BIOLOGY Ch. 1 Cell & Molecular Biology

Biochemistry, Cells & Organelles, Biothermodynamics, Cellular Respiration, Photosynthesis, Cell Division

electronegativity

the ability of an atom to attract shared electrons within a bond (pull closer to itself)

ionic bond

• complete transfer of electrons from one atom to another

• between atoms with very different EN

• exist between ions (charged atoms or molecules)

covalent bond

• electrons are shared between atoms with similar EN

• can be single, double, triple bonds

• nonpolar or polar bonds

nonpolar bond

equal sharing of electrons (highly similar EN)

polar bond

unequal sharing of electrons (slightly different electronegativity and formation of a dipole)

dipole

a difference in charge between two parts of a molecule

hydrogen bond

weak bond between molecules that meet two conditions:

1. molecule must have a hydrogen covalently bonded to a highly EN atom (F, O, N)

2. The same hydrogen atom is attracted to another highly EN atom (F, O, N)

   1. H-bonds can be intramolecular or intermolecular

intramolecular

within a molecule

intermolecular

between molecules

van der waals interactions

• weak, temporary attraction between atoms or molcules in close proximity

• occurs due to the transient, uneven distribution of electons in a molecule at any given time

• weak attraction individually, but can add up to a powerful force

bond strength, strongest to weakest

ionic/covalent > hydrogen > dipole-dipole > van der waals (london dispersion)

Stronger bonds have _____(lower/higher) energy, _____(shorter/longer) lengths, and _____(lower/higher) bond order

higher, shorter, higher

bond order, highest to lowest

triple > double > single

water properties

• excellent solvent

• high heat capacity

• liquid form is denser than solid

• cohesion → high surface tension

• adhesion → capillary action

micromolecules

essential nutrients that the body cannot produce in sufficient quantities

→ must be obtained from the diet

minerals

inorganic ions found intracellularly and extracellularly

ex: calcium, potassium

vitamins

organic micromolecules that are classified as either water-soluble or fat-soluble

fat soluble vitamins

excess deposited in body fat; overconsumption can lead to toxicity

ADEK

water soluble vitamins

excess not stored in the body and are excreted in urine

BC

Vitamin A

fat soluble

visual pigment and epithelial maintenance

Vitamin D

fat soluble

regulates calcium levels by promoting absorption from the intestine; synthesized when UV light strikes the skin

Vitamin E

fat soluble

antioxidant - neutralizes free radicals that can damage cells

Vitamin K

fat soluble

important for blood clotting

Vitamin B

water soluble

coenzymes or precursors to coenzymes; there are 8 different B-group vitamins

Vitamin C

water soluble

important for collagen synthesis; deficiency leads to scurvy

macromolecules

• large organic molecules composed of monomers that link together to form polymers

• 4 major: carbohydrates, lipids, proteins, and nucleic acids

dehydration synthesis

process by which monomers combine to form polymers, producing a water molecule

hydrolysis

process by which a water molecule is used to break polymer linkages

carbohydrates (monomer, polymer, linkage type, function)

• monomer: monosaccharide

• polymer: polysaccharide

• linkage type: gycosidic

• function: store energy

classes of carbohydrate

• monosaccharides: single sugar molecule (ex: glucose)

• disaccharides: 2 joined sugar molecules (ex: glucose + fructose = sucrose)

• polysaccharides: polymer of sugar molecules (ex: starch (α-glucose), glycogen (α-glucose), cellulose (β-glucose), chitin (β-glucose))

monosaccharides

single sugar molecule

• glucose

• fructose

• galactose

disaccharides

• glucose + fructose =

• glucose + galactose =

• glucose + glucose =

two monosaccharides joined by a glycosidic linkage

• sucrose

• lactose

• maltose

polysaccharides

series of connected monosaccharides that form long chains

• starch

• glycogen

• cellulose

• chitin

α-glucose polymers with branched structure

• starch: stores energy in plants

• glycogen: stores energy in animals

β-glucose polymers with no branching (linear polysaccharides)

