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218 Cards in this Set

  • Front
  • Back

What does cytology focus on?

Focuses on cellular structure and uses optical techniques

Biochemistry focus: ?

Focuses on cellular function

Genetics focus : ?

Focuses on information flow and genetics

What are two tools used by cytologists? (3)

•Themicrotome-- Allows the preparation of very thin slices of samples


•A variety of dyesand the development of immunohistochemistrytechniques -- Stain cells or cell compartments/molecules


•The smaller the limit of resolutiona microscope has, the greater its resolvingpower

electron microscope stats:

resolving power 0.1-0.2 nm


100 000x magnification

Tools used in Biochemistry (3):

RadioactiveIsotopes-- to trace the fate of specific atoms and molecules


Subcellularfractionation -- suchas centrifugationto separate/isolate different structures and macromolecules


Ultracentrifuges--capable of very high speeds (over 100,000 revolutions per minute)

Tools used in Biochem pt.2 (3):

Chromatography--Separates molecules from a solution based on size, charge, or chemical affinity••Electrophoresis--Uses an electrical field to move proteins, DNA or RNA molecules through amedium based on size/charge••MassSpectrometry --Determines the size and composition of individual proteins

Origin of genetics? Chromosone Theory of genetics come from this work

Gregor Mendel's Pea experiment in 1866. Described hereditary factors. Now known as genes.


- Chromosome Theory of Genetics would come from his work and others

Each gene is responsible for : ?

A single protein

Who proposed the DNA double helix?

Watson and Crick in 1953



What are two tools used in genetics that Separates DNA and RNA molecules: ?

Ultracentrifugation and electrophoresis

What is a tool used in genetics that Uses the ability of nucleic acid bases to bind to each other?

Nucleic acid hybridization

What is the technology used in genetics that uses Restriction enzymes to cut DNA at specific places forming recombinant DNA molecules,with DNA from different sources?

Recombinant DNA technology

What is a tool used in genetics to rapidly determine the base sequencesof DNA molecules?

DNA sequencing

In vitro is?

•using purified chemicals and cellular components

In vivo is?

•using live cells or organisms

Insilico is ?

• using computer analysis of largeamounts of data

Define Hypothesis

statement consistent with most of the data, may take the form of a model(an explanation that appears to account for the data); must be testable

Define a Theory:

a hypothesis that has been extensivelytested by many investigators, using different approaches, widely accepted

Define a Law:

•atheory that has been tested and confirmed over a long period of time withvirtually no doubt of its validity

Lecture 2. The Chemistry of the cell.

YAY!

What are the five principles of Cell biology?

--Characteristics of carbon and water.




-Selectively permeable membranes




–Synthesis by polymerization of small molecules




Self Assembly

Which 5 other atoms is carbon most likely to bind to ?

PHONS.

What is stability expressed as?

Bond energy - theamount of energy required to break 1 mole (~6x 1023) of bonds

•Bond energy is expressed as caloriesper mole (cal/mol)•Acalorie isthe amount of energy needed to raise the temperature of 1g of water by 1oC

:P

Which functional groups are negatively charged?

Carboxyl and phosphate

Which are positively?
amino
Which are (uncharged;but polar) ?

Hydroxyl, sulfhydroxyl, carbonyl, aldehyde

What is a configurational stereoisomer?

A non superimposable mirror image ( chiral)

A compound with nasymmetric carbons willhave how many possible stereoisomers?

2^n. Each asym C has two possible stereoisomers.

What is responsible for the high:


Surfacetension, Boilingpoint and Heatof vaporization of water?

The extensive network of Hydrogen bonding

How does water absorb so much heat with little change in temperature?

Heat is absorbed by breaking the many hydrogen bonds

What is heat of Vaporization?

•the amount of energy required to convert one gram of liquid into vapor

The high heat of vaporization of water makes it an excellent solvent for cells. Why?

B/c it protects proteins in solution from overheating

How do water molecules reduce the chances of re-association between dissolved ions?

They form spheres of hydration around the ions

Cell membrane consists of ? (3) + 3

phospholipids, glycolipids and membrane proteins.


