Cell Bio ch 5
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| DNA ---> RNA ---> protein | Gene ---> mRNA ---> polypeptide
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| DNA (gene) ---> RNA (mRNA) is known as what? | Transcription
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| RNA (mRNA) ---> protein (polypeptide) is known as what? | Translation
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| What is the genetic material? | DNA
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| What is all of the DNA in the cell referred to as? | Genome
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| Passed from one generation to the next; gives us our particular characteristics | Genome
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| Specific segments (sequences) of DNA; provide instructions | Genes
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| DNA gets copied into identical DNA molecules during _____ (prep for cell division) | Replication
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| A gene is used to make an RNA molecule | Transcription
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| One strand of DNA is _____ to make two identical strands | Copied
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| Copy of a structural gene | mRNA
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| Will be used by ribosomes as directions for making a specific protein | mRNA
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| Copy of a tRNA gene | tRNA
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| Involved in process of translation (carries amino acids to the ribosome) | tRNA
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| Copy of an rRNA gene | rRNA
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| Makes up part of the ribosome | rRNA
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| The specific sequence of nucleotides in an mRNA is "read" by what? | Ribosome
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| The sequence of nucleotides determines the sequence of _____ _____ in the protein | Amino acids
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| DNA is useful as the genetic material mainly because of its _____; easy to copy | Structure
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| DNA consists of two chains of nucleotides, which form what? | Double helix
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| Single ring containing C and T | Pyrimidine
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| Double ring containing A and G | Purine
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| What is the sugar in DNA? | Deoxyribose
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| DNA is made up of a _____ ring, _____, and a _____ group | Nitrogenous ring, sugar, phosphate group
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| The backbone of DNA is what? | Phosphate-sugar
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| The bases in DNA hang off what? | The backbone
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| How many hydrogen bonds do A and T form? | Two
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| How many hydrogen bonds do G and C form? | Three
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| The two nucleotide bases pair by _____ bonding | Hydrogen
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| What holds the two DNA strands together? | Hydrogen bonding between the bases
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| If the sequence of two strands of DNA is such that they can H-bond along their full length, then they are _____ | Complementary
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| A on one chain, T on the other; G on one chain, C on the other | Complementary
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| Each strand of DNA is directional, which is based on linkage of _____ _____ units (backbone) | Sugar-phosphate
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| Free phosphate group on 5' carbon | 5' end
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| The 5' end has a free _____ group on the 5' carbon | Phosphate
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| Free hydroxyl group on 3' carbon | 3' end
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| The 3' end has a free _____ group on the 3' carbon | Hydroxyl
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| The two complementary strands in a double helix run in opposite directions, thus making them what? | Anti-parallel
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| How many base pairs are in one full turn of the helix? | 10
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| There are _____ Angstroms per base pair (rise) | 3.4
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| There are _____ Angstroms per turn (rise) | 34
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| Bigger indentation in DNA | Major groove
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| Smaller indentation in DNA | Minor groove
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| Eukaryotes have many _____ chromosomes | Linear
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| DNA + histones + other associated proteins | Chromatin
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| What kind of chromosomes are very long and wrapped around proteins (histones) and packaged in an orderly fashion? | Eukaryotic
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| Usually has one circular chromosome | Bacteria
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| Not nearly as long as eukaryotic chromosomes; associated with proteins (but not histones) | Bacterial chromosome
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| Chromosome lengths range from _____ million to _____ million base pairs long | 50, 250
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| How many base pairs are in one copy of the human genome? | 3.2 x 10^9
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| How many copies of the human genome do we have? | Two
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| The entire genome, stretched out, would be about _____ meters long (this is in EVERY cell) | Two
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| Entire complement of genetic material in an organism (billions of base pairs) | Genome
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| Individual, linear segments (millions of base pairs) | Chromosome
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| Humans have _____ individual chromosomes and two copies of each, giving us a total of _____ chromosomes | 23, 46
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| Smaller segments (portions) of chromosomes (thousands of base pairs) | Gene
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| Approximately how many genes do humans have? | 25,000
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| Humans have 22 different _____ | Autosomes
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| Chromosomes that don't determine sex; we have two copies of each (one from mom, one from dad) | Autosomes
