cell bio exam 1

why do we use model organisms?

cheaper and easier than humans, share basic cellular processes with humans

what are the major macromolecules?

nucleis acids, protiens, fats and membrane lipids, polysaccharides

subunit of polysaccharide

sugar

subunit of fats and membrane lipids

fatty acids

subunit of protiens

amino acids

nucleic acids

nucleotides

most abundant molecule in a cell?

water

most abundant macromolecule in an animal cell?

protiens

most abundant macromolecule in an plant cell?

carbohydrates

transmission electron microscopy

very thin slices of a specimen are used, revealing the internal structure of microbial and other cells

scanning electron microscopy

an electron microscope in which a beam of electrons is sent across the surface of a specimen and the reflected electrons are focused to produce a three dimensional image of the specimen surface.

phase contrast light microscopy

variations in density with the specimen are amplified to enhance contrast in unstained cells; this is especially useful for examining living, unpigmented cells.

conofocal fluorescence light microscopy

builds image by scanning sample with laser beam

superresolution fluorescence light microscopy

labelled with molecules whose fluorescence can be turned on and off

what kind of miscroscope do you use to view unstained living animal cells?

phase contrast microscopy

what kind of miscroscope do you use to view ribsomes?

electron microscopy

what kind of miscroscope do you use to view electrons?

none

what kind of miscroscope do you use to view a living cell expressing GFP?

fluorescence microscopy

what kind of miscroscope do you use to do confocal microscopy?

fluorescence microscopy

what kind of miscroscope do you use to view DNA?

fluorescence microscopy

what reaction occurs between peptides to form a peptide bond?

condensation reaction

rank the following chemical bonds in a decreasing order of strength: hydrogen, ionic, covalent, Van der Waals forces

C>I>H>V

what are the chemical properties of nucleotides?

nucleotides are polar and negatively charged?

what do enzymes do?

allow reactions to occur that otherwise would not have occured; lower the energy barriers that block chemical reactions

formula for ΔG°

ΔG° = -2.58 ln Keq

formula for Keq

Keq = [products]/[reactants]

if k < 1, lnk is

negative

if k > 1, lnk is

positive

if k = 1, lnk is

0

formula for ΔG

energy level of product - energy level of reactant

if ΔG is positive -->

reaction is not energetically favorable, not spontaneous, favors products at equilibrium

if ΔG is negative -->

reaction is energetically favorable, spontaneous, favors reactants at equilibrium

if ΔG° is positive -->

reaction is not energetically favorable, not spontaneous, favors products at equilibrium

if ΔG° is negative -->

reaction is energetically favorable, spontaneous, favors reactants at equilibrium

two ways energetically unfavorable reactions can occur in the cells:

if it is driven by being coupled to a second, energetically favored reaction

1. by siphoning off the product in metabolic pathway

2. by enzymatically linking 2 reactions via common intermediate

activated carrier molecule

molecule that stores and transfers energy (eg: ATP, NADH)

what is primary structure of a protein

sequence of amino acids in a polypeptide chain

what is secondary structure of a protein

local folding patterns

what is tertiary structure of a protein

complete 3D shape of a single polypeptide chain

what is quaternary structure of a protein

structure made up of multiple polypeptide chains together

what interactions are involved in primary structure of a protein

peptide bonds join together the amino acids

what interactions are involved in secondary structure of a protein

hydrogen bonding between N-H and C=O groups in polypeptide backbone

what interactions are involved in tertiary structure of a protein

tertiary structure is held together by R-group interactions: hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces, and disulfide bonds

what interactions are involved in quaternary structure of a protein

quaternary structure is held together by the same types of interactions as tertiary structure, but they occur between separate protein subunits instead of within one chain

what structural level of a protein does cryo-electron microscopy help you determine

tertiary, quaternary

what structural level of a protein does circular dichroism help you determine

secondary

what structural level of a protein does mass spectrometry of peptides help you determine

primary

what structural level of a protein does x-ray crystallography help you determine

tertiary, quaternary

what structural level of a protein does nuclear magnetic resonance help you determine

tertiary, quaternary

explain the hydrolase enzyme class

break bonds using water

explain the nuclease enzyme class

cuts nucleic acid

explain the protease enzyme class

cuts proteins

explain the ligase enzyme class

joins 2 molecules together using ATP

explain the isomerase enzyme class

rearrange atoms within the same molecule

explain the polymerase enzyme class

builds polymers from smaller subunits

explain the kinase enzyme class

adds a phosphate group to a molecule

explain the phosphatase enzyme class

removes a phosphate group from a molecule

oxido-reductase

moves electrons

ATPase

breaks down ATP into ADP + inorganic phosphate

ion-exchange chromatography

molecules separated based on net surface charge

gel-filtration chromatography

separates proteins based on size

affinity chromatography

uses specific interactions to slow down select molecules (can make use of specific receptor-ligand, enzyme-substrate, and antigen-antibody interactions)

Km

Substrate concentration at 1/2 Vmax

Vmax

maximum initial velocity or rate of an enzyme-catalysed reaction.

competitive inhibition

- substance that resembles the normal substrate competes with the substrate for the active site

- think 2 cars fighting for one parking spot

- Km increases, Vmax stays the same

- increasing substrate can fix it

allosteric regulation

- 2+ binding sites, but molecule does not bind to active site

- think someone alters a parking spot so no car can fit

- Vmax decreases, Km value varies

DNA polymerase

enzyme that synthesizes new DNA

primase

enyzme that synthesizes RNA primer needed to start replication

nuclease

enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides

repair polymerase

enzyme that fills short, single stranded gaps in DNA created during damage repair

ligase

an enzyme that connects two fragments of DNA to make a single fragment using ATP

DNA helicase

enzyme that opens DNA double helix

single stranded binding protien

keeps DNA in a single-strand form (binds lagging strand)

sliding clamp

holds DNA polymerase in place during strand extension

DNA polymerase reads _______ and binds _______

3' to 5', 5' to 3'

how many hydrogen bonds in A-T bond

2 hydrogen bonds

how many hydrogen bonds in C-G bond

3 hydrogen bonds

chromatin

clusters of DNA and proteins in the nucleus of a cell that make up chromosomes

types of chromosomes

euchromatin - loosely packed, genes are accessible, transcriptionally active

heterochromatin - tightly packed, genes are mostly inactive, less accessible

𝛼-helix

common secondary protein structure where right handed coil formed from hydrogen bonding between an amino group and a carboxyl group of nearby amino acids (think like curly hair coil)

beta pleated sheet

common form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds (think like crimped hair)

four steps of transcription

RNA polymerase binding, initiation, elongation, termination

when is transcription terminated

when a stem loop structure is formed

transcription & translation in eukaryotes

pre mRNA occurs in the chromatin, processed into mature mRNA, then transported to cytoplasm for translation.

transcription & translation in prokaryotes

occur simultaneously in the cytoplasm

3 modifications made to RNA before it becomes mature

1) 5' cap

2) RNA splicing

3) poly A tail

3 sites on a ribsomeone

1) E site - exit site

2) P site - peptidyl tRNA site

3) A site - amino actyl tRNA site

siRNA

provide protection from viruses + proliferating transposable elements

tRNA

adaptors between mRNA and amino acids during protein synthesis

miRNA

regulate gene expression

rRNA

form the core of the ribosomes structure + catalyze protein synthesis

mRNA

code for proteins