bio 110 unit 1

Polymer

long chain of similar repeating sub units joined together by similar bond types

carbs

hexagon structure, cellulose (wood)

protein

• polymers of amino acids

• amino acid structure: carbon bonded to nitrogen, phosphate group, R group

peptide bond

join amino acids together

primary structure

• from first amino acid to the last

• proteins have only one

• linear chain

secondary structure

• proteins have many

• 3D helix of stable parts of the protein

• stabilized by polar interactions b/n protein backbone

tertiary structure

• overall 3D shape of protein

• stabilized by interaction of -R group

• easily influenced by external environment

Quaternary structure

• functional protein: groups separate subunit protein structures

nucleic acids

• polymers made of nucleotides

• info and data storage transmission

• DNA and RNA

  • RNA has OH

  • purines A, G; pyrimidines C, T (or U in RNA)

    • base pairing

      • A = T/U

      • G = C

• Phosphodiester bond

lipids

• not polymers; fats, oils (nonpolar)

• glycerides: made of a glycerol backbone bonded to fatty acid(s)

• phospholipids

  • amphipathic

    • P head, NP tail

    • shunned by water → minimize interactions with NP, maximize with P (surrounds)

  • micelles

    • spherical clusters of amphipathic molecules

    • dissolve in water, spontaneously forms

• steroids

  • found in our body

  • are many hormones

  • 3 hexagons, 1 pentagon

plants

• sugar / starch / carb

• less energy per gram

• easier to make and access

animals

• lipids / fats

• more energy per gram

• lighter, takes less energy to move around

• harder to access

cell theory

• all living organisms made of cells

• cells divide from preexisting cells

• cells can be cultures to produce more cells

plasma membrane

regulates what enters and leaves the cell

cytoplasm

gelatinous liquid that fills the inside of a cell

DNA

• molecule that contains genetic instructions

• blueprint for proteins

• naked DNA: not enclosed in nucleus, easily accessible

Ribosomes

• organelle that makes proteins

• free ribosomes are in cytoplasm

• bound ribosomes are attached to rough ER, temporarily

cytoskeleton

• found in eukaryotic cells

• tubes composed of proteins

• provide structural support for compression and expansion

• protein filaments

  • microfilaments

    • frequently interacts with myosin to do movement

      • protects cell from being stretched/tensed

  • microtubules

    • tracks for kinesin to transport proteins and vesicles

      • uses energy (ATP)

3 types of cells

• bacteria and archaean’s : prokaryotes

• eukaryotes

prokaryotic cells

• naked DNA

• no organelles

• smaller size

• bacteria, archaean’s

• produce through binary fission

• smaller ribosomes

• simpler organization

• parts

  • cell wall

  • capsule

  • pill

  • flagella

  • nucleoid

  • plasmids

eukaryotic cells

• DNA arranged as chromosomes and stores in nucleus

• many organelles

• larger size

• plants, animals, fungi, protists

• produce through mitosis

• larger ribosomes

• more complex and organized

• parts

  • nucleus

  • mitochondria

  • Endopasmic reticulum

  • golgi apparatus

  • lysosomes

  • chloroplasts

  • vacuoles

  • cytoskeleton

nucleus

• DNA (how to make proteins) is protected but less accessible

• only in eukaryotic cells

nuclear localization signal (NLS)

• molecular tag on proteins so they can get in and out of the nucleus

• process

  • protein with NLS in cytoplasm

  • binds to importin

  • goes to nucleus

pulse-chase experiment

• use labeled compounds (dyed proteins) to follow dynamics of cellular processes and pathways

endomembrane system

• make and distribute proteins, secretion

• parts

  • Endoplasmic reticulum: surrounds nucleus, network folds of membranes

    • rough ER

      • protein synthesis

        • mRNA copies info from DNA → cytoplasm → binds to free ribosomes and gives info to make protein

          • if protein needs to go to other parts of endomembrane system or secreted → binds to ribosome → signal sequence → binds SRP → binds receptor → protein made (“pooped”) into ER

            • bind to vesicle → transported

          • if protein needed in cytoplasm or nucleus → don’t have signal sequence → remains free ribosome

    • smooth ER

      • lipid synthesis

similar parts in eukaryotic and prokaryotic cells

• ribosomes

• DNA

• cytoplasm

• plasma membrane

golgi apparatus

• part of endomembrane system in eukaryotic cells

• distribution center of proteins from endoplasmic reticulum

  • transports to other parts of endomembrane system

• secretion out of cell

lysosomes

• recycling center

• breaks down molecules

endosymbiotic theory of origin of mitochondria and chloroplast

• similar in size to prokaryotes

• photosynthetic bacteria and oxygen breathing bacteria eaten

• symbiotic relationship

  • larger bacteria → more glucose and energy

  • smaller bacteria → protected

• oxygen breathing → mitochondria

• oxygen breathing AND photosynthetic → mitochondria AND chloroplast

cell wall

• structural support

• in plant cells, highly porous → doesn’t regulate

energy and enzymes

• energy of reaction doesn’t change because of enzyme

• enzyme speeds up reaction

ATP

• found in DNA and RNA

• 3 phosphate groups connected in a sequence

• RNA has OH

energy coupling

• use of exergonic progress to drive endergonic process

enzyme regulation

• enzymes can be turned off and on

• prevent unnecessary reactions

competitive inhibition

• competition for binding space on active site

• prevents regulatory molecule from binding to enzyme active site

• lowers enzyme activity

allosteric regulation

• 2nd binding site: allosteric site

• molecules binding to allosteric site change shape of enzyme

• allosteric activation; on

• allosteric inhibition; off

feedback inhibition

• product of pathway acts as inhibit of pathway

• prevents too much buildup of a product

• self-regulating system

• if product level gets too low in concentration, there isn’t enough product to bind to enzymes, thus the enzymes will start producing more product

enzyme and environment

• proteins, especially enzymes, easily affected by environment

• temperature

  • temperature optimum

    • when above, enzyme activity crashes

    • when below, enzyme activity unaffected

• pH

  • pH optimum

    • too high/low will denature enzyme

temperature optimum

temperature where enzyme operates at peak efficiency

pH optimum

usually around the pH of the environment found, the pH where the enzyme operates at peak efficiency