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| Are autosomes haploid or diploid? | Diploid
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| Humans have 2 _____ chromosomes | Sex
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| XX are the sex chromosomes for... | Females
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| XY are the sex chromosomes for... | Males
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| Two pairs of each chromosome are called _____ chromosomes | Homologous
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| Contain the same genes although they may be different versions | Homologous chromosomes
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| What are the only chromosomes that are not homologous (different genes)? | X and Y
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| A display of the full set of 46 chromosomes (can look for large abnormalities) | Karyotype
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| Prepared using cells in mitosis; chromosomes are stained in a variety of ways to aid identification | Karyotype
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| One chromosome breaks and attaches to the end of another | Translocation
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| More than two copies of a chromosome | Trisomy
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| There is some correlation between organism complexity and _____ _____ (but only on a larger scale) | Genome size
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| Eukaryotic genomes are usually much _____ than bacterial genomes | Bigger
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| Our genome is much _____ than some plants and amoeba | Smaller
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| There is no real _____ between gene number, genome size, and chromosome number (genomes can contain a few long chromosomes or many short ones) | Correlation
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| Bacteria and most unicellular organisms have very _____ genomes | Compact
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| Eukaryotes have lots of _____ in between genes, frequently called "junk DNA" | Space
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| Many scientists believe the sequence isn't important, but the spacing is | Junk DNA
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| During the cell cycle: everything except mitosis | Interphase
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| Dispersed chromosomes (less condensed); individual chromosomes can't be distinguished using a light microscope | Interphase
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| Chromosomes are very condensed; can see individual ones | Mitosis
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| Specialized area of a chromosome necessary for separation during mitosis | Centromere
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| Place where DNA copying starts; there are many on each eukaryotic chromosome | Origin of replication
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| End of the chromosome; allows the ends to be replicated and also provides a "cap" that marks the ends as ends (rather than breaks) | Telomere
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| During interphase, regions with genes that are expressed are _____ condensed; proteins and other enzymes involved in gene expression need access! | Less
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| Regions with genes that are silent are _____ condensed; no access needed | More
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| Nucleotide sequence of DNA that control a discrete hereditary characteristic of an organism | Gene
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| Encodes an RNA molecule (rRNA, mRNA, tRNA, etc.) | Gene
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| How many nucleotides are usually in one gene? | 1 x 10^4 to 5 x 10^5
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| Double membrane that surrounds the nucleus | Nuclear envelope
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| Channels through the nuclear envelope | Nuclear pores
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| Allow some molecules to pass through nuclear envelope; passage is regulated | Nuclear pores
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| Fibrous network of proteins lining the inside of the nuclear membrane | Nuclear lamina
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| Gives structural support for the nuclear membrane | Nuclear lamina
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| Abnormal nucleus shape is present in patients with mutations in _____ _____ proteins (causes disease called progeria) | Nuclear lamina
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| Chromosomes occupy _____ locations in the nucleus; very organized | Discrete
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| Area where genes for ribosomal RNA cluster (rRNA is synthesized) | Nucleolus
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| The DNA has to be packaged in specific structural units in order to fit inside the _____ | Nucleus
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| Stretched out, the DNA in our cells would be about _____ meters long | Two
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| The nucleus is usually less than _____ micrometers | 10
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| DNA is condensed through association with _____ proteins | Histone
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| What are the two types of associated proteins in chromatin? | Histones, non-histone proteins
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| DNA is highly _____ to allow it to fit in the nucleus | Condensed
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| What are the five main histones? | H1, H2A, H2B, H3, H4
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| Huge levels of expression; extremely highly conserved | Histones
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| What histones make up a histone octamer? | H2A, H2B, H3, and H4 (two of each)
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| DNA is wrapped around the _____ _____ | Histone octamer
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| Histones have a high proportion of _____ and _____ | Lysine, arginine
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| In histones: being positively charged amino acids, they bind to the negatively charged Pi groups that are more abundant in DNA | Lysine, arginine
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| The DNA makes _____ turns around the histone octamer | 1.7
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| How many base pairs of DNA are wrapped around each histone octamer? | 146
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| The DNA and histone octamer complex is known as... | Nucleosome core particle
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| DNA molecule wrapped around a histone octamer plus the linker region (DNA in between the histones) | Nucleosome
