Final exam topics/concepts which stand out as testable

(not necessarily an exhaustive list)

created by Dr. Racich 12/8/99

 

Life arose from non-life

The first organisms were single cells

Photosynthesis and sex changed the course of evolution

Eukaryotes are “cells within cells”

Cells evolved the ability to change their structures and specialize

The cells of an organism are constantly adjusting

Multicellular organisms develop and grow

Speciation has resulted in the diversity of life

Emergent properties of life

 

All above sub-headings within chapter 1.  Use the sub-headings or even the contents listings to pick out major concepts for review.

 

Emphasize your notes – 95% of material comes from them.  Use the book as support information, but focus on the lecture notes (and web material from Dr. Huskey).

 

Function in molecules follows from structure

 

Functional groups:  amine, carboxyl, hydroxyl, sulfhydryl

 

Core set of 33 basic biomolecules

Know the structure by sight for types of amino acids (polar, non-polar, charged, specials)

 

Know some particular aa’s which have been discussed recently (phe, tyr)

 

Know all 5 nitrogenous bases, for sure.

 

Alpha vs. Beta linkages in carbohydrates

 

Configuration vs. conformation

 

Dehydration synthesis

 

Molecules with information

 

1,2,3,4 structure of proteins

 

Diversity of proteins – n residues has 20 to the nth possibilities

 

Alpha helix – beta pleated sheet

 

Structural complementarity – ex. Antigen and Ig molecule

 

Enzyme specificity and action

 

Categories of proteins

Nucleotide structure and usage – know your pairing, which is pyrimidine, which is purine           CU,AG

 

Chargaff, Watson & Crick

 

Types of RNA

 

Crick’s Central Dogma

---

 

Cell Theory

 

Cell size limitations

 

Prokaryote characteristics

 

Eukaryote characteristics

 

          Nucleus

          Ribosomes

          Endomembrane system

          Rough ER

          Smooth ER

                    Path of secreted protein, from DNA to cell                                  membrane – signal sequences

          Golgi apparatus

          Lysosomes

          Vacuoles

          Mitochondria

          Chloroplasts

 

Cytoskeleton – Microfilaments, Intermediate Filaments, Microtubule

 

 

Plasma membrane structure!  Compartmentalization

 

Phospholipid structure

 

Integral membrane proteins

Peripheral membrane proteins

Glycoproteins, glycolipids external only

 

Fluid-mosaic model!   Pool covered with ping pong balls and tennis balls image

 

Functions of membrane proteins

 

Traffic across membranes

          Small molecules – osmosis

          Facilitated diffusion – osmosis driven

          Active transport – Na, K pump

          Secondary transport – dependent upon primary

 

Decrease entropy = feature of life

 

DG (will it happen?) vs. Kinetics - how fast will it happen?

 

A®B + energy

 

E of activation

 

DG = DH - TDS

 

DG of ATP hydrolysis = -7.3 kcal/mole

 

Coupled reactions

 

Ester and anhydride bonds

 

Enzyme properties:

          Catalytic power

          Specificity

          Regulation

 

Active site, induced fit hypothesis

E embraces S

Covalent catalysis

Microenvironment – localized pH changes

 

Allosteric regulation of enzymes

Feedback inhibition – negative allosteric effector

 

Covalent modification of enzymes, typ. by phosphorylation

 

Life is work

 

Relative potential energy for redox rx – oxidation of C

 

Glycolysis

Citric Acid Cycle

Oxidative Phosphorylation

 

NADH!

 

ATP!

 

Aerobic vs. Anaerobic respiration

 

Know your energy budgets!

 

ATP synthase machine – molecule of the year?

 

Pasteur effect

 

 

Photosynthesis relies on photoreactivity of chlorophyll

Takes place on membranes

 

Conversion of light E to chemical E as Phosphorylation power  (ATP) and reducing power (NADPH)

 

Biosynthetic pathways are reductive in nature!

 

Possible fates of captured energy in *P (4)

 

Photochemical event

 

PSI, PS II – which system, what order

 

Cyclic, noncyclic photophosphorylation

 

Ribulose bisphosphate and RUBISCO

 

Photorespiration

 

 

Cell signaling – signal transduction cascades

 

2 classes of hormones – membrane permeant, impermeant

 

Receptors trigger cascades of events

 

G protein coupled receptors!

Receptor tyrosine kinases!

 

Second messengers – cAMP!, Ca+2, etc.

 

Activate protein kinases – phosphorylate target proteins® activate gene expression

 

Homodimers and heterodimers in RTK responses

 

Transautophosphorylation

 

 

Cell cycle and Mitosis

 

n vs. 2n vs. 4n

 

G1, S, G2, mitosis, cytokinesis;  G0 arrest

 

Regulation of cell cycle – mitogens, cdk’s, cyclin, selective protein degradation

 

PMAT and its mechanisms

 

“Corpse at a funeral”

 

Apoptosis

 

Meiosis

 

Differences in Anaphase, Anaphase I, Anaphase II

 

Synaptanemal complexes – chiasmata

 

Aneuploidy

 

Turner’s, Kleinfelters, Trisomy 21

 

Mendel – why succeed?  What did he do?

