Biology Notes

Macromolecules: Structure and Function

Cells use smaller organic molecules (monomers) to create larger molecules (macromolecules or polymers). These macromolecules have a weight exceeding 100,000 Daltons (atomic mass unit).

The four major classes of macromolecules are:

a) Carbohydrates
b) Lipids
c) Proteins
d) Nucleic acids

Polymers: Synthesis and Breakdown

Polymers are long molecules consisting of similar building block molecules called monomers covalently bonded together.

  • Dehydration Reaction: Monomers connect through covalent bonds via a dehydration reaction, where one monomer provides a hydroxyl group (OH) and the other provides a hydrogen (H) atom, forming water (H_2O). This process requires energy and is aided by enzymes.
  • Hydrolysis: The covalent bonds connecting monomers in a polymer can be disassembled by hydrolysis (hydration). In this reaction, a water molecule is split, and a hydrogen atom and a hydroxyl group attach to where the covalent bond used to be. Hydrolysis reactions dominate the digestive process and are guided by specific enzymes.

Carbohydrates

  1. Monosaccharides: The simplest form of carbohydrates, also known as simple sugars, containing a single sugar molecule.
  2. Disaccharides: Contain two monosaccharides joined via dehydration reactions.
  3. Polysaccharides: Polymers of many monosaccharides.

Sugars are composed of carbon, hydrogen, and oxygen in a ratio of 1:2:1, represented by the molecular formula CnH{2n}O_n.

  • An OH group is attached to each carbon except one, which is double bonded to an oxygen (carbonyl).

Monosaccharide Classification

  • Aldoses: Monosaccharides with the carbonyl group (C=O) at the end of the carbon chain (e.g., Glucose).
  • Ketoses: Monosaccharides with the carbonyl group (C=O) within the carbon chain (e.g., Fructose).
  • Triose (3C): e.g., Glyceraldehyde
  • Pentose (5C): e.g., Ribose
  • Hexose (6C): e.g., Glucose, Fructose, and Galactose

Disaccharides

Consist of 2 monosaccharide molecules joined during a dehydration reaction.

  • Sucrose (table sugar): Consists of Glucose + Fructose. The covalent bond formed between Glucose & Fructose is called “glycosidic linkage”.

Polysaccharides

Consist of a few hundreds to a few thousands of monosaccharides joined by a dehydration reaction.

  • Storage Polysaccharides: Provide sugar for cells through hydrolysis (addition of water).
    • Starch: A storage polysaccharide of plants found within plastids, consisting of thousands of α glucose molecules. It gives glucose when hydrolyzed by special enzymes, and potatoes and grains are major sources of starch.
    • Glycogen: Stored in animal cells like liver and muscle, consisting of thousands of glucose molecules. It also yields glucose upon hydrolysis.
  • Structural Polysaccharides: Serve as building materials for organisms.
    • Cellulose: Forms micro-fibrils and cell walls in plants, consisting of thousands of β glucose molecules. Humans cannot digest it, but some bacteria and protozoa can. It serves as the building material of plant cell walls.
    • Chitin: Consists of thousands of glucose molecules with a nitrogen atom at one end. It is used to manufacture surgical threads and is the building material of the cuticle in insects.

Proteins (Polypeptides)

Proteins are polymers of amino acids.

  • Amino acids: are constructed from 20 amino acids.

Amino Acids Structure

The general formula of an amino acid includes a central carbon atom (C) bonded to a hydrogen atom (H), a carboxyl group (COOH), an amino group (NH_2), and a variable R group (or side chain).

  • Differences in the R groups produce the 20 different amino acids.
  • Hydrophobic Amino Acids: Have hydrophobic (non-polar) R groups.
  • Hydrophilic Amino Acids: Have polar R groups, making them hydrophilic.
  • Ionized Amino Acids: Have functional groups that are charged (ionized) at cellular pH (7).

Peptide Bond Formation

The peptide bond is formed between the carboxyl group of one amino acid and the amino group of another through a dehydration reaction.

  • Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of the other. The resulting covalent bond is called a peptide bond.
  • The repeated sequence (N-C-C) forms the polypeptide backbone.
  • Polypeptides range in size from a few monomers to thousands.

Levels of Protein Structure

a. Primary Structure (simple)
b. Secondary Structure (double)
c. Tertiary Structure (triple)
d. Quaternary Structure (quaternary)

Lipids

Lipids include fats, phospholipids, steroids, and waxes. They are generally insoluble in water.

  • Fats store large amounts of energy.
  • Phospholipids are major components of cell membranes.
  • Steroids include cholesterol and certain hormones.

Fatty Acids

Are long chains of mostly carbon and hydrogen atoms with a -COOH group at one end.

  • When they are part of lipids, the fatty acids resemble long flexible tails.

Fat Molecule Structure

  • In a fat, three fatty acids join to a single glycerol molecule by an ester linkage, creating a triacylglycerol.
  • Thus, the fat molecule is constructed from two kinds of smaller molecules: glycerol and fatty acids (so it is not a true polymer).
  • Hence, lipids are the one class of large biological molecules that does not include true polymers.

Saturated vs. Unsaturated Fatty Acids

  • Saturated Fatty Acids: Have no double bonds between the carbons. All carbons are linked with hydrogen. They are solid at room temperature and include most animal fats.
  • Unsaturated Fatty Acids: Have one or more double bonds between carbons in their fatty acids create “kinks” in the tails. They can be synthetically converted to saturated (solid) by adding H atoms (hydrogenation). They are liquid at room temperature and include most plant fats.

Other Lipids

  • Phospholipids: Have two fatty acids attached to a glycerol molecule and a phosphate group at the third position. The phosphate group carries a negative charge. The 2 fatty acid tails are HYDROPHOBIC, but the phosphate group and its attachments form a HYDROPHILIC head. Thus, it is AMPHIPATHIC: has both hydrophobic and hydrophilic regions. They are major components of cell membranes.
  • Steroids: (e.g., Cholesterol) are hydrophobic molecules, some of which form hormones (sex hormones).
  • Waxes: Are hydrophobic molecules used for waterproofing (protection).

Viruses

  • Viruses consist of a core of nucleic acid, either DNA or RNA, and a protective coat of protein.
  • Viruses do not show any of the expected signs of life.
    • do not respond to stimuli
    • do not grow
    • do not do any of the things we normally associate with life.
  • Viruses are not considered "living" organisms but are able to reproduce in a host cell.
  • Viruses are much smaller than bacteria (about 20nm in diameter).

Viral Structure

  • A virus is a genome enclosed in a protective coat.
  • Viruses are not cells.

Viral Genome

  • Viral genomes may consist of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), or single-stranded RNA (ssRNA).
  • The viral genome is usually organized as a single linear or circular molecule of nucleic acid.
  • The smallest viruses have only four genes, while the largest have several hundred.

Capsid and Envelopes

  • The capsid is a protein shell enclosing the viral genome. It can be rode-shaped, helical, polyhedral, or more complex.
  • Capsomeres are the protein units that form the capsid.
  • Some viruses are further wrapped in a membranous envelope (viral envelope), e.g., influenza virus. These envelopes are derived from the membrane of the host cell.

Viral Replication

  • A viral infection begins when the virus's genome enters the host cell.
  • The viral genome commandeers its host, reprogramming the cell to copy viral nucleic acid and manufacture proteins.
  • The nucleic acid molecules and capsomeres then self-assemble into viral particles and exit the cell.
  • Obligate Parasitism: Viruses replicate only in host cells.

Retroviruses

  • A retrovirus is an RNA virus that is duplicated in a host cell using the reverse transcriptase enzymes to produce DNA from its RNA genome. The DNA is then incorporated into the host’s genome by an integrase enzyme.
  • An example is the AIDS (HIV) virus, which includes an envelope with glycoproteins, a capsid containing two identical RNA strands as its genome, and two copies of reverse transcriptase.

