BIO 002 - Midterm 1

Amide

Draw, p/d state if it has, state properties

polar

Carboxylic Acid

Draw, p/d state if it has, state properties

can be protonated or deprotonated

acidic

Amine

Draw, p/d state if it has, state properties

can be protonated or deprotonated

basic

Phosphate

Draw, p/d state if it has, state properties

can be protonated/deprotonated

polar

methyl

Draw, p/d state if it has, state properties

nonpolar

thiol

Draw, p/d state if it has, state properties

polar

thioester

Draw, p/d state if it has, state properties

polar

hydroxyl

Draw, p/d state if it has, state properties

polar

draw an amino acid

circle backbone

What is pH?

numerical measurement of hydrogen ions concentration within a solution on a negative logarithm

Hydrolysis

Water added to polypeptide chain, breaks the peptide bond

Define primary structure

• draw

linked by peptide bonds( or amides), basic linear arrangement, is non functional

define secondary structure

• draw

held together by hydrogen bonds b/w backbone atoms, folds into alpha helixes or beta pleated sheets

define tertiary structure

• draw

the 3D shape of a protein held together by many electrostatic interactions b/w the R-groups of an AA. is a functional protein

define quaternary structure

• draw

multiple different protein subunits held together by the same interactions as tertiary structures, but interactions happen b/w the R-groups of the tertiary structure subunit proteins

enzyme

catalyzes rxns by binding reactants and lowering the activation energy of the rxn

allosteric enzymes

enzymes that can be up/down regulated, have an allosteric site

allosteric site

place where an allosteric molecule (activator/inhibitor) binds and changes the shape of the enzyme’s active site

What are the EN and EP elements?

How do we find the nonpolar covalent bonds or polar covalent bonds?

EN → higher EN #

• O, N, S

EP → lower EN #

• C, H, P

Nonpolar covalent bond: EN-EN or EP-EP

Polar covalent bond: EN and EP

How to find carbohydrates

• have C, H, O (fixed ration 1:2:1)

• have OH groups

• can be ring or linear

Monosaccarides

simple sugars

• 3-7 bonds

• very soluble

Disaccharides

two monosaccharides combined via a dehydration/condensation reaction

• forms glycosidic bonds/linkages

• broken via hydrolysis

how to find nucleic acids

• has a nitrogenous base (ring like structure with nitrogen), a pentose sugar and a phosphate group

How to find lipids

• contain many C-H bonds, no fixed ratio

• more carbons than oxygen

• has long chains of C-H bond

How to find proteins

• Have C, H, N, O

• have animo and carboxylic groups

• can be protonated/deprotonated

• have N-C-C backbone (or C-C-N)

N-terminus

• Start of polypeptide

• the free amino group (NH₂/NH₃)

C-Terminus

• End of polypeptide

• free carboxyl group (-COOH)

condensation reaction

• draw it

water removed from two amino acids coming together, forming a peptide bond (and new amide functional group)

hydrolysis

• draw it

water added to polypeptide chain, breaks the peptide bond

hydrophobic

water fearing

• nonpolar compounds

hydrophillic

water loving

• polar/charged compounds

phospolipids

polar “head” and nonpolar “tail”

saturated

• carbons are “saturated” with hydrogens

unsaturated

the carbons are lacking hydrogens

• lead to kinks in the tail

For redox rxns, when the one of the products gain e- → the number goes…?

when one of the products loses e- → the number goes…?

when the one of the products gain e- → the number goes down (reduction)

when one of the products loses e- → the number goes up (oxidation)

what are the functions of the Cytoskeleton?

• maintain and control cell shape

• control internal organization of the cell

• forced generation - transport of cargo, movement of cell, cytokinesis

Microfilament

made of actin monomers

• has motor proteins called myosin (travels - to + end)

Microtubules

made of alpha and beta tubulin

• has motor proteins called kinesin and dyneins

  • kinesin go - to + (kick out)

  • dynein go + to - (dine in)

intermediate filaments

made of keratin

plasma membrane

• defines the inside/outside of the cell

• offers protection

• allows cells to recieve/transmit signals to other cells

• increases SA by fold/encloses spaces to carry out biochemical equations

both plant and animals have this

nucleus

• contain and protect DNA

• site of DNA transcription and mRNA processing

• has pores in the nuclear envelope (semi permeability)

both animal and plant cells have this

ribosomes

• reading RNA transcripts (mRNA) and translating it to an amino acid sequence to make functional proteins

Mitochondria

• cell respiration ( food → usable E for the cell

• produces majority of the ATP for the cell

Chloroplasts

produces glucose

Peroxisomes

• carry out redox rxns (break down amino acids, fatty acids)

• detoxify the cell

Lysosome

• break down proteins, sugars, lipids, nucleic acids

vesicles

• storage and transport

• can fuse with plasma mebrane

vacuole

• break down some macromolecules

• provides structure/ ridigity to cell

endomembran system

• contains

  • RER

  • SER

  • vesicles

  • lysosomes

  • golgi apparatus

• function

  • packaging and transporting

what is the ideal molecules?

what is class 1 molecules

class 2? class 3?

ideal: small and nonpolar

class one: easily pass through

• small and nonpolar

• EX: diatomic gases

class two: can pass thru but not as easily

• small and polar

• large and nonpolar

• EX: cholesterol or H2O

class three: almost never passes

• large and polar

• charges ions

• EX:Na+ , K+, H+

draw passive transport

• diffusion

• facilitated diffusion

check it urself

draw active transport

• primary

• secondary

check ur self

delta G determines spontaneity,

what do they correlate with?

• spontaneous → negative delta G → exergonic → releases energy

• nonspontaneous → positive delta G → endergonic → absorbs energy