VM 602 Physiology

why do we need proteins?

provide structural support

function as enzymes

involved in signaling

proteins are made up of

amino acids

amino acids are linked together by _______ _________ bonds

covalent peptide

multiple peptides link together to form

polypeptide backbone

4 levels of structure of protein

primary, secondary, tertiary, quaternary

proteins are made up of amino acids written from N- to C- terminus

primary structure

a regular, repeating conformation in a protein

-includes a-helices, B-sheets

secondary structure

secondary structures found in proteins are a-helices and B-sheets. both have regular repeating patterns that maximize:

hydrogen bonding

adjacent chains in B-sheets are

anti-parallel

the overall 3D arrangement of amino acid residues

-3D folding of a single polypeptide chain

tertiary structure

tertiary structure bonds

H bonds

disulfide bonds

ionic bonds

van der Waals interactions

hydrophobic interactions

for multi-subunit complexes, this is the 3D arrangement of the subunits (multiple polypeptide chains with multiple subunits)

quaternary structure

ex of protein with quaternary structure

hemoglobin

based on the structural organization, what are the two main forms of protein?

globular proteins

fibrous proteins

globular proteins function as

catalysts, transporters, signal transducers (functional proteins)

globular proteins, soluble or insoluble in water?

relatively soluble

role of fibrous proteins

structural rather than dynamic role

ex of fibrous proteins

collagen and keratin

fibrous proteins, solubility in water?

low solubility

properties of collagen

-provides tensile strength

-major component of connective tissues

-distinct amino acid composition: glycine, proline, 4-hydroxyproline, 3-hydroxyproline

hydroxy acids enhance

hydrogen bonding

vitamin C deficiency leads to

scurvy

why does deficiency of vitamin C cause scurvy

-vitamin c is needed by an enzyme that converts proline to hydroxyproline

-hydroxyproline needed to form collagen

-collagen provides structural support

if Keq > 1 and delta G < 0

reaction is favorable

if Keq is < 1 and delta G is > 0

reaction is unfavorable

Keq =

[B] k1

---- = -----

[A] k-1

where B is product, A is substrate, k1 and k-1 are rate constants for forward and reverse reactions

chemical reactions have an energy barrier separating the reactants and products called the

transition state

enzymes ___________ the activation energy

reduce

enzymes _________ rate of reaction

increase

enzymes do/do not change overall delta G of a reaction

DO NOT

2 models of enzyme function

lock and key

induced fit model

lock and key model for substrate bonding

enzymes are able to select just ONE SUBSTRATE

induced fit model of substrate binding

substrate binding can change the active site structure of the enzyme leading to conformational change

-flexible active site

factors influencing rates of enzyme reactions

temperature

(higher=accelerates, too high will denature)

pH (can influence reaction rate, pH optimum of most enzymes)

helps in taking partially folded protein intermediates and folding them

chaperone

what is common amongst prion diseases

misfolded protein

prions are thought to propagate by transmitting a

misfolded protein

why do we need to study enzyme kinetics and inhibition?

drugs

drug therapies are based on ___________ enzymes

inhibiting

Km

Michaelis constant

Vmax

maximum rate

Km

affinity of enzyme for substrate

kcat

turnover number

_________ Km implies a lot of substrate must be present to saturate the enzyme, meaning the enzyme has _______ affinity for the substrate

high, low

_______ Km means only a small amount of substrate is needed to saturate the enzyme, indicating a ________ affinity for substrate

low, high

enzyme inhibition types

reversible inhibitor

irreversible inhibitor

allosteric inhibitor

types of reversible inhibition

competitive

noncompetitive

uncompetitive

competitive reversible inhibitor

-inhibitor binds reversibly in the active site

-inhibitor & substrate compete for access to enzyme

-Vmax unchanged

-Km increased

-affinity decreased

example of competitive reversible inhibitor

statins

noncompetitive reversible inhibitors

-bind to a site on the enzyme distinct from the active site

-inhibitors bind to both enzyme and enzyme substrate

-Vmax decreased

-Km unchanged

uncompetitive reversible inhibitors

-binds to enzyme-substrate complex only

-both Vmax and Km decreased

irreversible inhibitors

-suicide inhibitors

-covalently modify the enzyme, destroying its activity permanently

example of irreversible inhibitor

aspirin

allosteric inhibitor

-remote control

-inhibitor binds to different site than active site and control the active site (inhibitor binds and changes active site- less active)

allosteric activation

-makes it faster

-produces more products

allosteric inhibition show ___________ curve

sigmoid

maturity onset diabetes of the young (MODY) can be caused by mutations that either

