cell bio unit 1 exam study guide

4 types of noncovalent bonds

hydrogen bonds, ionic bonds, hydrophobic interactions, van der waals forces

hydrogen bonds

stabilize the protein backbone and secondary structures like alpha-helices and beta-sheets

ionic bonds

pull oppositely charged amino acid side chains together into specific, low-energy 3D structures

hydrophobic interactions/forces

help proteins fold by driving nonpolar parts away from water

van der waals forces

stabilize the folded protein by creating weak attractions between closely packed atoms

consequences of denaturation

protein loses its function and 3D shape

chaperone proteins

assist protein folding and prevent misfolding and aggregation.

primary level of folding

linear sequence of amino acids

secondary level of folding

beta pleated sheets and alpha helices

tertiary level of folding

overall 3D shape of the protein determined by side chain interactions

quaternary level of folding

multiple subunits come together to make on protein complex

disulfide bonds

strong covalent bond that helps stabilize a protein’s folded 3D structure

scaffold proteins

organize proteins into complexes by bringing them together and increasing their efficiency

ligand

A molecule that binds specifically to a receptor or other protein, often causing a cellular response.

ligand example

insulin

nonpolar amino acids

interact with nonpolar parts of ligands through hydrophobic and van der Waals interactions

polar amino acids

interact with ligands through hydrogen bonds

charged amino acids

interact with oppositely charged parts of ligands through ionic interactions.

amino acid side chains

determine the shape and chemical properties of the binding site

enzyme catalysis

how an enzyme speeds up a chemical reaction by lowering its activation energy

ways enzymes promote catalysis

bring substrates together and lower activation energy

feedback inhibition

final product of a metabolic pathway inhibits an earlier enzyme

protein modifications

phosphorylation, acetylation, methylation

how protein activity is controlled

changing protein, shape, location, or interactions

avery, macleod, and mccarty

destroyed different molecules from the heat-killed bacteria. Only destroying DNA stopped transformation

griffith

r strain into s strain

hershey and chase

used radioactive labels to track DNA vs. protein in bacteriophages and only DNA entered the bacteria and caused an effect

3 parts of a nucleic acid

phosphate group, 5 carbon sugar, nitrogenous base

chargaff’s rules

A = T (U with RNA)

G = C

5’ end

has a phosphate group attached to the sugar’s 5′ carbon

3’ end

has a free –OH group on the sugar’s 3′ carbon

chromosome painting

can reveal chromosome abnormalities and mutations

interphase

cell grows, carries out normal functions, and copies its DNA in preparation for division.

mitosis

cell separates its duplicated chromosomes so each future daughter cell gets an identical set of chromosomes

cytokinesis

cytoplasm divides, physically separating the cell into two daughter cells

replication origin

specific DNA sequence where DNA replication begins

centromere

region where sister chromatids are held together and where spindle fibers attach during cell division

telomere

repetitive DNA sequences at the ends of chromosomes that protect them from degradation

chromosome location

occupy organized territories within the nucleus, and their positioning is related to gene activity

nuclear pore

helps maintain separation between nuclear activities and cytoplasmic activities

nucleolus

makes rRNA and makes ribosome subunits that leave through nuclear pores

nucleosomes

DNA wrapped around histone proteins

8 histones

• 2 H2A

• 2 H2B

• 2 H3

• 2 H4

h1

linker histone that helps stabilize the DNA between nucleosomes and promotes further compaction

histone characteristics

positively charged, small proteins that help compact DNA and organize chromatin

structure of chromatin during interphase

loose/organized which allows access to DNA

heterochromatin vs euchromatin

heterochromatin maintains chromosome structure and stability while euchromatin allows genes to be expressed

histone modifications

when histones can have chemical groups added or removed which affects gene expression

histone modification examples

Acetylation, methylation, phosphorylation

histone tails

regions that stick out and are where most histone modifications occur

fruit fly eye example

heterochromatin spread into nearby regions and silenced genes which caused a mottled eye color that was both red and white

barr body

an inactive X chromosome that has been condensed into heterochromatin

importance of DNA replication

DNA replication is important because every new cell needs a complete, accurate copy of the organism's genetic information

meselson stahl experiment

found out DNA replication was semiconservative using heavy and light nitrogen

origin licensing

process of preparing replication origins during G1 so they can initiate DNA replication during S phase

form of nucleotides during DNA synthesis

dNTPs

energy for DNA synthesis

comes from breaking the high-energy phosphate bonds of the incoming dNTp

sequence of events for creating an Okazaki fragment

Primer added, fragment extended, primer removed, gap filled with DNA

DNA polymerase proofreading

DNA polymerase checks the newly added nucleotide and removes it if incorrect

polymerizing domain

adds the correct nucleotide to the growing DNA strand

proofreading domain

checks the newly added nucleotide and removes incorrect nucleotides

RPA

ssDNA binding protein that binds and stabilizes ssDNA during replication

CMG

acts as a helicase and unwinds the double helix

PCNA

forms a clamp around DNA that keeps DNA polymerase attached to it

topoisomerase

relieves torsional stress by cutting DNA so it can unwind

shelterin

proteins that bind/cap the telomere and prevent it from being recognized as DNA damage

t-loop

a loop formed by the 3′ G-overhang folding back into the telomere to hide and protect the chromosome end

hemoglobin

4 globin subunits: 2 α + 2 β chains.

DNA mismatch detection

a mismatch causes distorted geometry in the DNA double helix, which repair proteins can recognize

depurination

loss of a purine base that leaves an empty spot in DNA

deamination

a base loses an amino group which changes its identity

3 ways a cell responds to DNA damage

repair the DNA, stop cell cycle, apoptosis

non homologous end joining

directly joins broken ends; fast but can cause mutations

homologous recombination

uses a matching DNA template; accurate but requires a sister chromatid

alternative end joining

uses short matching sequences; more error-prone