• cellulose: structural molecule in plant cell walls

• chitin: structural molecule in fungi cells walls and arthropod exoskeletons

  • contains nitrogen atoms

humans cannot cleave _____ glycosidic linkages; some animals (ex: cows) can cleave these linkages because of bacteria in their gut

beta

lipids (monomer, polymer, linkage type, function)

functions: insulation, energy storage, cell structure, endocrine molecules, and membrane structure

monomer: hydrocarbon (not true monomers)

polymer: hydrocarbon chains (lipids are not true polymers)

linkage type: covalent carbon-carbon bonds

triglyceride

glycerol + 3 fatty acids

• saturated (single bonds; straight chain)

• unsaturated (double bonds, branched chain)

type of lipid

phospholipid

2 fatty acis + phosphate group attached to glycerol backbone

• amphipathic → polar head, nonpolar tail

• form phospholipid membrane bilayer

type of lipid

steroids

three 6-membered rings + one 5-membered ring

• ex: hormones, cholesterol, vitamin D, and bile acids

type of lipid

porphyrin

4 joined pyrrole rings with a metal center atom

• ex: hemoglobin (central Fe transports oxygen), chlorophyll (central Mg absorbs light)

• non-lipids, but commonly associated with lipid membranes

type of lipid

proteins (monomer, polymer, linkage type, function)

monomer: amino acid

polymer: peptide

linkage type: peptide bonds

function: structure, transport, defense, storage, enzymes

protein primary structure

linear sequence of AA’s connected by PEPTIDE bonds; determined by the sequence of translated mRNA codons

protein secondary structure

3D shape resulting from H bonding between amino and carboxyl groups of adjacent AA’s → alpha helix and beta sheet

protein tertiary structure

3D structure due to non-covalent interactions between amino acid R groups

• interactions: H-bonds, ionic bonds, hydrophobic effect, disulfide bonds (covalent exception), and Van der Waals forces

protein quaternary structure

3D structure that arises from multiple subunits joining together

______ are the only macromolecules with disulfide bonds (and sulfur atoms in general)

proteins

nucleic acid (monomer, polymer, linkage type, function)

monomer: nucleotide

polymer: nucleic acid (DNA, RNA)

linkage tpype: phosphodiester bond

function: encode, express, and store genetic info

nucleotide

nitrogenous base + five carbon sugar + phosphate group

purines

nucleotides w/ double ring nitrogen bases

GA

pyrimidines

nucleotides w/ signle ring nitrogen bases

CUT

DNA linkages

nucleotides on the same strand are connected by PHOSPHODIESTER bonds in 5’→3’ and the two strands are connected by H-BONDS between the bases

CUT the PYE

cytosine, uracil, thymine are pyrimidines

all cells contain

plasma membrane, DNA, ribosomes

prokaryotes

1. no nucleus

2. single, circular, naked, double-stranded DNA

3. ribosomes (50S + 30S = 70S)

4. cell walls (peptidoglycan); archaea (polysaccharides) - many have sticky capsules on the cell wall

5. flagella are constructed from flagellin, not microtubules

nuclear envelope

double membrane (two phospholipid bilayers) with pores allowing molecules to enter and exit

nuclear lamina

protein network that maintains the shape of the nucleus

nucleolus

region inside the nucleus where ribosomal RNA (rRNA) is made

_______ and ______ are the two organelles capable of post-translational protein modification

rough ER, Golgi

Nucleus

Contains the cell’s DNA, and coordinates cell activities such as protein synthesis & reproduction

Nucleolus

Site of ribosome (rRNA) synthesis

Cytoplasm

The fluid-filled area in which the cell's metabolic activities occurs; also includes the organelles

Mitochondria

Double layered, makes ATP, site of fatty acid catabolism. Has own circular DNA and ribosomes

Ribosomes

made of rRNA; makes proteins

Rough Endoplasmic Reticulum

Has ribosomes attached to the structure. Functions to synthesize and store proteins.

