Palm 320 Exam 1



What are the four major classes of biomolecules

proteinsnucleic acidslipidscarbs

What is CHNOPS

the atoms that are present in biomolecules

what are the three atoms that are major elements of the human body


covalent bonds

shared electron pair btw two atoms

non-covalent bonds

Hydrogen bondsVan der waals Ionic Bonds

what are proteins made up of

20 amino acids

how do amino acids form polymers

they are linked by peptide bonds

amino acid polymers______

fold into precise secondary and tertiary structures to form a protein


adenine (a)cytosine (c)guanine (g)thymine (t)


nucleosides with phosphate group added

deoxyribonucleic acid (DNA)

-2x helix-linked by phosphodiester bond

ribonucleic acid (RNA)

-single stranded-transcribed from DNA-gets translated into protein

lipids function

lies with dual nature hydrophobic and hydrophilic parts

lipids are critical ___ and are a form___

in the formation of cell membranes-energy

carbs are____ and its most common form is

fuel sources for cellsglucose

glucose is stored as___ and it plays a role in____

as glycogencell- cell recognition and interaction

The Central Dogma


Prokaryotic cells

-no nucleus -genetic info is free floating in cytoplasm as single strand of dna

Eukaryotic cells

-membrane bound organells-lots of genetic Information in nucleus

Membranes are a ____

lipid bilayer

difference in Eukaryotic and prokaryotic membrane

eukaryotic cells contain membrane enclosed compartments

similarities in eukaryotic and prokaryotic membranes

both have plasma membrane

the plasma membrane

protects the cell from the outside environment

Where is the cytoplasm located?

in the plasma membrane

The plasma membrane is _____ to most substances, but it is____

impermeable selectively permeability

selective permeabiliity

allowed by membrane proteins that facilitate the entrance and exit of critical molecules for the cell

the cytoplasm is the

site of many biochemical processes such as glucose metabolism, fatty acid synthesis and protein synthesis

how is the cytoplasm organized

cellular cytoskeleton

biochemical reactions are____

sequestered into cellular compartments called organelles


-largest organelle-double membrane bound-where cells entire genome is found

The pores in the nucleus allows for what

protein transport in and out of the nucleus

The nucleus regulates genomic information by

expressing the information at the correct tome and in the correct amount


-powerhouse of the cell-contains two membranes

inter membrane space

the space between the mitochondrial two membranes

how much of the cells energy is produced in the mitochondria


what is the main source of energy produced in the mitochondria and how is it made

ATP and oxidative phosphorylation

Smooth ER

processes extracellular chemicals

Rough ER

appears rough due to the ribosomes attached


take the proteins that are synthesized in the er to the lumen where folding occurs

transport vessicles

allow for folded modified and finalized proteins to leave the lumen

ribosomes are responsible for

the translation of RNA to proteins

After the proteins leave the rough ER, they move to the_____ to be sorted

Golgi complex

proteins in the Golgi that have been tagged for secretion will be contained by

secretory vesicles

secretory vesicles Duse with the plasma membrane and the contents get released with the correct signals. this process is called ---



vesicles formed when cells take up material through endocytosis


when large amounts are taken up by the cell


organelles that contain a wide array of digestive enzymes

____ AND _____ fuse together in order to digest the engulfed material

lysosomes and endosomes

Lysosomes also digest

damaged intracellular organelles

Overview of cellular metabolism

-cell need energy-energy is the capacity to work-energy is stored in chemical bonds-energy is used to form chemical bonds and released when breaking them

Anabolic metabolism

the buildingrequires energy

catabolic metabolism

degrading of largersome energy release


the most abundant energy carrier molecule in the cells


the field of study that isolates and analyzes protein structure and full range of functions