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| Regions of RNA in between nucleosome core particles | Linker region
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| How many base pairs are typically in linker DNA? | Can vary - usually a few to 80 base pairs
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| An enzyme that digests (cuts) DNA | Nuclease
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| Short digestion times: nuclease breaks down only _____ region, which frees individual nucleosome core particles | Linker
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| Region of core histones that extend out of the nucleosome | Histone tails
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| N-terminal end; subject to many COVALENT modifications (methylation, phosphorylation, ubiquitination) | Histone tails
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| Areas with no genes (centromeres and telomeres) are very highly _____ | Compacted
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| What is the first level of compaction of DNA? | Formation of nucleosomes
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| The formation of nucleosomes reduces the length of DNA to about _____ | 1/3
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| HISTONES: also known as "linker" histone | H1 histone
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| HISTONES: binds the linker region in between nucleosome core particles | H1 histone
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| HISTONES: thought to bring individual nucleosome core particles together | H1 histone
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| HISTONES: aids in further compaction of DNA | H1 histone
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| What is the second level of compaction of DNA? | 30 nm fiber
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| Individual nucleosomes packed close together | 30 nm fiber
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| Thought to be mediated by histone H1 | 30 nm fiber
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| The 30 nm fiber is folded into a series of _____ | Loops
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| The 30nm fiber folding into a series of loops is probably mediated by attachment of specific regions to _____ _____ or _____ _____ | Nuclear envelope, nuclear lamina
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| DYNAMIC CHROMATIN STRUCTURE: unfold enough for RNA polymerases and associated proteins to get in | Gene expression
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| DYNAMIC CHROMATIN STRUCTURE: unfold enough for DNA polymerases and associated proteins to get in | Replication
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| DYNAMIC CHROMATIN STRUCTURE: other times, proteins need access to _____ DNA damage | Fix
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| Protein machines that modify DNA structure | Chromatin remodeling complexes
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| Chromatin remodeling complexes use energy from ATP _____ to push on the nucleosomes | Hydrolysis
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| The overall result of chromatin remodeling complexes is that nucleosomes are _____ | Repositioned
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| Decreases compaction; exposes areas of DNA to other proteins | Chromatin remodeling complexes
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| Reversible COVALENT modification; N-terminus | Histone tail modification
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| Phosphorylation, acetylation, methylation done by enzymes present in the nucleus | Histone tail modification
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| RESULTS OF HISTONE MODIFICATION: "_____" positive charges on the histone tails (might make 30nm fiber less tightly packed) | Neutralizes
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| RESULTS OF HISTONE MODIFICATION: acts as a _____ (modified histones are recognized and bound by various proteins) | Code
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| RESULTS OF HISTONE MODIFICATION: sometimes used to "_____" regions of chromatin (newly replication, etc.) | Tag
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| Modification state of histones, in general, doesn't indicate whether a region will be tightly compacted; depends on the specific modification present and the combinations | Histone code
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| Modification state of histones depends on the activity of the modifying _____; these are usually signaled by other things going on in the cell | Enzymes
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| Histone acetylation state is determined by what two things? | Histone acetyltransferases (HATs) and histone deacetylases (HDACs)
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| Chromatin remodeling complexes and histone modifying enzymes are tightly _____ | Regulated
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| Processes in regulation are _____, allowing cell to modify chromatin structure, as needed | Reversible
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| Usually doesn't contain any genes; stains dark; usually ~10% of a chromosome | Heterochromatin
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| Centromeres, telomeres, and the inactive X chromosome (in females) are examples of what type of chromatin? | Heterochromatin
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| Everything that's not heterochromatin is... | Euchromatin
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| _____ chromosomes exhibit different levels of compaction in different regions (areas with genes expressed = less compact, areas with silent genes = more compact) | Interphase
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| Areas present as heterochromatin usually do not contain _____ | Genes
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| Tends to spread; modified regions attract enzymes that modify histone tails in adjacent regions | Heterochromatin
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| Associated with specific histone tail modifications; methylation of lysine (K) 9 on H3 | Heterochromatin
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| When heterochromatin spreads, nearby genes are subjected to _____ _____ | Positive effects
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| Chromatin structure can be inherited; histones from parent chromosomes are deposited onto daughter chromosomes during replication (meaning daughter chromosomes each get 1/2 "marked" histones) | Inherited
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| Marks on genome (DNA/chromatin) that affect gene expression but DO NOT change the DNA sequence | Epigenetic inheritance
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| _____ modifications are one type of epigenetic regulation and inheritance | Histone
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