Biochemistry Unit Summary

Macromolecules Overview

• General points

  • Polymers made w/ dehydration synthesis and undone with hydrolysis

Carbohydrates

• Composition

  • C, H, O combined using dehydration synthesis

• Function

  • Energy molecules (short term)

  • Raw materials

  • Structural material

    • Eg. cellulose in plant walls

• Types

  • Simple sugars (monosaccharides)

    • Sugars, starches, cellulose, glycogen

    • Classified by number of carbons

  • Polysaccharides

    • Polymer of carbs (multiple monosaccharides connected)

    • Eg. starch

Lipids

• Composition

  • Long, repeating C-H chains

    • Not made of repeating units → not technically polymers

• Function

  • Long-term energy storage

  • Insulation/cushioning

  • Membranes

• Types (Family Groups)

  • Fats

    • Saturated vs Unsaturated

    • Used for insulating/lining organs

  • Phospholipids

    • Phosphate head + fatty acid tails (Hydrophilic head, hydrophobic tails)

    • Used in cell membranes to regulate entry/exit in cell

    • Cell membrane

      • Fluid Mosaic Model: Representation of phospholipid bilayer with embedded proteins/sugars/etc

      • Components

        • Phospholipids

        • Cholesterol

          • Make membrane fluid/flexible

          • ↑ temp want ↑ cholesterol to be more fluid (allow motion)

          • ↓ temp want ↓ cholesterol for tighter packing of lipids

        • Proteins

          • Integral - all the way embedded

          • Peripheral - halfway embedded

        • Cytoskeleton/Exoskeleton

  • Steroids

    • Modified cholesterol molecules used for

Proteins

• Composition

  • Amino acid chains

    • Made of amino group, carboxyl group, R-group, H attached around a C

  • Polymer = polypeptide

• Structure

  • Primary - Chains of amino acids ordering themselves

  • Secondary - H-Bonds to form rough shape

  • Tertiary - 3D shape

  • Quaternary

• Function

  • Everything - used to lower activation energy, transport, structure, communication, antibodies

• Types

  • Enzymes (Proteins/RNA)

    • Biological catalysts that don’t - used to lower activation entry

    • Control starting/stopping reaction

    • Active vs Allosteric site

    • Reaction specific

      • Form determines function - can’t be used in different types of reactions

    • Affected by cellular environment

      • Anything that could denature a protein can screw up an enzyme

    • Eg. Pepsin - enzyme to break down

Nucleic Acids

• Function

  • Information storage - Central dogma theory (DNA → RNA → Protein)

• Composition

  • Made of nucleic acids (monomer) to form nucleic polymers

  • Nucleotide bases

    • Purines - 2 nitrogen-rings (A, G)

    • Pyrimidines - 1 nitrogen-ring (T or U, C)

Enzymes

• Models

  • Lock and Key - enzymes have specific shapes (lock) that only bind with substrates of a specific shape (key)

  • Inducted Fit - 3D structure of enzyme fits substrates that cause enzymes change shape

• Factors affecting function

  • Enzyme concentration

    • ↑ enzymes = ↑ reaction rate b/c ↑ enzymes = ↑ collision rate

    • Graph makes side-ways parabolic shape

  • Substrate concentration

    • ↑ substrate = ↑ reaction rate b/c ↑ collisions

      • Grows then levels off b/c too much substrate for enzymes

  • Temperature

    • ↑ temperature = ↑ reaction rate (to a degree before enzyme starts denaturing)

    • Bell-curve shape

  • pH

    • Bell-curve graph

  • Salinity

    • Enzymes intolerant of extreme salinity

      • Disruption of bonds = change in shape

    • Bell-curve graph

  • Activators

    • Cofactors

      • Non-protein, small inorganic compounds/ions that bind within enzyme molecule

      • Eg iron in blood

    • Coenzymes

      • Non-protein organic molecules

        • Temporarily or permanently bind to enzyme near active site

      • Eg. vitamins

  • Inhibitors

    • Molecules that decrease enzyme activity

    • Competitive

      • Substrate + inhibitor compete for active site

        • Eg. penicillin

      • Overcome by increasing substrate concentration

    • Non-competitive

      • Inhibitor binds to site other than active (eg allosteric)

      • Change shape to active site → substrate + enzyme can’t bind anymore

    • Irreversible

      • Permanent binds to enzymes

        • Competitor or allosteric (changes to active or allosteric site)

          • Allosteric Regulation

            • Conformational changes by regulator molecules (inhibitors/activators)

    • Feedback

      • Excess production of something shuts down the reaction

        • Negative feedback loop = off switch for

        • No build up

Cell Membrane

• Regulation of what enters/exits cell

  • Can pass: small, hydrophobic, non-polar molecules b/c can squeeze between polar molecules

    • Eg. O2

  • Can’t pass: large, hydrophilic, polar molecules, ions

    • If VERY small, can pass through very slowly

• Passive Transport

  • Diffusion due to random motion

  • Tonicity - based on water potential

    • Measure of free energy, if isotonic WP = 0

  • Facilitated Diffusion - diffusion with transport proteins

    • Channel

    • Carrier protein - change shape to move things through

    • Aquaporins - water pores

• Active Transport

  • Ability to move against concentration gradient - requires ATP

    • ATP can change shape of carrier (lose a phosphate to phosphorylase)

      • ATP synthase - enzyme that makes ATP

• Cotransport

  • Using the concentration of something to move another (circuit)

• Bulk Transport

  • Endocytosis

    • Vesicles being made from the cell membrane to release things inside the cell

  • Exocytosis

    • Vesicles joining with the cell membrane to release contents outside the cell

      • Add to cell membrane size (adding membrane)

  • Receptor-Mediated Endocytosis

    • Signals to take things into cells when something needed is sensed