biology

Structural lipids (fat molecule)

2 fatty acids

glycerol

phosphoglycerate (third carbon of the glycerol backbone is occupied by a polar phosphate group)

PHOSPHOLIPIDS (a major component of the cell membrane
creates a bilayer when immersed in water with hydrophilic (due to phosphate group) heads on the outside and hydrophobic tails on the inside.)

Subtopic

Phospholipids with unsaturated fatty acid tails- lipids not tightly packed together, can move in membrane

phospholipids with saturated fatty acids- tightly packed together

Low temp prevents packing btwn phospholipids

Proteins move slowly through membrane

Membrane proteins classified based on location

Membrane protein functions: transport, enzymatic activity, signal transduction, cell cell recognition, intercellular joining, attachment to ECM

Facilitated Diffusion- hydrophilic substances need help of proteins to cross membrane

Subtopic

Presence of cholesterol in membranes also has an effect on fluidity

It regulates movement of phospholipids in membrane

Plasma membranes are selectively permeable

Hydrophobic molecules dissolve in lipid bilayer of membrane easily, while hydrophilic molecules do not cross membrane easily

Transport proteins help hydrophilic molecules cross membrane

Passive transport- movement across membrane without any energy required, down concentration gradient

Diffusion- tendency for molecules of any substance to spread out evenly into the available space

Osmosis- diffusion of free water across a selectively permeable membrane

Membranes

Phospholipids move laterally in the membrane

Phospholipids with unsaturated fatty acid tails- lipids not tightly packed together, can move in membrane

phospholipids with saturated fatty acids- tightly packed together

Temperature affects membrane fluidity

Fluidity of membrane has an affect on its function

Low temp prevents packing btwn phospholipids

They are in a liquid crystalline phase

Proteins move slowly through membrane

Membrane proteins classified based on location

Membrane protein functions: transport, enzymatic activity, signal transduction, cell cell recognition, intercellular joining, attachment to ECM

Facilitated Diffusion- hydrophilic substances need help of proteins to cross membrane

movement of molecules from high to low concentration

Channel proteins- provide channels that allow specific molecule/ion to cross membrane.

Carrier proteins- undergo change in shape that translocates solute-binding site across the membrane

Presence of cholesterol in membranes also has an effect on fluidity

It regulates movement of phospholipids in membrane

Plasma membranes are selectively permeable

Hydrophobic molecules dissolve in lipid bilayer of membrane easily, while hydrophilic molecules do not cross membrane easily

Transport proteins help hydrophilic molecules cross membrane

Passive transport- movement across membrane without any energy required, down concentration gradient

Diffusion- tendency for molecules of any substance to spread out evenly into the available space

Osmosis- diffusion of free water across a selectively permeable membrane

Active transport- movement against concentration gradient

Uses energy

Low to high

Nutritional lipids (fat molecule)

3 fatty acids (triglycerol)

Unsaturated Fats - Non-saturated with hydrogens at every C, double bonds are present and liquid at room temp. usually derived from plant sources.

ISOMERS

CIS

The presence of double bonds cause a slight kink/
bend, explains why unsaturated fats are liquid at room temp. (cant be tightly packed because of these kinks/bends)

Hydrogenation - Hydrogenating Unsaturated fats with Saturated fats increase shelf life and creates a pleasing texture, but can create unhealthy trans fats in the process.

TRANS

Molecules with trans fatty acids are considered trans fats.
(extremely unhealthy as we can not break down trans fat)

Saturated Fats - Saturated with hydrogens for every C, commonly found in animal sources and are solids at room temp. No double bonds, associated with increase in cardiovascular disease.

glycerol (the backbone where each C
is attached to a fatty acid

bonded with fats through dehydration/
condensation synthesis

Catabolic Pathways (Pathways that release energy by breaking down complex molecules into simpler compounds)

Steroids (another type of lipid)

Created with four fused rings
(considered lipid because insoluble
in water and hydrophobic)

steroids have an –OH functional group attached

polysaccharides

Made of repeating glucose molecules

Long chains with helical shape

When 100+ monosaccharides are
bonded through glycosidic linkages,
polysaccharides are formed

