Study Guide 1

What are the structures and organelles of a typical eukaryotic cell?

plasma membrane, nucleus, nucleolus, nuclear membrane, smooth endoplasmic reticulum, nuclear membrane pore, rough endoplasmic reticulum, lysosome, mitochondrion, cytosol, filamentous cytoskeleton (microtubules), Golgi apparatus

What are the major differences between a prokaryotic and eukaryotic cell?

prokaryotes have no defined nucleus or membrane-bound organelles, eukaryotes are usually the cells of multicellular organisms and have membrane-bound organelles

What are the main features and functions of plasma membranes? Focus on lipid bilayers and proteins/glycoproteins of plasma membranes.

• hydrophobic and hydrophilic moiety

• cholesterol enhances mechanical stability and reduces membrane permeability

• membrane proteins responsible for functions

• carbohydrates present as glycolipids and glycoproteins

  • glycocalyx: a glycoprotein covering that surrounds the cell membranes for cell-cell recognition, communication, and intercellular adhesion

What are the main features and functions of cytoplasmic matrices? Focus on key proteins of the three types of cytoplasmic matrices and their relative position and size.

provides structural support to define shape

framework for positioning of organelles

network to direct the movement of materials and organelles within the cells

means of independent locomotion for specialized cells

pathway for intracellular communication

possible transfer of RNA and DNA

cytoskeleton components

• microtubules: smallest

  • protein: tubulin

• intermediate filaments

  • protein: various fibrous proteins

• microfilaments: largest

  • protein: actin

Structural arrangement of the matrix influences metabolic pathways such as…

• glycolysis

• hexose monophosphate shunt (pentose phosphate pathway)

• glycogenolysis

• fatty acid synthesis

• facilitate interactions between enzymes and molecules

What are the main features and functions of mitochondria?

• double membrane surrounds matrix

  • outer membrane is relatively porous

  • inner membrane is selectively permeable and the site of electron transport chain

• site of TCA cycle and fatty acid oxidation

• contains DNA through maternal inheritance

• can divide and change in size

TCA cycle

What are the main features and functions of cell nuclei?

• largest organelle

• surrounded by nuclear envelope

• nuclear structural components

• contains DNA

  • cell genome is the entire set of genetic information

protein synthesis facts

• not all genes are expressed at the same time

• not all genes are expressed to become proteins

• not all genes are expressed in the nucleus

• DNA sequences are not always equivalent to genes

What is the major function of a nucleolus?

• site of rRNA transcription and processing

• ribosome assembly and synthesis

Key steps and procedures of transcription and replication and where they occur

DNA replication

• duplex DNA unwinds and nucleotides are added to each strand to make two sets

• in the S-phase of the cell cycle

transcription

• mRNA created from sequence of one DNA strand (sense strand)

• genes

• introns: intervening sequences

• exons: containing coding sequences

• coding exons, but not intron, sequences to become protein

• transcription of a gene in the nucleus results in the synthesis of a strand of mRNA

Key steps and procedures of translation and where they occur

in translation and elongation, the mRNA strand leaves the nucleus, binds to ribosomes, and directs protein translation with the help of tRNA subunits and their associated amino acids. This elongation process results in the production of a polypeptide strand

• mRNA codes for amino acid one by one to form protein

• mRNA is synthesized in nucleus, then moves to RER in cytoplasmic matrix

• codon: a 3-base sequence codes for one amino acid

• tRNA brings amino acids to mRNA

  • tRNAs have their specific 3-base anticodon RNA sequence to match its codon, and carry the correct amino acids

  • the 61 different tRNAs (see the genetic code) are preloaded with their unique amino acid and wait for the next codon to come

• elongation

  • after amino acids are positioned, peptide bonds are formed between them

• “nonsense” (stop) codons signal the end of translation

• only a portion of the genes are expressed in cells of a given organ

  • regulation of gene expression occurs at various levels

    • transcription

    • mRNA processing (combinations of exons)

    • translation

exons during transcription

contain coding sequences

introns during transcription

intervening sequences

What is DNA replication?

the process by which the genome’s DNA is copied into cells

Why is DNA replication needed?

to ensure that when a cell divides, daughter cells have a full copy of the genome and therefore, successful inheritance of genetic traits

What are the main features and functions of endoplasmic reticulum?

• network of membranous channels used to communicate from the innermost part of the cell to the exterior

• protein quality control

• types

  • rough ER (studded with ribosomes): protein synthesis

  • smooth ER: lipid synthesis

  • sarcoplasmic reticulum (SER) in muscle: calcium ion pump

  • *ribosomes

    • on ER: for extracellular and organelle destination

    • free in cytosol: for cytosolic proteins

What are the main features and functions of Golgi complex?

