bio130 pt.1

section 1, fill in the blanks

____/__ have no nuclei, no membrane bound organisms, single celled, include bacteria and archaea

prokaryotic cells

_____/___ have a nuclei, membrane bound organelles, single or multicellular, and make up plants, fungi, animals, humans

eukaryotic cells

ectosymbiosis is a form of symbiotic behaviour in which an organism ___/_/__/___ of another organism

lives on body surface

the ____ is an organelle in eukaryotes that can use oxygen to generate ATP in a process known as ___/____

mitochondria, aerobic respiration

mitochondria were originally bacterial endosymbionts, or ___/___/____ able to use O₂ to help generate ATP

free living prokaryotes

The entangle-engulf-endogenize (E³) model includes an ancient anaerobic ____ cell, an ancient aerobic bacterium, and over evolutionary time, a symbiotic relationship between the two

archaeal

an ____ is a cell that lives inside another with mutual benefit

endosymbiont

mitochondria and chloroplasts still have remnants of their own ___ and ____/____ that resemble modern-day prokaryotes

genomes, genetic systems

a ___/____ is a living thing selected for intensive study as a representative of a larger group of species (model for other things)

model organism

general attributes of model organisms include:

• ___/____ w short life cycles

• __ adult (reproductive) size

• readily availble

• easily ___ or ____

• understandable genetics (simliar/simpler to understand)

rapid development, small, manipulated, modified

The Central Dogma of molecular biology states that information flow in the cell goes from

___ (transcription) → RNA (____)→ ___

DNA, translation, protein

a nucleotide consists of a ______ + ______ + ______

nitrogen containing base, 5 carbon (pentose) sugar (scaffold for base), phosphate group (backbone, 1 2 or 3)

nucleotides are the subunits of ___/____

nucleic acids

Cytosine (C), thymine (T), and uracil (U) are called ____ because they’re derived from a 6 membered ____ ring

Pyrimadines

U C The PYramids

guanine (G) and adenine (A), are ___ which bear a second five-membered ring fused to the six membered ring

purines

a nucleoside contains a ___ + ____

nitrogenous base + sugar

adenosine is a ___ which consists of a sugar + a base

nucleoside

nucleoside diphosphate is a ____ which consists of a sugar + base + 2P

nucleotide

DNA is synthesized from deoxyribonucleoside ___, otherwise konwn as dNTPs

triphosphate → made from 3 phosphate groups

note DNA has no oxygen on 2’ C in pentose sugar

RNA is synthesized from _____ triphosphates, or NTPs

ribonucleoside → has an O on 2’ of pentose sugar

Nucleotides are linked by ____ bonds

phosphodiester

a _____ bond links the 3’C of one nucloside triphosphate to the 5'C of the next

phosphodiester

Base pairing holds the DNA double helix together, with A - T forming _ hydrogen bonds, and G - C forming _ hydrogen bonds

2, 3, G - C is more “sticky” than A-T (takes more energy to break)

DNA is arranged ____, meaning the two strands are oriented with opposite chemical polarities to each other

antiparallel

the double helix of DNA contains 10 base pairs/helical turn, and has ___ grooves followed by ___ grooves making the conformation of DNA energetically favourable, and allowing proteins to recognize and make contact with specific DNA sequences

major, minor

*most protein interactions are made in major group as minor group is too narrow

Three forces that keep the DNA strands together are hydrogen bonds, ___ interactions and __/__/___ attractions (LD forces)

hydrophobic, van der waals

The sequence of the two DNA strands are ____

complementary

DNA strands can be ___, which is important for DNA replication and RNA synthesis

unzipped

The strands in a double helix are antiparallel, which means one strand is __ → __, while the other is __→__