Bacteriophages (Phages)

  • These are viruses that infect bacteria.
  • They have a 20-sided capsid head that encloses their DNA and a protein tail piece that attaches to the host and injects the phage DNA inside.

Lytic Cycle vs. Lysogenic Cycle

  • Lytic Cycle: The phage reproductive cycle results in the death of the host. The bacterium lyses (breaks open) and releases the phages produced within the cell.
  • Lysogenic Cycle: The phage genome replicates without destroying the host cell. Temperate phages (e.g., phage lambda (λ)) may use both lytic and lysogenic cycles.

Viral Host Specificity

  • Each type of virus infects a limited range of host cells (host range).
  • Most viruses of eukaryotes attack specific tissues.
  • A protein on the surface of the virus has a shape that matches a molecule in the plasma membrane of its host, allowing the virus to recognize the host cell.

Cell Structure and Classification (Prokaryotic vs. Eukaryotic)

Cell Theory

The cell theory states that:

  1. all living organisms are made of one or more cells
  2. cells are the basic units of structure and function, and
  3. cells come only from pre-existing cells. A cell is the smallest unit that can carry on all of the processes of life

Domains of Life

A) Prokaryota:

  • Contains 2 Kingdoms: Archaea and Bacteria (Eubacteria)

B) Eukaryota:

  • Contains 4 Kingdoms: Fungi, Protista, Plantae, and Animalia

Similarities Between Prokaryotic and Eukaryotic Cells

  • All cells are surrounded by a plasma membrane.
  • The semi-fluid substance within the cell is called “cytosol”, containing cell organelles.
  • All cells contain chromosomes which have genes in the form of DNA.
  • All cells have tiny organelles called “Ribosomes” that make proteins.

Differences Between Prokaryotic and Eukaryotic Cells

  1. Eukaryotes have a nucleus, while prokaryotes do not.
  2. Eukaryotes have membrane-bound organelles, while prokaryotes do not.
  3. Eukaryotic cells are, on average, ten times the size of prokaryotic cells.
  4. The DNA of eukaryotes is much more complex and therefore much more extensive than the DNA of prokaryotes.
  5. The DNA of prokaryotes floats freely inside the cell; the DNA of eukaryotes is held within its nucleus and associated with histones (proteins).
  6. Prokaryotes have a cell wall composed of peptidoglycan. Many types of eukaryotic cells also have cell walls, but none made of peptidoglycan.
  7. Eukaryotes undergo mitosis and meiosis; while prokaryotes divide by binary fission (simple cell division).

Prokaryotes

  • Prokaryotes are single-celled (Unicellular) organisms that do not have a membrane-bound true nucleus and can live in nearly every environment on earth.
  • they differ greatly in their genetic traits, their modes of nutrition, however, their habitats are similar
  • Based on genetic differences, prokaryotes are grouped into two Major Domains: Domain Archaea and Domain Bacteria.

Archaea

  • extremophiles, “ للظروف محبُ القاسية “of extreme environments
    • Extreme halophiles ( للملوحة محبُ ): live in saline places as the Great Salt Lake and the Dead Sea. Some species require an extremely salty environment to grow.
    • Extreme thermophiles ( للحرارة محبُ ): live in hot environments. The optimal temperatures for most thermophiles are 60 - 80°C.

Bacteria

  • Structure of Bacteria Cell
    • Plasma membrane
    • Cell Wall
    • Capsule
    • Ribosomes
    • Nucleoid
    • Cytoplasm (Cytosol)
  • Many bacteria secrete a sticky protective layer called the capsule outside the cell wall.

Capsule functions

  1. Adhere ( تثبيت ) bacterial cells to their substratum ( السطح ).
  2. Increase bacterial resistance ( المقاومة ) to host defenses ( العائل مناعة ).
  3. Stick ( تلصق ) bacterial cells together when live in colonies.
  4. Protect ( تحمى ) bacterial cell.

