Exam 1 Flashcards
Cells are diverse in their
1) Size
2) Shape
3) Chemical Environment
4) Level of specialization
Central Dogma
DNA - RNA - Protein
Which predates which? RNA // DNA and why was it able to do so?
RNA predates DNA and it was possible through autocatalysis
Early RNA could
1) store genetic information
2) catalyze intracellular processes without proteins
Describe RNA’s autocatylitic properties
RNA can recreate more of itself (catalyze its own synthesis) without the help of other types of molecules. It can also do RNA splicing and also DNA ligation
Ribozyme and how it differs from protein
RNA folded into a 3 dimensional shape that can carry out catalytic activity.
- not as diverse
- not made of amino acids (only 4 subunits)
Why is DNA more stable than RNA?
The deoxyribose in the phosphodiester bond
Function of Ribozyme
Peptide bond formation in protein synthesis
All cells are descendants from
one ancestral cell
Most diverse kingdom of life
Bacterium
Characteristics of bacteria
- Prokaryotes
usually smaller - smaller genome
- proliferate rapidly
- therefore mutate rapidly
- cell wall
Characteristics of Archea
Prokaryotes that live in extreme environments
Archea and Bacteria COMPARED
Both have cell walls and lack membrane enclosed organelles and have a similar appearance
Bacteria and Archea cell wall chemistry and internal cell chemistry differ greatly
Filament types that make up the cytoskeleton
- Action filaments- thin, abundant, muscle contraction
- microtubules- separate chromosomes in cell division
- Intermediate filaments- strengthen animal cells
Protozoan
free-living single celled eukaryote
Transport Vesicle
mediate exchange of materials between all organelles and exterior of the cell
organic vs. inorganic molecules
organic- contains caron
inorganic- does not contain carbon
small molecules and their macromolecules
Sugar- Polysaccharide or oligasachride
Fatty acid- lipds
Amino acid- Proteins
Nuceic a
Glycocidic bond
bond between two OH groups on a sugar
What reactions bring molecules together
Dehydration reactions- removal of a h2O molecule
What reactions berak molecules apart
Hydrolysis- addition of a water molecule
Which types of reactions are energetically favorable?
Hydrolysis- breaking bonds releases energy and is energetically favorable
Saturated vs. unsaturated fatty acids
Saturated- all single bonds, non-kinked tails, solid at room temperature
Unsaturated fats- double bonds, kinked tails, liquid at room temperature
Triaglycerol
3 fatty acid chains linked together by their carboxyl group heads
Fatty acids
Hydrocarbon tail, carboxyl head
Lipids
molecules soluble in fat and insoluble in water, non-polar and hydrophobic
Polypeptide chain
- N-C-C backbone with R groups attached to central carbon,
- R groups can rotate and change position but backbone CANNOT
Where does the peptide bond form along the polypeptide chain?
- Between the C with the carbonyl on it and the next nitrogen on the backbone
Which macromolecules are the most chemically diverse?
Proteins
Why are nitrogenous bases called bases?
They can each bind to an H proton and increase OH concentration
What macromolecule takes up most of the cells dry mass?
Proteins
Enzymes definition
promote reactions by providing a binding site and binding molecules together to increase the rate
Transporters
help passage of materials around cells and through membrane OR transport signals
Motor proteins
travel up and down cytoskeleton to move organelles
The protein’s shape is determined by its
amino acid sequence
What allows protein folding?
Noncovalent flexible bonds between R groups
What prevents protein folding
Bonds w/in the protein backbone (N-C-C)
Characteristics of a protein conformation
- final 3D shape of protein
- always the lowest energy conformation (releases heat when formed)
What causes protein denaturation
disruption of non covalent bonds and subsequent misfolding
How do chaperon proteins facilitate folding
They produce isolation chambers for the proteins to fold correctly or bind to partially folded chains to assist them
Alpha helix
- helix strand
- results from hydrogen bonding between O= and N on backbones
- R groups do NOT interact or are functional
- common in cell membranes with nonpolar R groups
Coiled coil
two alpha helixes sandwhiched together with the polar backbone on the outside and the nonpolar R groups on the inside
Beta Sheet
Made of adjacent alpha helices that maintain the N-O= bonding
- Side chains are nonfunctional and stick out above or below sheet
- can be parallel or nonparallel to each other
Levels of protein organization
Primary- just amino acid sequence
Secondary- ALPHA helix or beta sheets
Tertiary- 3-d structure, functional, shape influenced by R groups and their non-covalent bonds, contains unique shapes
Quatenary- contains multiple polypeptide chains and multiple protein domains
Protein domain
amino acid sequence that can fold into its own unique structure (not alpha helix or beta sheet)
Protein families can be defined by similar what
- shape
- amino acid sequence
- reflectional symmetry etc
Extracellular proteins characteristics
- fiborous- simple long structure)
- IE: collagen or relastin
- held together by DISULFIDE BONDS beween SH groups (cystine) that do not exist w/in the cytosol
Methods of regulating protein activity
- Regulate transcription
- Modify its degredation rate
- Confine protein to specific location
- Modify protein conformation
Feedback inhibition works when __
a product accumulates and its concentration shuts an earlier pathway off
What are the types of negative regulation
- allosteric inhibition- ligand binds to one binding site on protein and changes its conformation, resulting in the change in function of the other binding site
Phosphorylation- phosphate attaches to the OH group of seline, tyrosine or threonine, its negative change alters the position of the R group, and the ligand binding is altered and activity is inhibited
Which enzymes are used to initiate and reverse protein phosphorylation?