What are the 4 different groups that are attached to the central carbon

hydrogen atombasic amino groupacidic carboxyl groupside chain

Because all amino acids contain one asymmetric carbo atom, there are ___ isomers formed called ___ and ___


all amino acids in proteins are in the ___ conformation


What decides amino acid properties

the side chain

hydrophilic (polar) side chains

exposed on the surface of the protein

hydrophobic (non polar) side chains

buried in the interior of the protein

Amino acids are____ meaning they have ___ and ___ groups

amphoteric basic acidic

At pH 7. the ______ is the dominant species


at acidic ph, amino acids are protonated forming the____. at basic ph, amino acids produce ____


the overall charge of a protein depends on ____

the contribution form basic (+) and acidic (-) amino acids

charge varies with

pH of solution the molecule is in

The Henderson-hasselbalch equation

describes the titration of an amino acid and can be used to predict the net charge and isoelectric point of protein


the dissociation constant of a weak acid

The Henderson hasselbalch equation can determine

the acid base equilibrium of systems

The Henderson hasselbalch equation is useful in demonstrating

the net charge of an amino will vary with the pKa of the functional groups and the ph of solution


the point when the acidic and basic forms are in equilibrium


solutions that minimize pH (change in H+)

buffers consist of

a weak acid or base and its counter ion

when does the maximal buffering capacity occurs

at the molecules pKa

why are amino acids and proteins are excellent buffers

-the amphoteric nature-the basic and acidic components have their own pKa

isoelectric point

the point between the separate pKa values of an amino acid in the solution

buffering capacity is the weakest at the

isoelectric point

Why do we care about pH??

drastic changes in pH can alter the form pf proteins and enzymes and prevent chemical reactions from taking place

what are the three buffer systems in body

bicarbonate bufferprotein buffer (hemoglobin)phosphate buffer

bicarbonate buffer

very important blood buffer

protein buffer systems

-donate or accept protons-powerful buffers

phosphate buffer systems

-weak acid-conjugate base pair-have pKa 7.2

the primary structure of proteins

the linear sequence of a proteins amino acids

Amino acids are linked

from N terminus (amino group) to C terminus (carboxyl group)


each amino acid in a peptide chain

the sequence of amino acids are always written

left to rightn to c terminus

What determines the structure and function of a protein

its amino acid sequence

----- plays a large role in protein folding.



a measure of randomness

the hydrophobic effect

an entropy driven association btw molecules

Entropy of water molecules_____ when around non polar molecules


When the entropy of water molecules decrease, it drives non polar molecules to one another causing entropy to ___


hydrophobic interactions

form spontaneously (no energy required) because they increase the entropy of water

Many____ bonds like ____ and ____ form in the folding process to stabilize the 3d structure

weakhydrogenvan der Waals

How is the secondary structure of proteins determined

by hydrogen bond interactions btw backbone carbonyl and amide groups

what are the three types of secondary structures

- alpha helices-beta sheetsreverse turns and loops

alpha helix

a rod like structure in which the polypeptide chain is tightly coiled and amino side chains extend outward

in the alpha helix, each amino acid is_____ to another amino acid that is ____ residues away

hydrogen bonded4

what direction does an alpha helix wind

right handed turns

B pleated sheets

when hydrogen bonds are formed laterally between peptide bonds, polypeptides align parallel or anti-parallel to one another

proteins have ____ shapes that require requires direction reversals in the polypeptide chain called___ and ___

globular reverse turns and loops

where are reverse loops and turns found within the protein and why

on the surface so that they interact with other proteins and the environment

loops are composed of amino acids with____ groups because they are exposed to an ____ environment


tertiary structure of proteins

determined by interactions btw side chain functional groups

what all is include in tertiary structure

disulfide bondshydrogen bindssalt bridgeshydrophobic interactions

what does the tertiary structure of a protein define

a fully folded and functional protein

tertiary and secondary structures of a protein can be unfolded/destroyed by ___

denaturants or chaotropic agents

globular proteins

have a compact 3d structure and are water soulableperform most of the chemical transactions in the cell

myoglobin is a globular protein with only ____ interior residues, which binds with ___ and ___

2 polarheme iron and oxygen

the outside of myoglobin consists of

polar and non polar residues that interact with water making it soluble

van der Waals interaction contribute to

the stability of tertiary structure of proteins

protein structure =



combos of secondary structures that exhibit similar functions

an example of a motif

helix- turn- helix which are found in many proteins that bind with DNA


two or more compact regions that many be connected by a flexible segment or polypeptide chain

different proteins can have domains in common even if

their overall tertiary structure are different

Quaternary structure of proteins

define the combo of two or more tertiary structures to form a multi-subunit protein