Smooth Endoplasmic Reticulum

Functions to synthesize lipids and steroid hormones for export

sarcoplasmic reticulum

a specialized form of the SER found in muscle cells

• serves as a reservoir for Ca²⁺ cations that are utilized in the process of muscle contraction

Golgi

Modifies and packages proteins (i.e., glycosylate polypeptides)

Golgi cisternae

flattened sacs in the Golgi apparatus that bud off from the Trans Golgi Network before being transported to the cell membrane, or other membrane-bound structures in the cell

Lysosomes

Made by Golgi and contain digestive enzymes with low pH. Functions in apoptosis and autophagy, and break down of nutrients, bacteria, & cell debris

Peroxisomes

Common in the liver & kidney that function to breakdown substances

• uses hydrogen peroxide (H₂O₂) to oxidize substances

  • a byproduct that forms within peroxisomes when they oxidize substances. After it forms, the H2O2 is quickly broken down within the peroxisome by the enzyme catalase

Cytoskeleton

a network of tubules and filaments in the cytosol that functions in maintaining cell shape, faciltating movement of components within a cell, cell motility, an anchoring membrane proteins

Microtubules

Composed of tubulin.

• forms spindle apparatus during cellular division

• builds long distance transportation systems for kinesin and dynein

• supports cell shape, movement and structure of cilia and flagella

microtubule organizing centers (MTOCs)

• found in all eukaryotic cell types - mitosis/meiosis

  • bacteria divide via binary fission → doesn’t require microtubules

• in animal cells, MTOC = centrosome

• in plant cells, MTOC = spindle poly body

• organized in 9 × 3 array = 9 groups of 3 microtubules arranged in a circular pattern

Centrioles

development of spindle ffibers for cell division

centrosome

two perpendicularly arranged centrioles

Cilia

short hair like extensions from cell for movement

Flagella

thread-like extension from cell for movement

Intermediate filaments

maintain cell shape

keratin is one of the most common proteins

• desmosome and hemidesmosome cell junctions are attached to keratin intermediate filaments

Microfilaments

composed of actin. used for cell motility

three components of cytoskeleton

1. microfilaments: made of actin involved in cell motility; smallest diameter

2. intermediate filaments: support for maintaining cell shape; composed of keratin

3. microtubules: made of tubulin for support and motility; largest diameter

Vacuoles

vesicles inside cell that move materials & are membrane bound

• types: transport, food, central, contractile

contractile vacuole

large vesicle that collects and pumps excess water out of the cell to prevent it from bursting (lysis)

• commonly found in protists that reside in hypotonic environments

  • water from envir. constantly rushing into cell

Extracellular matrix

function to provide mechanical support & helps bind adjacent cells (most abundant = collagen)

Found in plants: ________ and ________

1. cell walls: provide support

2. plastids: variety of organelles serving various metabolic activities such as chloroplasts for photosynthesis

3 main components of cytoskeleton, in order of increasing diameter

microfilaments, intermediate filaments, microtubules

anchoring junction

includes desmosomes; connects 2 cell togethers

tight junction

encircles each cell, producing a seal that prevents the passage of materials between cells; is characteristic of cells lining the digestive tract

gap junction

narrow tunnels between animals cells; allow passage of ions and small molecules

glycocalyx

a carbohydrate coat that covers the exterior of some bacterial and animal cells

• functions in cell-to-cell recognition, adhesion, and it acts as a physical barrier to prevent pathogens from entering the cell

• can also be found on the inside of blood vessels to provide a protective barrier and maintain vascular walls

Glycoproteins

proteins with carbohydrates attached

• commonly used as cell surface markers because immune cells can check membrane glycoproteins to determine if a cell is foreign

• main functions of glycoproteins include cell-to-cell recognition, signaling, and cellular adhesion

microfilaments are made of ______, intermediate filaments are made of _________, microtubules are made of _______

actin, keratin, tubulin

cyclosis

the streaming movement of the cytoplasm that is generated by the contraction and relaxation of actin and myosin filaments in the cytoskeleton

biothermodynamics

the transfer of energy between and within living organisms

Anabolic

Small molecules assemble to form a larger molecule

Catabolic

Large molecules are broken into smaller molecules

Exergonic

Free energy is released (spontaneous with −ΔG)

Endergonic

Free energy is absorbed (nonspontaneous with +ΔG)

Chemical reactions can be combined to drive otherwise ____________ reactions. For example, ATP hydrolysis is an _______ reaction that facilitates __________ reactions.

nonspontaneous, exergonic, endergonic

Kinetic Energy

the energy of anything in motion

(e.g. flagella whipping back and forth).