Initiate- protein kinase (binds P from ATP to OH)
Reverse- protein phosphatase- removes P from protein
Which histone tail modification are most impactful
Modification at position 9 of lysine (K)
Constitutive heterochromatin
- permanently condensed (telomeres and centromeres)
Facultative heterochromatin
can be condensed or not condensed depending on chromosome, cell type, developmental stage or environment
Active euchromatin
actively being transcribed
Quiescent euchromatin
available for transcription, slightly more condensed than active euchromatin
What is epigenetic inheritance and why is it possible among daughter cells?
- cells produce daughter cells that will have changes in their gene expression w/o changing their DNA
- possible because nucleosome modifications in parent cell are equally distributed among daughter cells
Process of proofreading in DNA polymerase
Common sources of single-strand DNA damage (draw pictures)
- Depurination- loss of a purine base (A or G) and results in a deletion
-Deamination- loss of an amine group on a cytosine so it is read as uracil instead and ressults in a substitution - Thyme/Cytosine dimers- adjacent bases bond covalently to each other (cannot occur with adenine or guanine), result in two base pair deletion and occurs when UV radiation is received
Reciprocal Translocation
two segments of two different chromosomes are swapped
Characteristics of Interphase chromosomes
- long and thin
- not distinguishable in microscope
-decondensed aside from constitutive heterochromatin
replication origin
- location on chromosome where replication begins, many exist to allow for rapid replication
Telomeres and centromeres are simply ___
DNA sequences at the middle and ends of chromosomes that signal proteins to bind (IE centromere signals for kineticore binding)
How are interphase chromosomes organized within the nucleus?
- organized by type of chromosome, homologs are not necessarily located adjacent to each other
- The nucleolous contains RNA encoding DNA
Depurination- cause, characteristic and result
- loss of a purine group (a/g) as a result of addition of H2)
- results in a single base pair deletion
Deamination- cause, characteristic and result
Loss of a amine group on a thymine as a result of H20 addition that causes it to be read as a uracil. Results in single base pair substitution
Thymine/cytosine dimers
After receiving UV radiation, thymines or cytosines covalently bond to adjacent baes between their double bonded carbons. Results in double base pair deletion
Formation of dimers, deamination and depurination are what type of DNA damage?
Single strand damage
Where is heterochromatin located during interphase?
At the edge of the nucleus connected to the nuclear envelope
What does chromatin contain?
- DNA
- histone proteins
- none-histone chromosomal proteins
A nucleosome contains
- nucleosome core particle (DNA wrapped around octomeric histone proteins) and linear DNA that links the particles together
Describe the components of the histone octamer and its function
- made of four histone proteins- (two molecules each) H2A, H2B, H3 and H4, which have N terminus tails that extend outward from histone complex and can be covalently modified
- Histome proteins contain positively charged amino groups (seline, lysine etc) because it allows negatively charged DNA to bind to it easily
What does the H1 protein do?
Assists in DNA winding around the histone, is not actually a part of the histone protein complex
What is the function of the SMC ring complex? What are its components?
Contains
- Hinges that attach to DNA
- cohesin protein that creates loops of DNA strands
- two balls that feed DNA strand along into the loop
Hydrolyzes two ATP molecules to move
What are the function of clamp proteins
signal for cohesin to stop feeding the DNA loop and are located on either side of the SMC complex
also helps sinch chromatids to form centromeres
___ is used to create interphase chromatin and ____ is used to create mitotic chromosomes
- cohesin
- condensin II then I
Ways that nucleosomes can be modified
- through Chromatin remodeling complex- loosens or tightens DNA coil around the octamer to make DNA available for transcription, it is ATP dependent and requires a lot of energy
- Histone modifying enzymes- detects certain sequences to covalently modify histone tails to interfere with histone protein shape and therefore change DNA coiling
Examples of Histone tail modifications
- Lysine methylation
Lysine trimethylation - Lysine acetylation
(all at position 9)
Heterochromatin spread
continuous condensation of a string of euchromatin into heterochromatin
What factors regulate heterochromatin spread?
- Hstone tail modification, most commonly trymethylation of lysine at position 9 on H3 tail, modifies DNA that is heterochromatin
- Histone modifying enzymes detect the modification (reader) and propogates the modification (writer) to spread the condensation across connected histones
- When histone modifying enzyme reaches DNA barrier sequence that is modified to block the condensation (ie acetylation) it stops heterochromatin spread