In quaternary structures, each subunit can

have the the identical function or a completely separate function


the simplest quaternary structure (two subunits)

what are are the four things that protein purification is based on?

size, charge, solubility, ligand binding

why do proteins require purification?

to determine its primary, secondary, and tertiary structure


the separation of the protein of interest form complex biological mixtures (cells, blood, tissue)

what must happen to cells to remove the protein?

they must. be broken open to release their content


a mixture of all components of the cell but not intact cells


The (usually) clear liquid left behind after a precipitate has been spun down to the bottom of a vessel by centrifugation

differential centrifugation

the multiple centrifugation steps that provide supernatants of varying densities

crude extract

supernatant used for extraction of the protein

Proteins can be precipitated by change the salt [x] of the solution. What happens when you increase and decrease the salt [x]?

increase= more soluble decrease= less soluble

Protein precipitation may also occur when ______

adjusting pH

How are small molecules (salt) that are used for precipitation removed from protein solutions?

dialysis and ultrafiltration

What is a dialysis membrane and how is it used?

a membrane that has a molecular weight cut off (MWCO) meaning that molecules that are at or smaller than that molecular weight can pass through the membrane, where as proteins will remain separated inside of the membrane


uses the same process but adds pressure to the technique to force a solution thru a membrane

How does cel filtration chromatography separate proteins

on the basis of size

Gel filtration utilizes ____ to separate proteins

column of highly. hydrated polymers

what is the principle of gel filtration

its is based upon the differential migration of dissolved solutes through gels that have pores of defined sizes

gel filtration is _____ for protein purification and desalting

frequently used

What happens with the protein during ion-exchange chromatography?

proteins will bind to ion exchange matrices based on the charge to charge interactions

Proteins can be separated during ion-exchange chromatography based upon

on the basis of their bet charge

If the immobilized phase is positively charged during ion exchange chromatography and if its negative?

positive= anion exchange columnnegative= cation exchange column


positively charged proteins can be removed from an ion exchange column by increasing the salt [x] of the buffer poured over the column

affinity chromatography

purifies proteins based on ligand interactions

What characteristic does affinity chromatography take advantage of when purifying proteins?

the fact that some proteins have a high affinity for specific chemical groups or molecules

High-pressure liquid chromatography (HPLC)

is an enchanted version of the column techniques for purifying proteins that have already been discussed

the resolving power of HLPC

is the ability of a column to separate individual proteins

____ must be applied to the column during HLPC so that it is able to have adequate flow rates


What does HLPC result in

high resolution and rapid separation

What is gel electrophoresis?

the action of a molecule with a net charge moving in an electric field that allows for the visualization of proteins

the distance and speed the protein moves at during electrophoresis depends on what three things

electric field strengthnet charge of protein shape of protein

What happens to large and small molecules during gel electrophoresis

large- move slowly/ stay at the top of gelsmall- move quickly/ moves thru the gel towards the bottom

how is the pH adjusted during electrophoresis

ph is adjusted so that all proteins are negatively charged

During gel electrophoresis, proteins can be separated largely by size alone with the addition of the detergent_____

sds page

what does SDS do ?

binds denatured proteins at a ration of one SDS molecule per every two amino acid which gives all proteins the same charge to mass ratio

How are proteins separated during isoelectric focusing

they are separated electrophoretically based on their relative contents of acidic and basic residues

isoelectric point (pI)

the pH of a protein at which its net charge is zero

how sensitive is isoelectric focusing?

it is able to separate proteins differing by one net charge

two-dimensional electrophoresis

isoelectric focusing (1st step) combined with SDS-PAGE(second step)

what is two-dimensional electrophoresis normally coupled with and why?

mass spectroscopy to identify the protein responsible for each spot on the gel

What must happen to a protein before the primary structure analysis occurs?

the protein must be purified from contaminating proteins

how is the purity of a protein monitored


To determine the primary structure of a protein, what must happen

both sequence analysis and protein identification for primary structure is done by mass spectroscopy

Primary sequence info is critical for understanding the____ and therefore the_____

protein structure and function

Edman Degradation

removes one residue at a time form the N terminal end of a peptide and labels each removed residue then identifies by HLPC

