PCB 3023 Exam 1

Flow of genetic information in all living cells

DNA -> RNA -> Protein

Replication-> Transcription -> Translation

Miller-Urey experiment

recreated conditions thought to exist in the atmosphere of primitive earth. No Oxygen!

Used heat to simulate sun, electric discharge to simulate lightning, and cooling to condense molecules to liquid form.

7 simple molecules: water vapor, nitrogen, ammonia, co2, co, methane, and hydrogen.

Miller-Urey results

With each round of heating, energy radiation, and cooling, more complex organisms were formed:

1. aldehydes

2. simple acids

3. more complex acids

Suggests organic molecules can form under abiotic conditions.

Ribozome catalyzed reactions

observed in:

genome replication in some RNA viruses

intron splicing

ribosome function in translation

Evidence for RNA World

RNA can catalyze the polymerization of nucleotides, including the synthesis of complementary RNA, using itself as a template. Not observed in DNA.

The first cell

self-replicating RNA and other life-promoting molecules inside a phospholipid membrane

What Constrains the size of a cell?

The ratio of surface area to volume. Smaller cells have a greater surface area to volume ratio.

Surface area to volume ratio

radius = 1cm -> Surface area : volume ratio is ~ 3:1

Radius = 10cm -> Suface area : volume ratio is ~ 1:3

High sa : v ratio means

more membrane per unite of volume. important for the cell to interact with its environment. smaller cell interact more efficiently; less likely to lose energy as heat to surroundings.

prokaryotic cell

no nucleus

no organelles

single chromosome (in nucleoid area) +plasmids

cell wall

capsule

most diverse of cells

Photosynthetic bacteria

obtain energy from sunlight. have internal system of membranes where photosynthesis occurs.

chemosynthetic

derive energy from oxidation of H2S.

ex. Filamentous Beggiatoa

Mitochondria

organelles found in most eukaryotic cells and generate most of the cell's supply of usable energy. extract energy from food

DNA-containing organelles (endosymbionts)

enclosed by double membrane

chloroplasts

organelles found in plant cells and ukaryotic algae. harvest energy from sunlight by photosynthesis.

DNA-containing organelles

larger than mitochondria

two membranes + a 3rd membrane system, the thylakoid.

thylakoid

contains the photosynthetic pigment chlorophyll

endocytosis

import mediated by the formation of endocytic vesicles

exocytosis

export

endosymbiosis

mitochondria and chloroplasts were prokaryotes that entered eukaryotic cells and became specialized to perform specific cellular functions

Evidence of endosymbiosis

resemble present-day prokaryotes in size

-organelles contain their own DNA (organelle genomes)

-organelle genomic sequences resemble those of present-day prokaryotes

-organelles can divide independent of mitosis and cell division

-organelles are enclosed by double membranes

Animal cell

nucleus

chromosomes

mitochondria

centrioles (microtubule organizing center)

no cell wall

Plant cell

nucleus

chromosomes

mitochondria

chloroplasts

no centrioles

microtubule organizing center (but no centrioles)

large vacuoles (fluid filled compartments)

cell wall

Animal cell types

epithelial, connective tissues, blood cells, neurons, muscle cells

epithelial cells

cells are bound by tight junctions and form sheets that cover body surfaces and form the lining of internal organs (e.g. mouth, bile duct, intestine)

connective tissues

bone and cartilage

adipose tissue

fibroblasts

blood cell types

red (O2 transport)

white (immune)

neurons

cells that receive and transmit signals throughout the body and are capable of generating electrical activity

Muscle cells

multi-nucleated cells that generate force and movement.

three types:

skeletal

cardiac

smooth

Basic properties of cells

complexity

genetics

replication

metabolism

biochemistry

function

response

self-regulation

complexity

cells are highly complex and organized

genetics

cells possess a genetic program and the means to use it

replication

cells are capable of producing more of themselves

metabolism

cells are capable of acquiring and utilizing energy

biochemistry

cells carry out a variety of chemical reactions

function

cells engage in numerous mechanical activities

response

cells are able to respond to external stimuli

self-regulation

cells maintain their complex state by constant self-regulation

building blocks of the cell

sugars

fatty acids

amino acids

nucleotides

larger units of the cell

polysaccharides

fats, lipids, membranes

proteins

nucleic acids

sugars

polysaccharides

fatty acids

fats, lipids, membranes

amino acids

proteins

nucleotides

nucleic acids

ribonucleosides or deoxyribonucleosides + phosphates

formation of macromolecules by condensation reactions

subunits are added to one end of a growing chain by dehydration synthesis

formation of disaccharides

the condensation of two monosaccharides produces one disaccharide

reverse reaction of condensation

hydrolysis (water consumed instead of being expelled)

carboxylic acid head

hydrophilic

hydrocarbon tail

hydrophobic

triaglycerols

formed when fatty acids stored as energy reserves (fats and oils) through an ester linkage to glycerol

saturated fatty acids

tend to form aggregates and deposits within the walls of blood vessels causing atherosclerosis of coronary blood vessels (coronary heart disease)

Cis unsaturated fatty acids

cis unsaturated fatty acids do not form solid aggregates

e.g. oleic acid (comprises 80% of olive oil)

Trans unsaturated fatty acids

behave similar to saturated fatty acids = they tend to aggregate and form solid deposits.

e.g. elaidic acid (found in partially hydrogenated vegetable oils)

phospholipids

in biological membranes typically contain one saturated and one unsaturated fatty acid.

saturated fatty acid makes the membrane less fluid because they tend to aggregate.

cis unsaturated fatty acids reduce membrane rigidity because they do not form solid aggregates.