1. increase the Km (poor affinity for ligand)

2. decrease the Vmax (poor rate of conversion)

3. affect both Km and Vmax of glucokinase

-therefore the mutation of the enzymes cause their Km and Vmax to change, affecting glucose transport

3 stages of signal transduction

1. Reception

2. Transduction

3. Response

reception of extracellular signal by cell

needs receptor, binds to ligand

transduction

transduction of signal from outside of cell to inside of cell, often multi-stepped

cellular response

occurs entirely in receiving cell

cells that produce the signaling molecule referred to as

signaling cells

cells that receive the signal are

target cells

4 types of intercellular signaling

1. Contact-dependent

2. Paracrine

3. Synaptic

4. Endocrine

contact-dependent intercellullar signaling

very close to each other

paracrine intercellular signaling

one cell makes molecules

synaptic intercellular signaling

synapses released

endocrine intercellular signaling

stable molecules released into bloodstream via endocrine cells

-largest class of signaling proteins involved in many biological process and pathologies

- about 50% of all modern drugs target them

G-protein coupled receptors (GPCRs)

signal transduction by GPCRs

1. receptor binds to G proteins (a, B, Y) that contain GDP bound to a

2. G protein exchanges GTP for GDP and dissociates (GTP and GDP separate)

3. GPCR-G protein complex disassembles, releasing the G protein a-subunit from BY complex

4. Ga-subunit binds to target enzyme (adenylyl cyclase), enhancing its activity

5. GTP hydrolyzed to GDP causing dissociation of a-subunit from target enzyme

6. a reassoociates with B Y - subunits and GPCR

-the blueprint of life

-contains instructions for making proteins within the cell

DNA

DNA is a polymer which is made up of

nucleotides

3 parts of nucleotide

nitrogen base

-purines, pyrimidines

pentose sugar

-ribose in RNA

-deoxyribose in DNA

phosphate (PO4) group

nitrogen base with double ring

purines

-adenine (A)

-guanine (G)

nitrogen base with single ring base

pyrimidines

-cytosine (C)

-thymine (T)

-uracil (U)

bond between nucleotides

hydrogen bond

purine::pyrimidine

Chargraff's Rule: Adenine always joins with

Thymine

amount of H bonds between adenine and thymine

2

Chargraff's Rule: cytosine always bonds with

guanine

number of H bonds between cytosine and guanine

3

-stronger than adenine and thymine

one strand of DNA goes from 5' to 3' (sugars), the other strand is in what direction?

opposite

-antiparallel

central dogma of molecular biology

DNA -> RNA -> Protein

why do we need DNA replication?

cell reproduction

-mitosis

gamete production

-meiosis

DNA replication takes place in the _______ phase

S

S phase during _________ of the cell cycle

interphase

DNA has to be _________ before a cell divides

copied

new cells will need __________ DNA strands

identical

DNA replication begins at

origin(s) of replication

-in eukaryotes, hundreds/thousands of origin sites

each DNA strand can serve as a _____________ for a new strand

template

splitting of DNA during copying

replication forks

DNA strands are unwound by

DNA helicase

what prevent immediate reformation of the double helix?

single stranded binding proteins (SSB)

what "unties" the knots that form?

-attaches to the 2 forks of the bubble to relieve stress on DNA molecule as it separates

topoisomerase

synthesis RNA primer from a single template strand

-DNA polymerase can begin its chain after a few RNA nucleotides have been added

RNA Primase

___________________ add nucleotides to the end of an existing chain

-it cannot initiate synthesis

-requires a "primer" synthesized by primase

-can add only to 3' end

DNA polymerase

new DNA strand can only elongate in what direction?

5' to 3'

______________ is synthesized as a single strand from the point of origin toward the opening replication fork

leading strand

the _________________ is synthesized discontinuously against the overall direction of replication

-this strand is made of many short segments

-replicated from replication fork toward the origin

lagging strand

series of short segments on the lagging strand

-must be joined together by an enzyme

Okazaki Fragments

enzyme ___________ joins the Okazaki fragments together to make one strand

ligase