Also sterols. cholesterol in animals


•ergosterols (fungi), or phytosterols (plants)

What are the main 3 types of membrane proteins?

Transport


Enzyme


Receptor

Are membranes permeable to polar or nonpolar molecules?
Non polar because of the hydrophobic interiors

Why are even the smallest of Ions still unable to diffuse across the bilayer?

Because of their charge and the surrounding hydration shell.

Consider revising types of transports proteins. 7 in total

:P

In the polymerization of monomers, monomers must first be _______ before condensation can occur?

activated. Once activated it is in a higher energy state, and it consumes this energy during condensation sythesis

How does a monomer become activated?

Is must be coupled with a carrier molecule

Does this process use ATP?

Yes, or an alternative high E molec.

Remember that the carrier molecule is removed after condensation.

:P


What is the carrier molecule of protein synthesis?

tRNA

What is the carrier molecule of Polysaccharide synthesis?

sugars (monomer) are often activated by linking them with ADP and UDP.



What is the carrier molecule of Nucleic Acid synthesis?

–nucleotides themselves are high-energymolecules (ATP, GTP)

Assisted self-assembly has what?

molecular chaperones

What class are many chaperones a part of ?

Heat shock

What are two advantages to heirarchical self assembly, in terms of simplicity and efficiency?

relatively few subunits are used for a wide variety of structures




a small number of condensation reactions are needed

What is another advantage in terms of quality control?

Early mistakes can be repaired or omitted before being incorporated into larger structures

There are 8 types of proteins. The follow are the less obvious ones

Lets get em

Structural Proteins

-- physical support and shape (e.g., cytoskeletal proteins)

Motility Proteins

-- contraction and movement (e.g., muscle proteins: myosin & actin)

Regulatory Proteins

control and coordinate cell function (e.g., cell signaling, cell death, gene transcription/repression)

Transport Proteins

move substances in and out of cells (e.g., membrane transporters and channels)

Communication Proteins

communication between cells (e.g., hormones, neurotransmitters)

Receptor Proteins

enable cells to respond to chemical stimuli from the environment

Defensive Proteins

Defensive Proteins

Storage proteins -

reservoirs of amino acids

All proteins are made from the same 20 amino acids. But some do not. What is this the result of?

Modification

9 AA have unpolar hydrophobic groups

What are the two acidic AAs?

Aspartate and glutamate


Asp and Glu




GluAsp

What are the three basic AAs?

Lys Arg and His




LAH

Describe a peptide bond?

C-N covelent bond b/w two AAs

Two cystein residues may form which type of bond?

covalent disulfide bonds

How are the formed?

With the removal of two hydrogens. (Oxidation)

Are these bonds intermolecular

Yes, but also intramolecular

Polypeptides form in which direction?

N-terminus --> C-terminus

Which bonds and forces maintain quaternary structure?

The same as tertiary.


H bond


van der waals


ionic


hydrophobic


covalent (s-s)

What are the two Purine bases?

Adenine and guanosine


A and G

What are the Pyrmidines?

Thymine, cytosine and uracil

What is a sugar base portion of DNA?

A nucleoside

A nucleside + ________ = nucleotide?

Phosphate

What is the difference in the sugar b/w DNA and RNA?

DNA 2' C-H


RNA 2' C-OH

Adenine forms __ H-bonds with __?

2,Thymine


Uracil if RNA

Cytosine forms __H-bonds with ___ ?

3 H - bonds with Guanine

Polysaccharides consist of ____ repeating unit(s)

1 sometimes two in alternating fashion

What is the most common sugar?
aldohexose. D-glucose, which is the most stable stereoisomer

In the cell does D-glucose exist as a ring?

No. It exists in an equilibrium b/w linear and ring form.


Fisher projection shows linear form and makes aldehyde obvious

How is alpha D glucose defined?

In alpha D glucose the 1 C OH group is downwards

How is beta D glucose defined?