alanine

one of the simplest amino acids

polypeptide

held together with peptide bonds. N-terminus capped by amino group and C-terminus capped by carboxyl group

Adenosine triphosphate

a nucleotide. ATP. used as an energy carrier in the cell

Ribonucleosides

Guanosine

Adenosine

Cytidine

Uridine

Deoxyribonucleosides

deoxyguanosine

deoxyadenosine

deoxycytidine

deoxythymidine

cyclic adenosine monosphosphate

cAMP. a cyclic nucleotide

Relative abundance of macromolecules in cells

30% chemicals:

DNA (1%)

polysaccharides (2%)

phospholipids (2%)

ions, small molecules (4%)

proteins (15%)

70% water

formed from the covalent bonding of their monomeric subunits

polysaccharides, polypeptides, and polynucleotides

interactions between macromolecules

mediated by noncovalent bonds of compatible groups. results in macromolecular complexes in cells.

e.g. molecule A randomly encounters other molecules (B,C, D). Surfaces of molecules B and C do not match A. A few weak bonds are formed but thermal motion breaks them apart. Surface of D matches Surface of A. Forms a lot of weak bonds that are able to withstand thermal jolting.

nonpolar side chains

tend to cluster at the interior of a folded polypeptide, away from the aqueous surroundings. also form the transmembrane domains of membrane proteins.

polar and charged amino acids

tend to be near the outside of the protein, the surface exposed to the aqueous surroundings.

globular protein

(folded conformation in aqueous environment)

hydrophobic core region (contains nonpolar side chains)

hydrogen bonds can be formed to the polar side chains on the outside of the molecule.

alpha helix

polypeptide structure. each N-H is bonded to the C=O of a neighboring peptide bond located four amino acids away in the same chain.

Beta sheet

polypeptide structure. individual polypeptide chains in each sheet are held together by hydrogen bonding between peptide bonds in different strands, and the amino acid side chains in each strand project alternately above and below the plane of the sheet.

protein maturation involves:

correct folding

proteolytic cleavage

chemical modifications

formation of quaternary structures

association with co-factors

protein regulation

each step in protein synthesis and maturation can be a target for regulation of protein function.

protein degradation

under tight control

chaperones

bind to nascent polypeptides and maintain a stable unfolded state. when synthesis is complete, the polypeptide is released and allowed to fold correctly.

if a protein is to be transported through a membrane:

1) chaperones stabilize the newly synthesized polypeptide.

2) the polypeptide is transported

3) chaperones on the other side maintain the unfolded state until translocation is complete

4) only then is the polypeptide allowed to fold into 3D shape

cross-linking

disulfide bonds form between adjacent cysteine residues.

they can link two domains of the same polypeptide or different polypeptide chains

denaturants

can unfold (denature) a polypeptide by breaking noncovalent interactions between amino acids. (e.g. urea or heat)

reducing agents

can break disulfide bonds. (e.g. beta-mercaptoethanol)

urea

produced in the liver of mammals as a way to excrete ammonia (a toxic metabolic waste product). can reversibly break noncovalent interactions between amino acids.

fibrillar collagens

the major structural proteins of connective tissues. build of triple helices of procollagen polypeptides.

prions

proteinaceous infectious particle. infectious agent.

protein-only hypothesis

diseases are caused by incorrectly folded versions of the prion protein

TSE

family of fatal brain diseases characterized by lesions that appear as small cavities (spongy appearance) caused by protein aggregates

Regulation of gene expression

determines the amount of protein produced by the cell by limiting transcription and/or translation

regulation of protein function

the protein is synthesized but its activity is restricted according to needs of the cell.

PKA

protein kinase A. promotes glycogen metabolism. cAMP activates PKA by binding to the regulatory subunits, causing the release of the catalytic subunits. the kinase activity of the released catalytic subunits phosphorylate multiple effector proteins

feedback inhibition

the end product of a biosynthetic pathway inhibits the enzyme that catalyzes the first step, causing the entire pathway to shut down.

allosteric regulation

a change in the conformation of a protein that affects its activity due to the binding of a regulatory molecule.

regulation of glucose metabolism

enzyme activity responds to elevated ADP levels

protein kinases

enzymes that transfer a phosphate group from ATP to proteins

two types of kinases

1. serine/threonine

2. tyrosine

phosphatases

enzymes that remove phosphate groups from phosphorylated proteins.

ubiquitin

a small protein that is attached to a target protein as a label for regulation or destruction

ubiquitylation and proteasomal degredation

1) target protein has several ubiquitins attached by ubiquitin ligase enzyme.

2) a cap domain of the proteasome recognizes the polyubiuitylated target protein

3) the ubiquitins are removed and recycled

4) the proteasome degrades the target protein by sequential ATP-dependent steps.

centromere

the point of junction between sister chromatids. also the attachment site for mitotic spindle proteins.

telomeres

the stable ends of linear chromosomes

replication origins

sequences where DNA replication begins

levels of organization of DNA in chromosomes:

1) nucleosomes

2) chromatin

3) chromatin fibers

4) condensed chromosomes

condensed chromosome

highest level of DNA organization.

ATP dependent enzyme complexes

can displace nucleosomal dna to expose specific sequences that can then be recognized by DNA-binding proteins

chromatin remodeling complexes

use energy from ATP hydrolysis to push the histone-bound DNA along the histone core, thereby exposing the underlying DNA.

emrbyonic stem cells

capable of becoming any type of cell because they have not undergone any differentiation

(totipotent)

adult stem cells

have limitations on which cell types they are capable of becoming because they have under-gone some differentiation (pluripotent)

e.g. blood stem cells

terminally differentiated cell types

can not become any other cell type (neurons, muscle cells, endocrine cells, blood cells, etc)