Functions of polysaccharides: storage & structure

Storage:
Glycogen, Starch, Dextran

Structure:
Chitin & Cellulose

monosaccharides

Aldoses: Have CO group at the end of the chain

Ketoses: Have CO group
in the middle of the group

Trioses: 3-Carbon Sugars

Pentoses: 5-carbon sugars

Hexoses: 6-Carbon sugars

Joined by dehydration reaction

Functions

Energy generation - ENERGY

Glycolysis

Occurs in cytosol

Prokaryotes

Eukaryotes

Inhibited by ATP

Anaerobic

Aerobic

Krebs Cycle

calvin cycle

Anabolic Pathways (Pathways that consume energy to build larger, complicated molecules from simpler ones)

Kinetic (If energy is associated with the relative movement of objects it is called kinetic energy.)

Potential (An object that is not moving can also have energy – potential)

LAW OF THERMODYNAMICS - First law: Energy can be transferred and transformed, but it cannot be created or destroyed!
Second law: Every energy transfer or transformation increases the entropy of the universe!

Gibbs Free Energy - Energy in cells that is used for a cell to function.

Free-energy Change
Delta (g) - difference
between the free
energy of the final state
and the free energy
of the initial state

ATP acts as coupler to couple reactions

Endergonic - overall Delta
G is positive, absorb energy
(non spontaneous)

Exergonic - overall
Delta G is negative,
release in
energy (spontaneous)

Enzymes (can speed
up exergonic reactions)

Catalytic Cycle

1.) Substrates enter the
active site
2.) Substrates are held
in the active site by
weak interactions
3.) The active
site lowers
EA and
speeds up
the reaction
4.) Substrates are
converted to
products
5.) Products are released
6.) Active
site is
available for
two new
substrate
molecules

Ph and Temp

How efficiently an
enzyme functions is
affected by
environmental conditions

Enzyme regulation

Inhibition

Competitive

A competitive inhibitor
mimics the substrate, competing
for the active site.

Non-competitive

noncompetitive inhibitor
binds to the enzyme away
from the active site,
altering the shape of
the enzyme so substrate
can no longer bind
stopping the pathway

Feedback inhibition

end product of a
metabolic
pathway shuts
down pathway

Allosteric regulation

Cooperativity - binding of one
substrate molecule to the
active site of one subunit
locks all other subunits
into the active shape

ATP

Transport Work

Mechanical Work

ATP cycle

ATP synthesis
from ADP + P
requires energy.

ATP hydrolysis
to ADP + P
yields energy.

disaccharides

Dehydration reactions that join monosaccharides form disaccharides

INTERMOLECULAR

INTRAMOLECULAR

DNA carries genes

Used to form mRNA by transcription

mRNA used to form proteins through translation

Amount of Purines (A+G) is equal to amount of pyrimidines (T+C)

Double stranded

Complementary base pairing

Sugar phosphate backbone and nitrogenous bases

Nitrogenous base pairs held by hydrogen bonds

Phosphodiester bond connects each nucleotide

SSB keeps DNA single stranded

RNA

ribose sugar

mathwa

DNA

double stranded

hydrogen bond holds base pairs together

complimentary base pairing

(A-T) (C-G)

nucleotides (monomers)

phosphate group

phosphodiester linkage

condensation reaction

bonds in-between two pentose sugars at (3,5)

pentose sugar

beta

nitrogenous base

AGCT

purine

(A or G)

glycosidic linkage from base to carbon (n-9,c-1)

pyrimidine

(c or G) (uracil in rna)

glycosidic linkage from base to carbon (n-1,c-1)

nucleoside

glycosidic linkage

nitrogenous base

pentose sugar

provides directions for its own replication

directs synthesis of mRNA, controls protein synthesis, a process called gene expression.

amino acids

primary structure

main chain

amino group

carbonyl group

peptide bonds

secondary structure

main chain

beta pleated sheets

alpha helices

tertiary structure

interactions of R groups

quaternary structure

DNA carries genes

Used to form mRNA by transcription

mRNA used to form proteins through translation

Amount of Purines (A+G) is equal to amount of pyrimidines (T+C)

Double stranded

Complementary base pairing

Sugar phosphate backbone and nitrogenous bases

Nitrogenous base pairs held by hydrogen bonds

Phosphodiester bond connects each nucleotide

SSB keeps DNA single stranded

Additional info

R group

main chain

hydrophobic interactions

ionic bonds

hydrogen bonds

Van der Waals interactions

covalent bonds

polypeptide

RNA polymerase (RNAP)