Mass Spectroscopy

powerful technique that can be used to determine a protein's mass, identity, and sequence

how are mass measurements during mass spectroscopy obtained

they are obtained by determining how readily an ion accelerate through an electric field

What happens during MALDI-TOF

1. a protein is mixed with metrix2. a flash of laser expels molecules form the surface 3. the molecules capture electrons and become negatively charged

what does the TOF stand for in MALDI-TOF

the ions are accelerated toward a detector

How is protein identification accomplished during MALDI-TOF

Through the analysis of the whole protein in addition to cleaved fragments

How is the protein sequence determined during MALDI-TOF

through tandem mass spectroscopy

What is used to determine the 3D structure of proteins

x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy

X-ray crystallography

depends on the diffraction of x-rays by the electrons of the atoms constituting the molecule


technique used for the determination of structure of a protein in a solution that complements x ray crystallography information

____ and ____ are major sources of energy

carbs and lipids

____ are hydrophilic meaning they are ___ in water, whereas ____ are hydrophobic meaning they are____ in water

carbs and soluble lipids and insoluble

carbs and lipids can both______ and play ____ and _____ functions

bind to proteinsstructural and regulatory

_____ are the simplest carb. What are their functions?

monosaccharides-serve as fuel molecules and functioning cellular components

Monosaccharides are____ or ____ that have _____ hydroxyl groups

aldehydes or ketones2 or more

____ contain keto groups and _____ contain aldehyde group

ketoses and aldoses

What are the six common Monosaccharides

D-ribose, D-deoxyribose, D-glucose, D-mannose, D-galactose, and D-fructose

What role does D-ribose and D-deoxyribose play?

components of DNA

D-glucose, D-mannose, D-galactose

abundant six-carbon aldoses


most abundant ketohexose

ketoses have____ than aldoses with the same number of carbons

have one less asymmetric center

The predominant forms of ribose, glucose, fructose, and many other sugars____

cyclize into rings

When does the cyclization of sugars occur

when an aldehyde reacts with an alcohol r form a Hemiacetal

In aldohexoses ( glucose) during the cyclization

the same molecule provided both the aldehyde and alcohol

Pyranose rings

hexameter rings that has c-1 as the anomeric carbon atom

Ketones react with an alcohol to form ____. what is an example?


furganose rings

pentamer rings with c2 as the anomeric carbon atom

What are three common monosaccharide reactants

alcohols, amines, and phosphates

O-glycosidic bond

a bond formed between the anomeric carbon atom of glucose and the oxygen atom of an alcohol


the product formed during the formation of glycosidic bond

When are O-glycosidic bonds prominent?

when carbs are linked together to form long polymers and when they are attached to proteins

N-glycosidic bond

formed when the anomeric carbon of a sugar is linked to the nitrogen atom of an amine

carbs can also form _____ to phosphates

ester linkage

Sugars contain many ____ groups allowing _____ bonds to join one monosaccharide to another

hydroxyl and glycosidic


formed by the linkage of two or more monosaccharides by O-glycosidic bonds


a disaccaride linked by glycosidic bind


enzymes that catalyze the formation of glycosidic binds and are responsible for the oligosaccharide formation


two sugars joined by an o-glycosidic bond

What are three common disaccharides

sucrose, lactose, maltose

sucrose is cleaved by ____. lactose is cleaved by____. maltose is cleaved by____


The cleavage products of disaccharides can be further processed to form_____


___ and ___ are ___ that plat a vital role in energy storage and structural integrity of organisms

glycogen and starch polysaccharides


if all of the monosaccharides in the polysaccharide are the same

what is an example of an homopolymer? What is it?

glycogen and the storage form of glucose

what is the plant version of glycogen? what are its two forms> how's is it hydrolyzed ?

starchamylose and amylopectin alpha- amylase


a major polysaccharide pf glucose found in plants

What allows for cellulose to form very long and straight chains

the glycosidic linkages

____ and ___ produce a hollow helix

glycogen and starch


carbs covalently attached to a protein

What are the three classes of glycoproteins

1. Glycoproteins- protein is the largest2. Proteoglycans- mainly carb3. Mucins- mainly carb

When a sugar attaches to an amino acid, what happens


What are the two linkages formed during glycosylation and where are they formed

amide nitrogen atom (N-linkage)hydroxyl oxygen atom (O-linkage)

