipase (pancreas), Lactase (lactose intolerance), G6PD (deficiency).