70 s ribosome

f MET first starting amino acid

Nucleotides in DNA to the right are labeled by positive numbers and this area of the DNA is referred to as downstream. To the left of the transcription start site nucleotides are numbered by negative numbers and this is called as the upstream

INITIATION

RNA polymerases bind to a region on the DNA upstream of the start site. This region is called the promoter. one direction only 5’ to 3’. The enzyme binds the promoter and picks one of the two strands as the template to use to form mRNA. It reads the template in 3’ to 5’ direction and forms mRNA in 5’ to 3’ direction.

ELONGATION

new nucleotides being added to the 3’ end of the new strand. The original strand is called as the template strand.

TRANSLATION

First, a correct match between a t R N A and an amino acid, done by the enzyme aminoacyl-t R N A synthetase, Second, a correct match between the t R N A anticodon and an mRNA codon. Flexible pairing at the third base of a codon is called wobble and allows some tRNA’s to bind to more than one codon

. The RNA is called ribosomal RNA (or rRNA). Each ribosome is made of two parts or subunits – large and small. These are typically separated, but come together when translating an mRNA.

E SITE

the exit site, where discharged tRNA’s leave the ribosome

P SITE

holds the tRNA that carries the growing polypeptide chain

translation brings together mRNA, tRNA bearing the first amino acid of the polypeptide, and two subunits of a ribosome

The mRNA is read in 5’ to 3’ direction
while the amino acids are added from
N to C direction

A SITE

site holds the tRNA that carries the next amino acid to be added to the chain

TERMINATION

Once a stop codon is reached in the A site there is no tRNA that corresponds to a stop codon. Instead a Release factor sits in the A site, dissociating the complex stopping translation. This is a GTP driven process.

RNA polymerase II – pre mRNA,
snRNA, microRNA

dn

signal for the cell to make a cut in the
newly formed pre mRNA and release
it from DNA. At the 5’ end a modified
G nucleotide is added, this is called
CAP and at the 3’ end near the AAUAAA
sequence a polyA tail is added by the
enzyme polyA polymerase. The 5’cap
will be used for translation and the
3’polyA tail helps with stability of the mRNA.

RNA SPLICING

Before the pre mRNA exits the nucleus
to be translated it has to go through
RNA processing. This process involves
removal of introns and joining togethe
r of exons. ONLY IN EUKARYOTES

ALTERNATE SPLICING
to form different mRNAs and hence different proteins.

80 S ribosome

MET first starting amino acid

DNA carries genes

Used to form mRNA by transcription

mRNA used to form proteins through translation

Amount of Purines (A+G) is equal to amount of pyrimidines (T+C)

Double stranded

Complementary base pairing

Sugar phosphate backbone and nitrogenous bases

Nitrogenous base pairs held by hydrogen bonds

Phosphodiester bond connects each nucleotide

SSB keeps DNA single stranded

linker DNA

histones

H1

H2A
H2B
H3
H4

transcription factors

general

background/basal
expression

specific

activators

INCREASE levels of
transcription

repressors

REDUCE levels of
transcription

control elements

proximal

distal

operons

operators

positive regulation

activator present

transcription occurs

activator NOT present

transcription does
NOT occur

negative regulation

repressor present

transcription does
NOT occur

repressor NOT present

transcription occurs

intracellular receptor

membrane receptor

G Protein Coupled Receptor

signal molecule

GPCR

G protein

GDP

GTP

activated G protein

enzyme

cellular response

GTP

G protein

GDP

Tyrosine Kinase Receptor

signal molecule

receptor tyrosine
kinase receptor

dimer

activated tyrosine
kinase regions

ATP

ADP

fully activated
tyrosine kinase
receptor

inactive relay proteins

phosphate groups

activated relay proteins

cellular response

Ion Channel Receptor

ligand-gated ion
channel receptor

signal molecule

channel opens

specific ions to
flow through

cellular response

signal molecule

channel closes

paracrine signaling

signal binds to receptors

stimulate adjacent cells

synaptic signaling

occurs between cells
with synapses

cell releasing signal is close to target cell

reception

signal molecule binds to receptor

transduction

relay molecules

response