N-linked oligosaccharides all have a common _____ core consisting of _____ and ______

pentasacchraridethree mannoses two N-acetylglucosamines

____ can be added to the common core of N linked oligosaccharides. What does this due to the molecule?

addition sugars and it forms great variety

What is an example of a glycoprotein?

erythropoietin (EPO)

lipids functions

used to store energykey components of membranesplay role sin signal-transduction pathways

lipids _______ form polymers

do not

What are the five classes of lipids

free fatty acids, triacylglycerols, phospholipids, glycolipids, steroids

what is the most common steroid


Fatty Acids (FA)

chains of hydrogen bearing carbon atoms called hydrocarbons

hydrocarbon chains

vary in lengths and may have one or more double bond in them

FA are ____ because the reduce more than carbs yielding____ than carbs

good fuels more energy

saturated FAs

Fas composed of single bonds only

notation 18:0 indicated____, whereas 18:2 means

C18 fatty acid with no 2x bondsc18 with 2 2x bonds

what are carbons atom 2 and 3 called and what is the last carbon refereed to ?

2= alpha3= betalast= w-carbon

FAs are ionized at

physiological pH

FAs in biological system contain

an even number of carbon atoms

the configuration of 2x bonds in the most unsaturated FAs is ____


How are the 2x bonds in a polyunsaturated FAs separated by

they are separated by at least one methylene group

what do properties of FAs and the lipids made from them depend on

the chain length and the degree of saturation

What does the presence of a cis 2x bind introduce to FAs and what does this cause ?

forms a kink in the FA that makes tight packing between chains impossible which lowers its melting temp

_____ of FAs are key elements in the control of the_____ of cell membranes

melting tempsfluidity

_____ is essential for the membrane function


what two characteristics enhance the fluidity of FAs and their derivates

short chain length cis unsaturation

What types of fats in the diet can lead to high blood levels of cholesterol and cardiovascular diseases

saturated and trans-unsaturated fats

trans unsaturated fatty acids

trigger inflammatory pathways

what types of fatty acids are essential to have in our diets because we cannot synthesize them


what are some examples of cis-polyunsaturated fatty acids

w-3 fatty acids (cold water fish)alpha-linolenate (vegetable oils)etcosapentaenote and docosahexaenotae (fatty fish and shellfish)

Why are polyunsaturated fatty acids essential ?

they are precursors for important hormones


formed by the attachment of three FA chains to a glycerol molecule via ester linkages


the Linkage of FAs to glycerol via ester linkages

What happens to triacylglycerols when energy is required

FAs are cleaved form it and carried in the cells


without water

Why are glycerols the major energy reservoir compared to glycogen

glycerols are anhydrous meaning that they do. not hold water so they are able to store 6x more energy than the same amount of carbs

adipose tissue

the site of accumulation of triacylglycerols

What do triacylglycerols within a fat cell

the droplets coalesce to form a large globule in the cytoplasm

adipose tissue are specialized for

the synthesis and storage of triacylglycerol and their mobilization unto fuel molecules once transported to other tissue

____ also serves as a thermal insulator

adipose tissue

What are the three major kinda of membrane lipids


What are the four components of a phospholipid

1. one or more FAs2. a platform to which the FAs are attached 3. phosphate4. an alcohol attached to the phosphate

what are the two platforms for phospholipids

glycerol and sphingosine


phospholipids derived from glycerol


simplest phosphoglyceride that is a key intermediate in the biosynthesis of others and triacylglycerols


phospholipids built on a sphingosine backbone


an amino alcohol that contains a long, unsaturated hydrocarbon chain


common sphingolipid found in membranes

Glycolipids are_____. they are _____ in all cell membranes and are derived form____

sugar containing lipidsubiquitous sphingosine

Steroids____. They facilitate the digestion of____ in the diet. They are key_____ constitutes

are powerful hormoneslipidsmembrane

Steroids exhibit _____ rather than linear structure which leaves them with ______

cyclical steroid nucleus

steroid nucleus

consist of three cyclohexane rings and one cyclopentane ring joined together

All biochemically important steroids are modified versions of the______ structure