In beta D glucose the 1C OH group is upwards

What type of bond links disaccharides?

glycosidic bonds (with the elimination of water)

Glycosidic bonds involving A-D-glucose are called glycosidic bonds

Glycosidic bonds involving B-D-glucose are called B glycosidic bonds

if a A-D-glucose bonds with a B-D-Fructose, what type of bond will form?

an A-glycosidic bond

The most common storage polysaccharide in animals is?

glycogen

The most common storage polysaccharide in plants is ?

Starch

How would one describe the bonding of starch and glycogen ?

A 1-->4 glycosidic




With branching at A(1--->6)

How often does glycogen branching occur?

Every 8-10 glucose units



Where is glycogen stored in animals?

In liver, for glucose, and in muscle as a fuel source for muscle contraction

In what two forms does starch occur?

As branched (every 12-25 glucoses) Amylopectin (70-90%) and amylose (10-30%)

Where is starch stored?

In the plastids as starch grains. In amyloplasts and in chloroplats

What is the compositon of cellulose?

B-D-Glucose

Bacterial cell walls contain which two kinds of sugars?

GlcNAc (N-acetylglucosamine) and MurNAc (N-acetylmuramic acid)

And they are derivatives of what?

B-glucosamine,

Linked alternately with what type of bond?

B(1--->4)

What is chitin's composition?

GlcNAc, B (1--->4)

Polysaccharide Structure Depends on the Type of Glycosidic Bonds Involved
Sure does.

A-glycosidic are loose

B-glycosidic are rigid linear rods that aggregate into microfibrils, about 5-20 nm in diameter

Lipids

yay!

What are 3 functions of lipids?

energy storage, membrane structure and signal transmission

few polar groups, but some are amphipathic, with polar and nonpolar regions

ya

There are 6 classes of lipids

un mas

What is the structure of a fatty acid?

Long unbranched hydrocarbon with a carboxyl group at one end

12 to 20 carbonsEven numbers of carbons are favored because fatty acid synthesis occurs via the stepwise addition of two-carbon units

Fatty acids are highly reduced and generate a large amount of energy upon oxidation

What are 2 functions of triaglycerols?

Energy storage and insullation

Animals triacylglycerols are semi solid at room temp

Plant TGCs are fluids. They are predominantly unsaturated fatty acids

What are two types of phospholipids?

Phosphoglycerides and sphingolipids

Draw a phosphatic acid. Which is the backbone of phosphoglycerides, which are the predominant phospholipid in membranes

2 fatty acids and a phosphate group attached to a glycerol

The R group is usually serine, ethanolamine, choline, or inositol, which contributes to the polar nature of the phospholipid head group

Usually have 1 sat and 1 unsat tail

Where are sphingolipids found?

On the outer leaflet of the plasma membrane

What are glycolipids?

Lipids with a carbohydrate group instead of a phosphate group

What are they derived from?

Glycerol and sphingosine

Carb group 1-6 sugars long

Occur largely on the outer monolayer of the plasma membrane

What is the base structure of steroids?

tetracyclic hydrocarbon

Are they polar?

No, they arn't

How do they differ from one another?

Functional groups and location of double bonds

Whats the most common steroid in animals?

Cholesterol, it plays a large role in membrane fluidity

What is cholesterol the precursor of?

Steroid hormones. Such as M and F sex hormones, glucocorticoids and mineralcorticoids

What are estrogens and androgens?

Female SH and male SH

What do glucocorticoids do?

they promote glucosneogenesis and reduce inflammation

What do mineralcorticoids do?

They promote reabsorption of HCO3-, Na, and Cl by the kidneys

What are terpenes synthesised from?

Isoprene, a 5 C compound

Terpenes and its derivatives are joined in various combinations to produce substances such as____?

Vitamin A and Cartenoid pigments

While archaea and bacteria are both prokaryotes, rRNA sequence analysis reveals how widely divergent archaea are from bacteria

:P



Where are archaea commonly found?

In extreme condition where they have developed diverse metabolic strategies

What are methanogens?
Archaea who get energy from H2 and convert CO2 into methane

What are Halophiles

Archaea who occupy extremly salty environments

What are Thermacidophiles?

Archaea who live in acidic hot springs

Archaea emerged from a common ancestor of eukaryotes long after diverging from bbacteria

ya!

Cells are small because?