5’ → 3’, 3’ → 5’

the 5’ end of DNA has a ___ group (-PO₄) while the 3’ end contains a hydroxyl group (OH)

phosphate

separating and rejoining DNA strands is a ___/___ that is performed by proteins in the cell, and with heat in the lab

reversible process

the study of model organisms helps us to understand humans because we share fundamental ___/___ and it’s easier to study and pool research on simpler species

cellular processes

human biologi can be explored more directly using ___/__/___ (in vitro) and in direct-care methods (in vivo)

human cell cultures

mitochondria and chloroplasts have kept some of their ___ and ___ synthesis components

protein, DNA

membranes in mitochondria and chloroplasts often ____ to those in prokaryotes and appear to have been derived from engulfed bacterial ancestor

similar

the position of amino acids that forms a protein determines its __/___, which is stabilized by noncovalent interactions between different parts of the molecule

3D confomation

a protein molecule is made from a long chain of amino acid, covalently held together by ____/___

peptide bonds

proteins are also referred to as ____ or ____ chains

polypeptides

the ___/___/___ refers to the unique order in which amino acids are presented in a protein, this is the same from on molec to the next.

amino acid sequence

The ____ is the end of the peptide chain carrying the amino group (NH₂). Polypeptide chains start with the amino group.

N-terminus

The ____ is the end of the peptide chain carrying the carboxyl group (COOH). Polypeptide chains will end with a carboxyl group

C-terminus

side chains of the amino acid are not involved in forming ___/____, but give each amino acid it’s unique properties, e.g. (+)/(-) charged, polar uncharged, or nonpolar

peptide bonds

The amino acid __/___, or R group, is variable, and determines the type of amino acid

side chain

the α helix and β sheet are common due to the ____/__ that form between the N-H and C=O groups in the polypeptide backbones

hydrogen bonds

in an α helix, a hydrogen bond is made between every ____ amino acid, linking the C=O of one peptide bond to the N-H of another within the same segment of pp chain. This causes a complete turn every 3.6 amino acids

fourth

a β sheet is made when H-bonding between C=O of 1 amino acid and N-H of another in ____/___.

there are parallel, and antiparallel β sheets.

neighbouring strands/different segments

a coiled coil forms when 2 or 3 α helices wrap around each other and form a more stable, amphipathic structure, minimizing exposure of ___ aa side chains to aq environment

hydrophobic

the primary structure of a protein consists of its ___/__/____

amino acid sequence

the ___ structure of protein consists of α helices and β sheets

secondary

the tertiary structure of a protein consists of the full, __/____ formed by an entire polypeptide chain

3D conformation

The ___ structure of a protein refers to protein molecules existing as a complex of more than one polypeptide chain

quaternary

The first three structures of a protein refer to a ___ polypeptide chain, while the fourth refers to more than one.

single

proteins will fold into the shape dictated by their amino acid sequence, but ____/____ make the folding process more efficient and reliable. e.g. hsp60, hsp70 (heat-shock proteins)

chaperone proteins

proteins will generally fold into a conformation that is most ____/____, where free energy (G) is minimized

energetically favourable

A ____/___ is a segment of a polypeptide chain that can independently fold into a stable structure and serves as (unique) purpose

Protein domain

Eukaryotic ____ often have 2 or more domains connected by intrinsically disordered sequences (no specific shape, not part of either domain)

Proteins

Protein families are groups of proteins that have a __/____ and an ____/__/____ that closely resemble those of other family members

3D conformation, amino acid sequence

A ___ is a molecule made up of smaller similar or identical subunits linked together

Dimer

The overall 3D structure of a protein is held together by _____ interactions, non-covalent bonds, and covalent ____/___

Hydrophobic, disulfide bonds

Cysteine is characterized by its R chain: _____, which can form disulfide bonds to adjacent cysteine side chains

CH2SH

Disulphide bonds do not form in cell cytosol (high conc. of ____ agents) but will form in the endoplasmic reticulum or outside the cell

Reducing

Multi protein complexes and molecular machines can be:

• many ___ subunits

• _____ of different proteins and DNA/RNA

• Very dynamic assemblies of proteins to form molecular machines

Identical, mixtures

To study proteins,

1. Purify protein(s) of interest using ____ and affinity _____

2. Determine amino acid sequence, e.g. mass spec.

3. Discover precise 3D structure using X-ray crystallography, NMR, cryogenic-electron microscopy, etc

Electrophoresis, chromatography

______ changes by ATP/GTP also enable certain specialized proteins to drive directed movements of cells and their components

