unit 1

energy, macromolecules etc

1st law of thermodynamics

energy is not created or destroyed

2nd law of thermodynamics

entropy increases (disorder increases)

entropy

disorder

metabolic reactions

energy changes. the breaking of bonds to form new bonds. impacted by the amount of entropy

enthalpy

difference in bond energy

potential energy

chemical bonds

energy that’s stored

kinetic energy

muscle contraction

energy is moving

endothermic reactions

take in energy to break bonds

exothermic reactions

releases energy to join bonds

exergonic reaction

negative

the release of energy/increase of entropy

(graph starts positive, goes up and decreases in the end. -change in G)

hydrolysis

Endergonic reaction

positive

builds energy

reduces disorder/creates organization

(starts out negative, goes up and neutralizes. +change in G)

condensation

Hydrolysis reaction

exergonic reaction / releases energy. weak bonds.

(energy required)

condensation reaction

builds energy. strong bonds

endergonic

Anabolic reaction

reduces entropy

increases energy

catabolic

increases entropy

decreases energy

relation of stronger bonds to energy

more energy

relation of weaker bonds to energy

less energy

Change in G

combined enthalpy and entropy

traits of nucleic acids

information storage

genetic code expression

The building blocks of a Nucleoside

sugar base +ribose or deoxyribose

the building blocks of nucleotide

sugar base, phosphate + ribose or deoxyribose

whats the difference between a ribose and a deoxyribose

Ribose has OH deoxyribose has H attatched to the base sugar

what does tp in eg: atp, gtp stand for?

Triphosphate

what are base sugar pairs bonded by

hydrogen bonds

(2 little lines)

RNA

copying the dna and then transcribing

single stranded

hydrogen bonds form the 3d structures

central dogma

describes how rna and dna flow ???????????

in what direction do you synthesize

5’ → 3’. but you read it in the perspective of the strand (3’ → 5’)

what are the bonds in RNA folds

hydrogen bonds

what are the bonds inside a polymer peptide chain

covalent bond

what are the base letters for DNA

AT GC

base letters for RNA

AU GC

secondary structure

bending to form hydrogen bonds (backbone)

alpha helix/beta sheets

a → spiral

b →pleated

tertiary

r-groups

interacts to form final version

diverse bonds because of different amino acids'

3d shape of polypeptide

quaternary

more than 1 polypeptide. group of different subunits of tertiary

disulfide bridges

cysteine /side chains

exergonic

-G, energy released, entropy increased, more stable

endergonic

+G, gain energy, entropy decreased, unstable

enzymes

lowering activation energy

usually highly specific/catalyzing 1 reaction

reactants

substrates → bind to a specific site on the enzyme

active site

specific site on the enzyme that reactants(substrates) bind to

enzymes lowering activation energy

including physical strain

substrate orientation

adding chemical groups

physical strain on substrate

pressure on substrate to get it into the unstable transition state

substrate orientation

substrates are brought together into the site for the reaction to form

adding chemical groups

r groups are involved in the reaction

changes in protein structure

ligand binding

r grouo moditifcation\

addition of cofactor

proteolysis

ligand binding

r group moditifcation

addition of cofactor

proteolysis

ways to control enzyme activity

regulate the amount → turn synthesis on or off

irreversible inhibition

the inhibiter covalently binds to the side chain of the active site.

permanent inactivation of the enzyme

competitive inhibitor

competes for the natural substrate for the active site

noncompetitive

enzyme binds at a different site than the active site. it changes the enzymes shape and function

allosteric regulation

allosteric regulation

can activate/inactivate enzymes

non competitive active site

not just inhibiting

feedback inhibition

regulation with metabolic pathway

when you hit the cap of the final product it goes back to turn off the beginning of the pathway.

inhibition from the result of the final product

smaller cells

higher surface area to volume

membrane fluidity in colder temps

decreases fluidity

head

hydrophillic

tails

hydrophobic

proteins affiliated or embedded in the membrane

peripheral membrane protein

integral membrane protein

transmembrane proteins

peripheral membrane protein

on the side

integral membrane protein

slightly embedded

transmembrane protein

through the bilayer

glycolipid glycoprotein

passive transport

doesnt need metabolic energy

-simple diffusion

-facillitated diffusion (channel /carrier proteins)

active transport

needs metabolic energy

energy input to go against the concentration grain

facilitated diffusion

moving cross the membrane using a channel or carrier proteins

diffusion

moving the molecules cross the membrane to get to an equilibrium

direction of diffusion

high concentration to lower concentration

the movement of solute

trying to get to equilibrium

simple diffusion

typically small nonpolar/noncharged molecules that move freely across the membrane by itself.

eg: gasses

osmosis

instead of diffusion of solutes, its diffusion of water across membranes.

passes through aquaporins (membrane channel)

water moves toward higher concentration of solute.

isotonic solution

equal solute concentration to cell

(the basic ratio)

equilibrium. same solute inside and out

hypertonic

less solute inside. more outside

water is attracted outside of the cell because of more solute outside

water leaving

hypotonic

more inside, less outside.

water attracted to inside, more solute inside.

examples of diffusion/osmosis

plants using osmosis to move water by moving solutes around to drive the waters where it needs to go.

active transport

you cant do active transport with a channel protein.

only does facilitated diffusion.

channel protein is just an opening in and out, doesn’t control direction.

channel protein

only for facilitated diffusion

ion channels

ligand-gated channel (regulated by stimulus)

voltage gated channel (electrical signal propagation)

primary active transport

use of atp directly

secondary active transport

2 things moving, 1 along the concentration gradient and the other is against

prokaryotes

without membrane enclosed compartments(organelles)eg: nucleus

dna in nucleoid

cytoplasm= cytosol+ribosomes

eukaryotes

has membrane enclosed compartments(organelles) eg: nucleus

complexity in structure

animal vs plant cells

plant cells-plant wall(made of cellulose), vacuoles(more prominent), chloroplast, plasmodesmata

nucleus

eukaryotic, largest organelle often, internal structure

endomembrane system

includes the nuclear envelope, er, golgi apparatus, lysosome

the membranes are connected and moving things through vesicles

rough er (rer)

ribosomes attached

transporting proteins

lots of surface area

protein synthesis

smooth er (ser)

tubular with no ribosomes

synthesis of lipids and steroids

glycogen degradation in animal cells

golgi apparatus

protein modification sorting and getting things into final forms so it can go where it needs to go

lysosomes

can originate from golgi,

digesting/breaking stuff down

mitochondria / chloroplast

chemical energy into atp

double membrane

energy transformation

divides autonomously