Beyond a certain threshold they would not be able to take in enough nutrients and release enough wastes

Many molecules rely on diffusion to move around the cell. Larger molecules have a slower rate of diffusion.

>.>


What are some steps cells take to avoid the limitations of diffusion?

Carrier proteins to actively transport materials through the cytoplasm.




And vesicles transported along microtubules

Cells must also stay small because of the necessity to maintain adequate reactant and enzyme concentrations, so as to maintain a high level of collisions b/w reactants and enzymes

yay!

As cell size increases the number of molecules must increase proportionate to__________?

Cell volume, which grows a lot

How do organelles avoid the issue of concentraions?

They are specialized compartments for specific functions

The nucleolus, which is a distinguishing feature of eukaryotes from prokaryotes, also is the site of what synthesis and assembly?

rRNA synthesis and ribosome assembly

Eukaryotes have a nuclear membrane, which has 2 membranes.


How is bacterial DNA arranged?

the genetic information is folded into a compact structure called the nucleoid and is attached to the cell membrane

How is bacterial DNA organized?

Circular with few protein interactions

How is EUK DNA organized?

linear and complexed with large amount of histones

How is Archaea DNA organized

circular and complexes with proteins similar to EUK histones

Bacterial and Archaeal cell duplicate their DNA and divide by ________?

binar fission

Eukaryotic cells replicate DNA and distribute their chromosomes into daughter cells by mitosis & meiosis, followed by cytokinesis, division of the cytoplasm

:PPP

This type of cell transcribes genetic information into RNA, and each RNA molecule may contain information for several polypeptides.


What type is it ?

Bacterial

RNA molecules become involved in protein synthesis before transcription is complete.




What type of cell does this?

Archaea and Bacteria

CMMMMembrane !

woop woop

What type of proteins would the cytoskelton connect to in the plasma membrane?

Anchor Proteins

Nucleopores are lined with what complex?

nuclear pore

When are chromosomes most visible?

During mitosis

When are chromosomes least visible? and what form are they in during said phase

During interphase when they are dispersed as chromatin

Mitochondria contain small circular molecules of DNA, which encodes some RNAs & proteins needed for mitochondrial function

yup

Mitochondria also have their own_________ to carry out protein synthesis?

ribosomes

How is ATP produced in the mitochondria?

By the oxidation of sugars and other fuel

What are the cristae of the mitochondria?

infoldings of the inner mitochondrial membrane

What is the mitochondrial matrix?

The fluid that fills the inside of the mitochondrion

Where are most proteins of the mitochondria localized?

The cristae and the matrix

Tissues with high demand for ATP have many mitochondria, located within the cell at the site of greatest energy needsE.g.: sperm cells

---------_-_-_> also e.g. muscle cells

Chloroplasts and Mitochondria are surrounded by both ________ and ____________ membranes?

inner and outer

Chloroplasts contain a system of __________ that are stacked into __________

thylakoids stacked into grana

In or on thylakoid membranes are the site of what reactions?

Solar energy dependant reactions

Reactions involved in the reduction of CO2 to sugar occur within the__________

stroma, which is asemifluid in the interior of the chloroplast

Chloroplasts also reduce NO3- from soils into __________
(hint: is it needed for protein synthesis)

NH3

Chloroplast function is the reverse of mitochondrial reactions that __________ glucose into CO2

oxidize

How do chloroplasts relate to mitochondria?

They have a small amount of circular DNA which codes for a few of their own ribosomes and proteins
DNA not associated with histones

The inner membrane of MIT and CHLO has what type of lipids?

Bacterial lipids

tubular membranes and flattened sacs of the ER are called what?

cisternae

The internal space of the ER is the

lumen

The ER is continuous with other parts of the cell

OK!

The RER is studded with _____________ and their role is ____________?

ribosomes that synthesize polypeptides



Where do those polypeptides go?