steroid nucleus

cholesterol is in the class of molecules called ____ which means it is a steroid with an _____ functional group

sterol alcohol

Cholesterol is found in ____ animal membranes


____ cholesterol does not exists outside of the membrane. Why is that?

freeit is esterified to a FA for storage and transport

Membrane lipids are amphipathic which means

they have hydrophilic and hydrophobic moiety

Hydrophobic part of membrane lipids

two fatty acid chains that run parallel to each other

hydrophilic part of membrane lipids

phosphorylcholine head points in opposite direction

shorthand of membrane lipid

hydrophilic (polar) circle headhydrophobic (non polar) tails

What happens when a lipid attaches to the protein

this allows proteins to associate with the hydrophobic environment within the membrane

How do cell membranes act like a barrier

they separate cellular interior and outside environmentthey compartmentalize organelles form cytoplasm

What are the 7 key aspects of a cell membrane

1. contains lipids, proteins, and carbs2. hydrophobic and hydrophilic 3. specialized protein families4. held together noncovalently 5. asymmetric6. fluidity7. electrically polarized

the bilayer membrane is ____

amphipathic (hydrophilic and phobic parts)

what are the two major bilayer lipids

phospholipids a nd glycolipids

hydrophobic effect

the major driving force of membrane bilayer formation

what does the permeability of small. molecules depend on

the solubility in h20 and non polar solvents

bilayers are highly


______ content of bilayers control fluidity

fatty acids

what regulates the fluidity from rigid to fluid in bilayers


_____ also interferes with tight packing which increases the fluidity and lowers the Tm


____ carry out nearly ALL of membrane functions


integral membrane proteins

proteins imbedded in the hydrocarbon chains of membrane lipids that normally span bilayer

perphial membrane proteins

bound to the head groups by electrostatic or hydrogen bonds or can bind to exposed integral proteins

____ are commonly used motifs for proteins that span membranes

alpha helices

_____ are typically used to form hollow tubes to form pores or channels

beta sheets

proteins can also be embedded ____ into the membrane


fluid mosaic model

basis of membrane protein motility by defining the membrane

according to the fluid mosaic model, define the membrane and lipid portions of the cell membrane

membrane= 2d structure with oriented lipids and globular proteinslipids= permeability barrier fro integral membrane proteins

Membrane proteins and lipids are in constant motion what is this motion called

lateral diffusion

lateral diffusion was discovered by _____


how does FRAP work

A fluorescent marker is bound to the phospholipids that make up a cell membrane.Next, a laser is used to bleach a small patch of membrane (stop the patch from fluorescing) Within seconds, patch will again show fluorescence due to dispersion of phospholipids throughout the membrane meaning that there is lateral diffusion

transverse diffusion

flip flop, very slow

bilayers are____ whereas biomembranes are____

mostly impermeablenot impermeable

Intergral (transmembrane) proteins

play important roles in transporting molecules thru the membrane and often maintain molecule and ion [x] gradients

the maintenance of [x] gradients requires ____

the usage of ATP

What are the two classes of membrane transporters

channels and pumps

what are the two factors that determine molecular movement across the membrane

[x] gradient and molecular solubility

lipophilic (lipid loving) molecules pass ___ through the membrane via _____

freelysimple diffusion

polar molecules need help from ____ and ____ to get through the membrane via a process called ____

channels and porespassive transport

If a molecule must go against a [x] gradient , a ____ is needed to preform ____

pumpactive transport

Na/K ATPase pump generates ____

na/k gradients in the cell

what are the three things that Na/K ATPase pump controls

cell volume, membrane potential, and drives transports

secondary transporters

uphill movement of one molecule coupled to downhill movement of another

two types of secondary transporters

antiporters and symporters


downhill movement drives uphill movement of another molecule


movement down a gradient used to drive movement of another molecule of the same direction

what is an example of a molecule that uses a symporter and what is it called

glucose sodium-glucose linked transporter (SGLT)

Ion transporters are rapid like_____ and are very ____ and ___ to their environment

free diffusion specific and sensitive

two examples of ion transporters

voltage gated channelsligand gated channels

voltage gated channels

opened in response to membrane potential changes

ligand gated channels

open in response to binding to small molecule