 

Traits – dominant and recessive

 

Law of Segregation

 

Law of Independent Assortment

 

Testcross

 

Phenotype examination – arm’s length to molecular!

 

Sex determination

 

X linked recessives

 

 

DNA replication mechanism

 

DNA Pol I, II, III

 

RNA Pol

 

Helicase, Topoisomerase

 

Proofreading, UV errors

 

Transcription mechanism

 

Translation mechanism!

 

Codon triplet concepts

          Initiation

          Termination

          Degeneracy

 

Regulation of Translation in Prokaryotes

 

DNA/chromosomal mutation types and consequences

 

Virus structure

 

Lytic cycle

Lysogenic cycle

 

 

Bacterial sex – F factor plasmid

 

Integration of plasmid into bacterial chromosome

 

Phage transduction of DNA

 

Episome concept

 

Transposons

 

Regulation of gene expression:

          Lac operon

          Trp operon

 

Mutants for above operons

          Inducible

          Repressible

 

 

Eukaryote gene expression

 

Introns and Exons

 

Post transcriptional splicing in nucleus

 

Psuedo genes

 

Clustered genes – ex. Globins

 

Cap, methylate and poly-A tail before sending mRNA to cytoplasm for translation

 

Splicing controlled by snRNP’s

 

Leader sequence if targeted for secretion

 

Exon shuffling

 

TATA, CAAT box; enhancers, repressors

 

Temporal expression!

 

X inactivation – mosaicism in females

 

Methylation of bases for control

 

Gene amplification (rRNA early in embryogenesis)

 

Post transcriptional control

 

Proteins binding to DNA

 

Binding motifs

          Leucine zipper

          Zn finger

          Helix-turn-helix

          Helix-loop-helix

 

Heterodimers

 

Determination and differentiation

 

Dolly

 

Drosophila segmentation determination through maternal gene expression

 

Homeotic genes – determination

 

Gap genes can feedback to homeotic genes (Kruppel, hunchback)

 

Evolutionary conservation of functional gene set

 

Sex development in humans

          Penis at 12 syndrome

 

Recombinant DNA tools

 

Cleave          Join              Separate

 

Palindromes

 

Restriction enzymes: recognition sites, blunt vs. sticky cuts

 

Gel electrophoresis

          Inverse relationship of velocity to length

 

Cloning vectors

 

Sequencing DNA

 

PCR reaction – cyclic process

 

Expression vectors inserted into target animal – pharming

 

RFLP’s

 

VNTR’s

 

Molecular medicine generalizations!!

          Know in depth at least one example for each generalization AND for each exception

Mutations and Disease

 

Methylation and dangers thereof

 

Transposons

 

Triple repeats

          Know example

 

Genomic imprinting – sex wars!

 

Detection of mutants

          Phenotypes

 

Cancer is a genetic disease – not all inherited!

 

Somatic mutation

 

Oncogenes and proto oncogenes

          Know examples and their types

 

Gain of function – stimulators of cell growth

 

Not usually inherited!

 

Tumor suppressor genes

          Inherited!  One bad allele

If no functional gene product ® develop tumor

 

Loss of function!

 

3 ways to generate loss of heterozygosity

 

Know examples, esp. BRCA1,2 APC in colon cancer, Rb

 

 

Treating genetic diseases

          Modify phenotype

          Supply missing product

          Fix the genotype – gene therapy

 

Defenses against Disease

 

Koch’s postulates!

 

Three lines of defense

          Surface barriers

          Nonspecific

          Specific immune response

 

Skin, Fluids, Flushing

Complement proteins

Interferons

Phagocytes

Natural Killer cells

Inflammation response

          ­heat ­redness      ­swelling, pressure

          ­pain

 

Pyrogens and fever

 

Liver and spleen – remove Fe

 

Immune response

          T cells

          B cells

          Macrophages

 

Interstitial cell space – site of infections

 

Lymphatic system = circulatory system

 

T cells – thymus, surface active – cell mediated response

 

B cells – bone marrow, internally active – antibody response

 

B presents to T; T activates B

 

4 Characteristics of lymphocytes

          specificity

          diversity

          tolerance

          memory

 

MHCI – all cells BUT B, macrophages

MHCII – B, macrophages

 

TCR’s

 

DNA removed in splicing – can’t go back!

Variation without immense gene bank

 

Immunoglobulins (Ig’s)

          Light and heavy chains

          Again DNA splicing, variation

          5 classes

 

And any further concepts yet to come…exam will cover Chapter 18 completely and any topics discussed Friday, Dec 10^th.