Either the accumulate in the membrane or are transported to the lumen

What is the role of the SER

Lipids synthesis e.g. cholesterol and its derivatives

It is also responsible for __________ and ___________ harmful substances?

deactivating and detoxifying

Sarcoplasmic reticulum does what ?

sequesters Ca2+ ions critical for contraction tissues

What is the main function of the GA ?

processing & packaging secretory & membrane proteins



What is another, similar role of the GA?

complex polysaccharide synthesis

It also accepts __________ that bud off from the _________

vesicles


ER

Secretory and membrane proteins are often glycosylated. Where does this occur?

It begins in the ER and then is completed in the GA

How do these processed materials move to other parts of the cell?

In vesicles that bud off the GA

Exocytosis releases contents into the ECM

hey ho

What are the 4 components that constitute the endomembrane system, which trafficks substances through the cell

ER, GA, vesicles and lysosomes

What do lysosomes store?

Hydrolases

What are hydrolases?

enzymes that can digest any kind of biological molecule

How is the lysosome protected from the hydrolases that it sequesters?

A special carbohydrate coating

How is H2O2, a harmful by-product of cellular respiration managed within the cell?

H202 is converted into H20 and 02 by catalse enzyme which is present in peroxisomes

What else do peroxisomes do?




(hint: related to SER)

detoxify toxins

Where in the body are peroxisomes found in high concentration?

Liver and kidneys

What is the role of vacuoles in animal and yeast cells?

Temporary storage or transport

A phagosome is the result of __________?

phagocytosis

If a phagosome (vacuole) fuses with a lysosome its contents are _____________to provide _____________ for the cell

hydrolyzed


nutrients

Why are ribosomes not organelles?

B/c they are not enclosed by a membrane

They are found in all cells but differ in bacteria, archaea and eukarya in their size & composition

nice

EUK cell ribosome sediment coefficients are approx ?

60s and 40s

50s and 30s in _________ and ___________ ?

Bacteria and Archaea

Other than structural support, what are 3 roles of the cytoskeleton?

Cell division


Cell movement


Intracellular transport

What are the largest structural elements of the cytoskeleton

microtubules

mitotic spindle fibers and axoneme of cilia are both _____________ based structures?

microtubule

draw and label a microtubule and its monomers
do it
Atub+Btub= tubulin dimer --> protofilament
--> microtubule


What are the smallest components of the cytoskeleton

microfilaments?

What is the monomer of mircofilaments?

Actin

Draw and label a microfilament and its monomers

Microfilaments Are polymers of the protein actin




Actin is synthesized as a monomer called G-actin (globular)




These subunits are polymerized into F-actin (filamentous), with a helical appearance




G-actin ---> F-actin ----> Microfilament

These filaments are the most stable and least soluble. What are they?

Intermediate filaments

Where are they found

Areas of mechanical stress such as muscle cells

There are six classes of intermediate filaments and animal cells from different tissues can be distinguished on the basis of the types of intermediate filament proteins they contain

just stop

Animal cell ECM consists of _______ fibers and ___________

collagen and proteoglycans

What is role of proteoglycans?

They confer mobility and elasticity

What does the primary cell wall consist mainly of ?

Cellulose fibrils embedded in a polysaccharide matrix

Secondary Cell Wall: Formed once the cell reaches its final size & shape by ?

deposition of additional cellulose and pectin on the inner surface of the primary cell wall

How are plant cells connected?

Plasmodesmata

How large molecules can pass through plasmodesmata?

H2O and small solutes

How do animal cells communicate?

Gap junctions.




Tight and adhesion jctns also connect animal cells

Viruses are noncellular parasitic particles incapable of _________________________?

Free living existence

consist of only a few different molecules of____________?

nucleic acid and protein

they use invaded cells' machinery to produce more virus particles

uh oh

Viruses consist of a ____________ (protein coat) that encapsulates a core containing _______ and ______

capsid


DNA


RNA

Enveloped viruses are ones that _________

are surrounded by a membrane

Viruses have no ________, _________ and can only reproduce via the machinery of other cells

metabolism


irritability ( ability to perceive and respond to outside stimuli)

Asymetric carbons allow for the formation of ________ which are mirror images of eachother

configurational stereoisomers

Which of thefollowing can only be viewed by electron microscopy? A) Frog eggs B) Viruses C) Nuclei D) Mitochondria E) Bacteria

B)