Conformational

in humans, there are ___ billion base pairs per genome, with a standard cell having 2 genomes

three

genomes size is not always correlated with number of genes, organisms ___, or organisms ___

complexity, size

50% of human genome is ___ DNA, with less than 1% coding for proteins

repetitive

LINEs

long interspersed nuclear elements, >500 bp

SINEs

short interspersed nuclear elements, <500 bp

____/____/____ (selfish genetic elements): can move around in a genome, sometimes spliced out of DNA, copied, and/or pasted back in (over an evolutionary period). e.g. LINEs, SINEs, retrotransposons, DNA-only transposons

mobile genetic elements

protein-coding exons are segments of gene that are ____ and ____

transcribed, translated'

introns are ____ but spliced out of final RNA

transcribed

____/___ is a structure in prokaryotic cells that contains DNA and proteins in a folded manner

prokaryotic nucleoid

_____/_/__/____ (FISH): diagnostic technique for testing presence of a particular sequence

fluorescence in situ hybridization

1. obtain probe sequence, binds to sequence you want to detect

2. label w/ dye

3. take sample from patient

   1. denature DNA, mix, renature, if sequence is present there will be fluorescence, else, no sequence

____ is a single, long, linear DNA molecule and associated proteins

chromatin

chromatin is tightly packed, and ____, BUT the DNA must remain _____ for transcription, replication, and repair

dynamic (can become more/less condensed), accessible

a _____ is an arrangement of chromosomes lined up

karyotype

DNA wraps around a nucleosome ____ times/turn, ~147 bp long

5/3

_____ = histone octamer core + double stranded DNA wrapped around + linker DNA + H1 linker histone

nucleosome

a chromatin fiber of packed nucleosomes is ___ long

30nm

In ____, not all but a lot of DNA is 30nm chromatin fiber

interphase

____ are small proteins rich in lysine and arginine, positive charge neutralizes negative charge of DNA

histones

pair of ___ histone proteins (H2A, H2B, H3, H4) form an octamer core.

four

ONE ___/___ (H1) binds to outside of octamer core, helps chromatin be more compact (kinda like paperclip, NECESSARY)

linker histone

____/____/____ = histone octamer + DNA wrapped around

nucleosome core particle, DOES NOT include linker DNA & H1 linker histone

the ___ (structural maintenance of chromosomes) proteins forms rings to package chomatin fibers into series of loops

SMC

____ is the SMC ring complex that organizes the structure of interphase chromosomes into loops

cohesin

____ and ____/____/____/____ regulate the size of chromatin loops

cohesin, sequence-specific clamp proteins

as cells enter mitosis, ____ replace cohesins to form loops within loops to fold mitotic chromosome into more compact configuration

condensins

Each DNA molec is packaged into ____/_____ that is 10,000x shorter than fully extended length, packing/unpacking requires energy (ATP)

mitotic chromosome

_____/____/____ can reposition the DNA wrapped around nucleosomes to make it more/less accessible to other proteins in cell

protein-modeling complexes

____/____/____ and chromatin remodeling complexes are examples of proteins that can make changes in chromatin structure and alter access to DNA for replication or transcription

histone modifying enzymes

____ are the most highly condensed form of interphase chromatin

heterochromatin

____ is the chromatin that exists in a less condensed state than heterochromatin

euchromatin

_____ heterochromatin in the centromere and telomeres remain permanently condensed

constitutive

_____ heterochromatin is condensed temporarily

facultative

heterochromatic regions of interphase chromosomes are areas where gene expression is _____

suppressed

____ euchromatin are stretches of the gene are inactive

quiescent

_____ euchromatic regions of interphase chromosomes are areas where genes tend to be expressed

active

localized covalent modification of histones, presence of chromatin remodeling complexes, and RNA polymerase (transcription) complexes modulate the reversible switching from ______ to ______ regions along chromosomes

euchromatic, heterochromatic