Cell Wall Functions (Prokaryotes)

  1. Maintains ( تحافظ ) the shape of the cell.
  2. Affords ( توفر ) physical protection ( الحماية الطبيعية ).
  3. Prevents the cell from bursting ( إنفجار ) in a hypotonic (البيئة ذات التركيز األسموزى المنخفض ) environment.
  • Most bacterial cell walls contain peptidoglycan (a polymer of modified sugars cross-linked by short polypeptides).
  • The walls of Archaea lack ( تـفـتـقـد ) peptidoglycan.

Gram's Stain

  • A tool for identifying ( تعريف ) bacteria, based on differences in their cell walls.
    • Gram-positive (Gram +ve) bacteria: cell walls quantities of peptidoglycans (appear violet-stained (تصبغ بنفسجيا ً)).
    • Gram-negative (Gram -ve) bacteria: cell walls small amount of peptidoglycan (appear stained red (تصبغ باللون األحمر )).
  • Most Gram-negative species are pathogenic ( ممرضة ) more threatening ( خطورة أكثر ) than gram-positive species.
  • Gram-negative bacteria are commonly more resistant ( ممانعة أكثر ) to antibiotics ( الحياتية للمضادات ) than gram-positive ones.

Bacteria Shapes

  • Spiral-shaped ( الشكل حلزونية ) bacteria in the form of spirilla or vibrio (comma like).
  • Sphere-shaped ( الشكل كروية ) bacteria are called cocci.
  • Rod-shaped ( الشكل عصوية ) bacteria are called bacilli

Bacteria Reproduction

  • Prokaryotes reproduce ( تـتـكاثر ) only asexually ( جنسيا ال ) by binary fission (اإلنقسـام الثـنائي البسيط).
  • A single cell produces a colony of offspring.

Bacterial Nutrition

  • Nutrition refers to how an organism obtains energy and a carbon from the environment to build the organic molecules of its cells.

Ways That Prokaryotes Are Grouped According to How They Obtain Energy and Carbon.

  • Phototrophs ( التغذية ضوئية ): Organisms that obtain energy from light.
  • Chemotrophs ( التغذية كيميائية ): Organisms that obtain energy from chemicals in their environment.
  • Autotrophs ( التغذية ذاتية ): Organisms that obtain carbon from CO_2.
  • Heterotrophs ( التغذية متعدد ): Organisms that obtain carbon from organic nutrients.
    • Photoautotrophs ( ذاتية التغذية الضوئية ): use light energy as an energy source, and CO_2 as a carbon source to synthesize ( تخلق ) organic compounds.
    • Chemoautotrophs ( الكيميائية التغذية ذاتية ): use chemical inorganic substances as an energy source, and CO_2 as a carbon source.
    • Photoheterotrophs ( الضوئية التغذية متعدد ): use light as an energy source, and organic substances as carbon sources.
    • Chemoheterotrophs ( الكيميائية التغذية متعدد ): use organic substances as a source for both energy and carbon.

Cellular Organelles:

  • An eukaryotic cell has internal membranes, which partition the cell into compartments.
  • These membranes also participate in metabolism as many enzymes are built into membranes.
  • The general structure of a cell membrane is a double layer of phospholipids and diverse proteins.
  • Each type of membrane has a unique combination of lipids and proteins for its specific functions.
    • Those in the membranes of mitochondria function in cellular respiration.

Cytoskeleton: Structure and Function network of fibers ( االلياف من شبكة ) that provides structural support ( تدعيم ) to the cell.

  • The cytoskeleton also functions in cell motility ( الخلية تحرك ) and regulation. It is made up of 3 types of fibers

Types of Microfilaments.

  • Microfilaments (Thin)
  • Intermediate filaments (Middle)
  • Microtubules (Thick)

Microfilaments function (Actin protein) to

  • Support cell motility
  • Transport materials within the cell.

Intermediate filaments function (Fibrous protein) to

  • Reinforcing the cell shape
  • Fixing position of organelles.

Microtubules function (Tubulin protein) to

  • Responsible for cell motility
  • Separation of chromosomes during cell division
  • Cell Membrane: membrane is a selective barrier that allows passage of oxygen, nutrients, and wastes for the whole volume of the cell. has a Fluid Mosaic Model, Carbohydrate