Cell Biology -- Study Guide for Exam #1 Structures of biomolecules

Cell Biology -- Study Guide for Exam #1
Structures of biomolecules
Basic principles of chemical bonding
Be able to identify important parts of deoxyribonucleotides, ribonucleotides,
dinucleotides, amino acids, dipeptides.
Important features of double-stranded DNA; supercoiling
Define levels of protein structure (primary, secondary, tertiary, quaternary and domains).
Allostery, phosphorylation/de-phosphorylation and Guanine nucleotide
binding/hydrolysis as ways of controlling protein activity. Definition of protein family,
paralogs, orthologs.
Gene Expression
Different classes of eukaryotic genes and their corresponding RNA polymerases.
Molecular structure of gene (promoter, transcribed region). Orientation of DNA strands
with respect to the foregoing parts of the gene.
Definition of transcription; Transcription process (Chemistry of phosphodiester bond
formation), transcription “bubble”, supercoiling and role of topoisomerases).
RNA processing (general idea of 5’ capping, intron removal, exon splicing and
Definition of translation; Reading frames; ORF; genetic code (be able to use the table);
tRNA structure; basic ribosome structure (large subunit, small subunit, P-site, A-site);
Stages of translation (initiation, elongation and termination). Chemistry of peptide bond
Ubiquitin-dependent proteolysis.
Be able to do the kind of gene expression problem we did in class!
Definition of amphipathic molecule. Phospholipid structure. Be able to identify and
explain hydrophobic and hydrophilic parts of phospholipids. Hydro-carbon tails
(variation in number of carbon atoms, saturated, unsaturated tails, be able to identify cis
and trans double bonds).
Lipid bilayer structure and why it forms spontaneously. Causes of membrane fluidity.
Properties of lipids that affect fluidity.
Know what kinds of molecules can and can not pass freely through a lipid bilayer.
Cellular location of lipid synthesis. Activity of “flippases”.
Asymmetric nature of lipid bilayer, and membrane in general (i.e., glycocalyx and cell
Be able to identify the cytosolic and non-cytosolic halves of the bilayer for the cell
membrane, vesicles and organelles of the cell.
General characteristics of integral and non-integral membrane proteins. General features
of membrane-spanning domains of membrane proteins.
Concept of lateral diffusion as it applies to lipids and integral membrane proteins.
Experiment demonstrating lateral diffusion of membrane proteins.