• protein trafficking and sorting

  • how do proteins know their final destinations? add oligosaccharides, lipids, or a few amino acids

• 4-8 cisternae (stacks)

• tubular networks at either end

  • cis-Golgi network: entrance

  • trans-Golgi network: exit

• connected to ER by transport vesicles

What are the main features and functions of lysosome?

• enzyme-filled organelles

• lysosomes serve as cell’s “digestive system”

  • capable of degrading proteins, polysaccharides, nucleic acids, and phospholipids

What are the main features and functions of peroxisome?

enzyme-filled organelles

site of oxidative catabolic reactions

• ex: oxidation of ethanol to acetaldehyde

  • using H2O2 as a substrate through catalase

What are the three types of protein receptors?

ion channel receptors, GPCRs, and enzyme-linked receptors

• those that generate internal chemical signals

• those that function as ion channels

• those that internalize stimuli

receptors info

• internal chemical signal

  • ex: 3’-5’-cyclic adenosine monophosphate (cyclic AMP, cAMP)

• ion channel

  • ex: receptor for acetylcholine- to open and allow for Na+ entry

  • the proton pump

• internalize stimulus: Clathrin-coated pit

  • variety of biologically active molecules

    • several hormones

receptors

modify cell’s response to environment

enzymes

catalysts for biochemical reactions within cells

ligands

proteins or chemicals that stimulate and attach to receptors

receptors steps

1. ligand binds with its receptor on the cell membrane

2. ligand and receptor move into a clathrin-coated pit

3. pit closes off and forms a clathrin-coated vesicle

4. the vesicle forms an endosome

5. ligand can be used by the cell or undergo lysosomal degradation

6. receptor is recycled to the surface of the cell membrane

   ex: virus; bacterial toxins

catalytic proteins (enzymes)

• functionality depends on protein and prosthetic group( non-protein part) or coenzyme

• enzyme’s active site has high specificity

• velocity defined by an equilibrium constant

  • Km (Michaelis constant)

  • concentration of substrate when reaction is at half of maximum velocity

• reversibility

  • most are reversible

    • enzyme (E) + substrate (S) <→ E-S complex → E + products

• mechanisms of regulation

  • covalent modification of enzymes: at active site

  • modulation of allosteric (change binding affinity to substrate upon effector binding, with conformational changes) enzymes

    • ex: phosphofructokinase, inhibited by citrate but stimulated by AMP/ADP

  • increase in enzyme concentration by induction

    • enhance the amount of proteins

      • vitamin D can increase Ca bioavailability

six classes of enzymes

1. oxidoreductases: reactions in which one compound is oxidized, another reduced

   1. Gpx1

2. transferases: functional group transferred from one substrate to another

   1. adenyl cyclase

3. hydrolases: hydrolysis of bonds between carbon and other atoms by adding water

4. lyases: cleavage of C-C, C-S, and C-N bonds (no hydrolysis/O-R)

5. isomerases: interconversion of optical or geometric isomers (R vs. L)

6. ligases: catalyze formation of C and other bonds (O, S, N, others)

examples of using proteins as clinical markers of diseases

• tumor markers

  • substances produced as a result of a malignant disease

    • telomerase

  • enzymes and isoenzymes, hormones, protein antigens such as carcinoembryonic antigen (CEA; a glycoprotein in association with intestinal cancer), and products of oncogenes

    • oncogenes: mutated genes that encode abnormal, mitosis-signaling proteins that promote unregulated cell division

What is apoptosis?

programmed cell death

What is senescence?

permanent termination of cell proliferation

• also known as cell aging

  • during the aging process, most somatic cells take longer and longer to proliferate and eventually reach senescence

• causes

  • aged cells

    • persistent DNA damage response due to shortened telomeres (located at chromosome ends)

  • acute stress

    • oxidative stress; acute damage to DNA, protein, or lipids

Know what biological energy is about (energy-requiring processes, high energy phosphate bonds, and energy-requiring processes).

• ATP: major storage form of energy in cells

• energy needed for:

  • physical exertion

  • anabolism

  • active transport

  • transfer of genetic information

  • enzymatic reactions

• energy comes from macronutrients (and alcohol!)

• transferred from one form to another

• heat by combustion vs chemical energy inside a cell

  • units of energy (cal, kcal, J, kJ)

    • 1 cal=4.18J, or 1kcal=4.18kJ

  • free energy (G)

    • potential energy released from chemical bonds of nutrition